mirror of
https://github.com/msberends/AMR.git
synced 2026-09-27 21:38:23 +02:00
Compare commits
63
Commits
v1.7.1
...
e63defe324
@@ -23,8 +23,11 @@
|
||||
^data-raw$
|
||||
^\.lintr$
|
||||
^tests/testthat/_snaps$
|
||||
^vignettes/AMR.Rmd$
|
||||
^vignettes/benchmarks.Rmd$
|
||||
^vignettes/datasets.Rmd$
|
||||
^vignettes/EUCAST.Rmd$
|
||||
^vignettes/MDR.Rmd$
|
||||
^vignettes/PCA.Rmd$
|
||||
^vignettes/resistance_predict.Rmd$
|
||||
^vignettes/SPSS.Rmd$
|
||||
|
||||
@@ -26,15 +26,15 @@
|
||||
on:
|
||||
push:
|
||||
branches:
|
||||
- premaster
|
||||
- master
|
||||
- development
|
||||
- main
|
||||
pull_request:
|
||||
branches:
|
||||
- master
|
||||
- main
|
||||
schedule:
|
||||
# run a schedule everyday at 3 AM.
|
||||
# run a schedule everyday at 1 AM.
|
||||
# this is to check that all dependencies are still available (see R/zzz.R)
|
||||
- cron: '0 3 * * *'
|
||||
- cron: '0 1 * * *'
|
||||
|
||||
name: R-code-check
|
||||
|
||||
@@ -50,22 +50,18 @@ jobs:
|
||||
fail-fast: false
|
||||
matrix:
|
||||
config:
|
||||
# these are the developmental version of R - we allow those tests to fail
|
||||
# test all systems against all released versions of R >= 3.0, we support them all!
|
||||
- {os: macOS-latest, r: 'devel', allowfail: true}
|
||||
- {os: windows-latest, r: 'devel', allowfail: true}
|
||||
- {os: macOS-latest, r: '4.1', allowfail: false}
|
||||
- {os: macOS-latest, r: '4.0', allowfail: false}
|
||||
- {os: macOS-latest, r: '3.6', allowfail: false}
|
||||
- {os: macOS-latest, r: '3.5', allowfail: false}
|
||||
- {os: macOS-latest, r: '3.4', allowfail: false}
|
||||
- {os: macOS-latest, r: '3.3', allowfail: false}
|
||||
- {os: macOS-latest, r: '3.2', allowfail: false}
|
||||
- {os: macOS-latest, r: '3.1', allowfail: true}
|
||||
- {os: macOS-latest, r: '3.0', allowfail: true}
|
||||
- {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
|
||||
# these are the current release of R
|
||||
- {os: macOS-latest, r: 'release', allowfail: false}
|
||||
- {os: windows-latest, r: 'release', allowfail: false}
|
||||
- {os: ubuntu-20.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
|
||||
# these are the previous release of R
|
||||
- {os: macOS-latest, r: 'oldrel', allowfail: false}
|
||||
- {os: windows-latest, r: 'oldrel', allowfail: false}
|
||||
- {os: ubuntu-20.04, r: 'oldrel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
|
||||
# test against all released versions of R >= 3.0, we support them all!
|
||||
- {os: ubuntu-20.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
- {os: ubuntu-20.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
- {os: ubuntu-20.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
@@ -75,7 +71,16 @@ jobs:
|
||||
- {os: ubuntu-20.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
- {os: ubuntu-20.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
- {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
|
||||
- {os: windows-latest, r: 'devel', allowfail: true}
|
||||
- {os: windows-latest, r: '4.1', allowfail: false}
|
||||
- {os: windows-latest, r: '4.0', allowfail: false}
|
||||
- {os: windows-latest, r: '3.6', allowfail: false}
|
||||
- {os: windows-latest, r: '3.5', allowfail: false}
|
||||
- {os: windows-latest, r: '3.4', allowfail: false}
|
||||
- {os: windows-latest, r: '3.3', allowfail: false}
|
||||
- {os: windows-latest, r: '3.2', allowfail: true}
|
||||
- {os: windows-latest, r: '3.1', allowfail: true}
|
||||
- {os: windows-latest, r: '3.0', allowfail: true}
|
||||
env:
|
||||
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
|
||||
RSPM: ${{ matrix.config.rspm }}
|
||||
@@ -87,6 +92,8 @@ jobs:
|
||||
- uses: r-lib/actions/setup-r@v1
|
||||
with:
|
||||
r-version: ${{ matrix.config.r }}
|
||||
|
||||
- uses: r-lib/actions/setup-pandoc@v1
|
||||
|
||||
- name: Install Linux dependencies
|
||||
if: runner.os == 'Linux'
|
||||
@@ -94,12 +101,11 @@ jobs:
|
||||
# we don't want to depend on the sysreqs pkg here, as it requires quite a recent R version
|
||||
# as of May 2021: https://sysreqs.r-hub.io/pkg/AMR,R,cleaner,curl,dplyr,ggplot2,ggtext,knitr,microbenchmark,pillar,readxl,rmarkdown,rstudioapi,rvest,skimr,tidyr,tinytest,xml2,backports,crayon,rlang,vctrs,evaluate,highr,markdown,stringr,yaml,xfun,cli,ellipsis,fansi,lifecycle,utf8,glue,mime,magrittr,stringi,generics,R6,tibble,tidyselect,pkgconfig,purrr,digest,gtable,isoband,MASS,mgcv,scales,withr,nlme,Matrix,farver,labeling,munsell,RColorBrewer,viridisLite,lattice,colorspace,gridtext,Rcpp,RCurl,png,jpeg,bitops,cellranger,progress,rematch,hms,prettyunits,htmltools,jsonlite,tinytex,base64enc,httr,selectr,openssl,askpass,sys,repr,cpp11
|
||||
run: |
|
||||
sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev
|
||||
|
||||
sudo apt install -y libssl-dev libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev
|
||||
|
||||
- name: Restore cached R packages
|
||||
# this step will add the step 'Post Restore cached R packages' on a succesful run
|
||||
if: runner.os != 'Windows'
|
||||
uses: actions/cache@v1
|
||||
uses: actions/cache@v2
|
||||
with:
|
||||
path: ${{ env.R_LIBS_USER }}
|
||||
key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-v4
|
||||
@@ -119,10 +125,8 @@ jobs:
|
||||
as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
|
||||
shell: Rscript {0}
|
||||
|
||||
# - name: Only keep vignettes on release version
|
||||
- name: Remove vignettes
|
||||
# if: matrix.config.r != 'release'
|
||||
if: always()
|
||||
- name: Remove vignettes on R without knitr support
|
||||
if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2'
|
||||
# writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R < 3.3 as writeLines() cannot overwrite
|
||||
run: |
|
||||
rm -rf AMR/vignettes
|
||||
|
||||
@@ -26,11 +26,11 @@
|
||||
on:
|
||||
push:
|
||||
branches:
|
||||
- premaster
|
||||
- master
|
||||
- development
|
||||
- main
|
||||
pull_request:
|
||||
branches:
|
||||
- master
|
||||
- main
|
||||
|
||||
name: code-coverage
|
||||
|
||||
@@ -45,15 +45,23 @@ jobs:
|
||||
- uses: r-lib/actions/setup-r@v1
|
||||
with:
|
||||
r-version: release
|
||||
|
||||
- uses: r-lib/actions/setup-pandoc@master
|
||||
|
||||
- uses: r-lib/actions/setup-pandoc@v1
|
||||
# with:
|
||||
# pandoc-version: '2.7.3' # The pandoc version to download (if necessary) and use.
|
||||
|
||||
- name: Query dependencies
|
||||
# this will change once a week, so it will cache dependency updates
|
||||
run: |
|
||||
writeLines(paste(format(Sys.Date(), "week %V %Y"), sprintf("R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/week-R-version")
|
||||
shell: Rscript {0}
|
||||
|
||||
- name: Restore cached R packages
|
||||
# this step will add the step 'Post Restore cached R packages' on a succesful run
|
||||
uses: actions/cache@v1
|
||||
uses: actions/cache@v2
|
||||
with:
|
||||
path: ${{ env.R_LIBS_USER }}
|
||||
key: macOS-latest-r-release-v5-codecovr
|
||||
key: ${{ matrix.config.os }}-${{ hashFiles('.github/week-R-version') }}-v4
|
||||
|
||||
- name: Unpack AMR and install R dependencies
|
||||
run: |
|
||||
@@ -68,26 +76,14 @@ jobs:
|
||||
as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
|
||||
shell: Rscript {0}
|
||||
|
||||
# - name: Test coverage
|
||||
# env:
|
||||
# CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
|
||||
# run: |
|
||||
# library(AMR)
|
||||
# library(tinytest)
|
||||
# library(covr)
|
||||
# source_files <- list.files("R", pattern = ".R$", full.names = TRUE)
|
||||
# test_files <- list.files("inst/tinytest", full.names = TRUE)
|
||||
# cov <- file_coverage(source_files = source_files, test_files = test_files, parent_env = asNamespace("AMR"), line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
|
||||
# attr(cov, which = "package") <- list(path = ".") # until https://github.com/r-lib/covr/issues/478 is solved
|
||||
# codecov(coverage = cov, quiet = FALSE)
|
||||
# shell: Rscript {0}
|
||||
|
||||
- name: Test coverage
|
||||
env:
|
||||
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
|
||||
R_RUN_TINYTEST: true
|
||||
run: |
|
||||
install.packages("covr", repos = "https://cran.rstudio.com/")
|
||||
library(AMR)
|
||||
library(tinytest)
|
||||
covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
|
||||
x <- covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
|
||||
print(x)
|
||||
shell: Rscript {0}
|
||||
|
||||
@@ -26,11 +26,11 @@
|
||||
on:
|
||||
push:
|
||||
branches:
|
||||
- premaster
|
||||
- master
|
||||
- development
|
||||
- main
|
||||
pull_request:
|
||||
branches:
|
||||
- master
|
||||
- main
|
||||
|
||||
name: lintr
|
||||
|
||||
@@ -42,7 +42,7 @@ jobs:
|
||||
steps:
|
||||
- uses: actions/checkout@v2
|
||||
|
||||
- uses: r-lib/actions/setup-r@master
|
||||
- uses: r-lib/actions/setup-r@v1
|
||||
|
||||
- name: Query dependencies
|
||||
run: |
|
||||
@@ -52,7 +52,7 @@ jobs:
|
||||
shell: Rscript {0}
|
||||
|
||||
- name: Cache R packages
|
||||
uses: actions/cache@v1
|
||||
uses: actions/cache@v2
|
||||
with:
|
||||
path: ${{ env.R_LIBS_USER }}
|
||||
key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
|
||||
|
||||
@@ -25,3 +25,4 @@ data-raw/taxon.tab
|
||||
data-raw/DSMZ_bactnames.xlsx
|
||||
data-raw/country_analysis_url_token.R
|
||||
data-raw/country_analysis2.R
|
||||
data-raw/taxonomy.csv
|
||||
|
||||
+80
-56
@@ -1,68 +1,92 @@
|
||||
Package: AMR
|
||||
Version: 1.7.1
|
||||
Date: 2021-06-03
|
||||
Version: 1.7.1.9062
|
||||
Date: 2021-12-06
|
||||
Title: Antimicrobial Resistance Data Analysis
|
||||
Authors@R: c(
|
||||
person(role = c("aut", "cre"),
|
||||
family = "Berends", given = c("Matthijs", "S."), email = "m.s.berends@umcg.nl", comment = c(ORCID = "0000-0001-7620-1800")),
|
||||
person(role = c("aut", "ctb"),
|
||||
family = "Luz", given = c("Christian", "F."), email = "c.f.luz@umcg.nl", comment = c(ORCID = "0000-0001-5809-5995")),
|
||||
person(role = c("aut", "ths"),
|
||||
family = "Friedrich", given = c("Alexander", "W."), email = "alex.friedrich@umcg.nl", comment = c(ORCID = "0000-0003-4881-038X")),
|
||||
person(role = c("aut", "ths"),
|
||||
family = "Sinha", given = c("Bhanu", "N.", "M."), email = "b.sinha@umcg.nl", comment = c(ORCID = "0000-0003-1634-0010")),
|
||||
person(role = c("aut", "ths"),
|
||||
family = "Albers", given = c("Casper", "J."), email = "c.j.albers@rug.nl", comment = c(ORCID = "0000-0002-9213-6743")),
|
||||
person(role = c("aut", "ths"),
|
||||
family = "Glasner", given = "Corinna", email = "c.glasner@umcg.nl", comment = c(ORCID = "0000-0003-1241-1328")),
|
||||
person(role = "ctb",
|
||||
family = "Fonville", given = c("Judith", "M."), email = "j.fonville@pamm.nl"),
|
||||
person(role = "ctb",
|
||||
family = "Hassing", given = c("Erwin", "E.", "A."), email = "e.hassing@certe.nl"),
|
||||
person(role = "ctb",
|
||||
family = "Hazenberg", given = c("Eric", "H.", "L.", "C.", "M."), email = "e.hazenberg@jbz.nl"),
|
||||
person(role = "ctb",
|
||||
family = "Knight", given = "Gwen", email = "gwen.knight@lshtm.ac.uk"),
|
||||
person(role = "ctb",
|
||||
family = "Lenglet", given = "Annick", email = "annick.lenglet@amsterdam.msf.org"),
|
||||
person(role = "ctb",
|
||||
family = "Meijer", given = c("Bart", "C."), email = "b.meijerg@certe.nl"),
|
||||
person(role = "ctb",
|
||||
family = "Ny", given = "Sofia", email = "sofia.ny@folkhalsomyndigheten.se"),
|
||||
person(role = "ctb",
|
||||
family = "Schade", given = c("Rogier", "P."), email = "r.schade@amsterdamumc.nl"),
|
||||
person(role = "ctb",
|
||||
family = "Souverein", given = "Dennis", email = "d.souvereing@streeklabhaarlem.nl"),
|
||||
person(role = "ctb",
|
||||
family = "Underwood", given = "Anthony", email = "au3@sanger.ac.uk"))
|
||||
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
|
||||
data analysis and to work with microbial and antimicrobial properties by
|
||||
using evidence-based methods and reliable reference data such as LPSN
|
||||
<doi:10.1099/ijsem.0.004332>.
|
||||
Depends:
|
||||
R (>= 3.0.0)
|
||||
Suggests:
|
||||
cleaner,
|
||||
curl,
|
||||
dplyr,
|
||||
ggplot2,
|
||||
ggtext,
|
||||
knitr,
|
||||
microbenchmark,
|
||||
pillar,
|
||||
readxl,
|
||||
rmarkdown,
|
||||
rstudioapi,
|
||||
rvest,
|
||||
skimr,
|
||||
tidyr,
|
||||
tinytest,
|
||||
xml2
|
||||
Authors@R: c(
|
||||
person(given = c("Matthijs", "S."),
|
||||
family = "Berends",
|
||||
email = "m.s.berends@umcg.nl",
|
||||
role = c("aut", "cre"),
|
||||
comment = c(ORCID = "0000-0001-7620-1800")),
|
||||
person(given = c("Christian", "F."),
|
||||
family = "Luz",
|
||||
role = c("aut", "ctb"),
|
||||
comment = c(ORCID = "0000-0001-5809-5995")),
|
||||
person(given = "Dennis",
|
||||
family = "Souverein",
|
||||
role = c("aut", "ctb"),
|
||||
comment = c(ORCID = "0000-0003-0455-0336")),
|
||||
person(given = c("Erwin", "E.", "A."),
|
||||
family = "Hassing",
|
||||
role = c("aut", "ctb")),
|
||||
person(given = c("Casper", "J."),
|
||||
family = "Albers",
|
||||
role = "ths",
|
||||
comment = c(ORCID = "0000-0002-9213-6743")),
|
||||
person(given = c("Judith", "M."),
|
||||
family = "Fonville",
|
||||
role = "ctb"),
|
||||
person(given = c("Alex", "W."),
|
||||
family = "Friedrich",
|
||||
role = "ths",
|
||||
comment = c(ORCID = "0000-0003-4881-038X")),
|
||||
person(given = "Corinna",
|
||||
family = "Glasner",
|
||||
role = "ths",
|
||||
comment = c(ORCID = "0000-0003-1241-1328")),
|
||||
person(given = c("Eric", "H.", "L.", "C.", "M."),
|
||||
family = "Hazenberg",
|
||||
role = "ctb"),
|
||||
person(given = "Gwen",
|
||||
family = "Knight",
|
||||
role = "ctb",
|
||||
comment = c(ORCID = "0000-0002-7263-9896")),
|
||||
person(given = "Annick",
|
||||
family = "Lenglet",
|
||||
role = "ctb",
|
||||
comment = c(ORCID = "0000-0003-2013-8405")),
|
||||
person(given = c("Bart", "C."),
|
||||
family = "Meijer",
|
||||
role = "ctb"),
|
||||
person(given = "Sofia",
|
||||
family = "Ny",
|
||||
role = "ctb",
|
||||
comment = c(ORCID = "0000-0002-2017-1363")),
|
||||
person(given = c("Rogier", "P."),
|
||||
family = "Schade",
|
||||
role = "ctb"),
|
||||
person(given = c("Bhanu", "N.", "M."),
|
||||
family = "Sinha",
|
||||
role = "ths",
|
||||
comment = c(ORCID = "0000-0003-1634-0010")),
|
||||
person(given = "Anthony",
|
||||
family = "Underwood",
|
||||
role = "ctb",
|
||||
comment = c(ORCID = "0000-0002-8547-427")))
|
||||
Depends: R (>= 3.0.0)
|
||||
Enhances:
|
||||
cleaner,
|
||||
skimr,
|
||||
ggplot2
|
||||
Suggests:
|
||||
curl,
|
||||
dplyr,
|
||||
ggtext,
|
||||
knitr,
|
||||
readxl,
|
||||
rmarkdown,
|
||||
rvest,
|
||||
tinytest,
|
||||
xml2
|
||||
VignetteBuilder: knitr,rmarkdown
|
||||
URL: https://msberends.github.io/AMR/, https://github.com/msberends/AMR
|
||||
URL: https://msberends.github.io/AMR, https://github.com/msberends/AMR
|
||||
BugReports: https://github.com/msberends/AMR/issues
|
||||
License: GPL-2 | file LICENSE
|
||||
Encoding: UTF-8
|
||||
LazyData: true
|
||||
RoxygenNote: 7.1.1
|
||||
RoxygenNote: 7.1.2
|
||||
Roxygen: list(markdown = TRUE)
|
||||
|
||||
@@ -5,6 +5,7 @@ S3method("!=",ab_selector)
|
||||
S3method("!=",mic)
|
||||
S3method("%%",mic)
|
||||
S3method("%/%",mic)
|
||||
S3method("&",ab_selector)
|
||||
S3method("&",mic)
|
||||
S3method("*",mic)
|
||||
S3method("+",mic)
|
||||
@@ -35,6 +36,7 @@ S3method("[[<-",mic)
|
||||
S3method("[[<-",mo)
|
||||
S3method("[[<-",rsi)
|
||||
S3method("^",mic)
|
||||
S3method("|",ab_selector)
|
||||
S3method("|",mic)
|
||||
S3method(abs,mic)
|
||||
S3method(acos,mic)
|
||||
@@ -120,7 +122,11 @@ S3method(print,rsi)
|
||||
S3method(prod,mic)
|
||||
S3method(quantile,mic)
|
||||
S3method(range,mic)
|
||||
S3method(rep,ab)
|
||||
S3method(rep,disk)
|
||||
S3method(rep,mic)
|
||||
S3method(rep,mo)
|
||||
S3method(rep,rsi)
|
||||
S3method(round,mic)
|
||||
S3method(sign,mic)
|
||||
S3method(signif,mic)
|
||||
@@ -151,33 +157,44 @@ export("%like%")
|
||||
export("%like_case%")
|
||||
export("%unlike%")
|
||||
export("%unlike_case%")
|
||||
export(NA_disk_)
|
||||
export(NA_mic_)
|
||||
export(NA_rsi_)
|
||||
export(ab_atc)
|
||||
export(ab_atc_group1)
|
||||
export(ab_atc_group2)
|
||||
export(ab_cid)
|
||||
export(ab_class)
|
||||
export(ab_ddd)
|
||||
export(ab_ddd_units)
|
||||
export(ab_from_text)
|
||||
export(ab_group)
|
||||
export(ab_info)
|
||||
export(ab_loinc)
|
||||
export(ab_name)
|
||||
export(ab_property)
|
||||
export(ab_selector)
|
||||
export(ab_synonyms)
|
||||
export(ab_tradenames)
|
||||
export(ab_url)
|
||||
export(administrable_iv)
|
||||
export(administrable_per_os)
|
||||
export(age)
|
||||
export(age_groups)
|
||||
export(all_antimicrobials)
|
||||
export(aminoglycosides)
|
||||
export(aminopenicillins)
|
||||
export(anti_join_microorganisms)
|
||||
export(antifungals)
|
||||
export(antimicrobials_equal)
|
||||
export(antimycobacterials)
|
||||
export(as.ab)
|
||||
export(as.disk)
|
||||
export(as.mic)
|
||||
export(as.mo)
|
||||
export(as.rsi)
|
||||
export(atc_online_ddd)
|
||||
export(atc_online_ddd_units)
|
||||
export(atc_online_groups)
|
||||
export(atc_online_property)
|
||||
export(availability)
|
||||
@@ -207,24 +224,7 @@ export(eucast_dosage)
|
||||
export(eucast_exceptional_phenotypes)
|
||||
export(eucast_rules)
|
||||
export(facet_rsi)
|
||||
export(filter_1st_cephalosporins)
|
||||
export(filter_2nd_cephalosporins)
|
||||
export(filter_3rd_cephalosporins)
|
||||
export(filter_4th_cephalosporins)
|
||||
export(filter_5th_cephalosporins)
|
||||
export(filter_ab_class)
|
||||
export(filter_aminoglycosides)
|
||||
export(filter_betalactams)
|
||||
export(filter_carbapenems)
|
||||
export(filter_cephalosporins)
|
||||
export(filter_first_isolate)
|
||||
export(filter_first_weighted_isolate)
|
||||
export(filter_fluoroquinolones)
|
||||
export(filter_glycopeptides)
|
||||
export(filter_macrolides)
|
||||
export(filter_oxazolidinones)
|
||||
export(filter_penicillins)
|
||||
export(filter_tetracyclines)
|
||||
export(first_isolate)
|
||||
export(fluoroquinolones)
|
||||
export(full_join_microorganisms)
|
||||
@@ -248,13 +248,13 @@ export(is.rsi.eligible)
|
||||
export(is_new_episode)
|
||||
export(italicise_taxonomy)
|
||||
export(italicize_taxonomy)
|
||||
export(key_antibiotics)
|
||||
export(key_antibiotics_equal)
|
||||
export(key_antimicrobials)
|
||||
export(kurtosis)
|
||||
export(labels_rsi_count)
|
||||
export(left_join_microorganisms)
|
||||
export(like)
|
||||
export(lincosamides)
|
||||
export(lipoglycopeptides)
|
||||
export(macrolides)
|
||||
export(mdr_cmi2012)
|
||||
export(mdr_tb)
|
||||
@@ -294,15 +294,16 @@ export(mo_year)
|
||||
export(mrgn)
|
||||
export(n_rsi)
|
||||
export(oxazolidinones)
|
||||
export(p_symbol)
|
||||
export(pca)
|
||||
export(penicillins)
|
||||
export(polymyxins)
|
||||
export(proportion_I)
|
||||
export(proportion_IR)
|
||||
export(proportion_R)
|
||||
export(proportion_S)
|
||||
export(proportion_SI)
|
||||
export(proportion_df)
|
||||
export(quinolones)
|
||||
export(random_disk)
|
||||
export(random_mic)
|
||||
export(random_rsi)
|
||||
@@ -314,11 +315,15 @@ export(rsi_predict)
|
||||
export(scale_rsi_colours)
|
||||
export(scale_y_percent)
|
||||
export(semi_join_microorganisms)
|
||||
export(set_ab_names)
|
||||
export(set_mo_source)
|
||||
export(skewness)
|
||||
export(streptogramins)
|
||||
export(susceptibility)
|
||||
export(tetracyclines)
|
||||
export(theme_rsi)
|
||||
export(trimethoprims)
|
||||
export(ureidopenicillins)
|
||||
importFrom(graphics,arrows)
|
||||
importFrom(graphics,axis)
|
||||
importFrom(graphics,barplot)
|
||||
|
||||
@@ -1,7 +1,74 @@
|
||||
# `AMR` 1.7.1
|
||||
# `AMR` 1.7.1.9062
|
||||
## <small>Last updated: 6 December 2021</small>
|
||||
|
||||
### Breaking changes
|
||||
* Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version
|
||||
* Removed the `key_antibiotics()` and `key_antibiotics_equal()` functions, which were deprecated and superseded by `key_antimicrobials()` and `antimicrobials_equal()`
|
||||
* Removed all previously implemented `ggplot2::ggplot()` generics for classes `<mic>`, `<disk>`, `<rsi>` and `<resistance_predict>` as they did not follow the `ggplot2` logic. They were replaced with `ggplot2::autoplot()` generics.
|
||||
|
||||
### New
|
||||
* Support for EUCAST Intrinsic Resistance and Unusual Phenotypes v3.3 (October 2021), effective in the `eucast_rules()` function. This is now the default guideline (all other guidelines are still available).
|
||||
* Function `set_ab_names()` to rename data set columns that resemble antimicrobial drugs. This allows for quickly renaming columns to official names, ATC codes, etc. Its second argument can be a tidyverse way of selecting:
|
||||
```r
|
||||
example_isolates %>% set_ab_names(where(is.rsi))
|
||||
example_isolates %>% set_ab_names(AMC:GEN, property = "atc")
|
||||
```
|
||||
* Support for Danish, and also added missing translations of all antimicrobial drugs in Italian, French and Portuguese
|
||||
|
||||
### Changed
|
||||
* Updated the bacterial taxonomy to 5 October 2021 (according to [LPSN](https://lpsn.dsmz.de)), including all 11 new staphylococcal species named since 1 January last year
|
||||
* The `antibiotics` data set now contains **all ATC codes** that are available through the [WHOCC website](https://www.whocc.no), regardless of drugs being present in more than one ATC group. This means that:
|
||||
* Some drugs now contain multiple ATC codes (e.g., metronidazole contains 5)
|
||||
* `antibiotics$atc` is now a `list` containing `character` vectors, and this `atc` column was moved to the 5th position of the `antibiotics` data set
|
||||
* `ab_atc()` does not always return a character vector of length 1, and returns a `list` if the input is larger than length 1
|
||||
* `ab_info()` has a slightly different output
|
||||
* Some DDDs (daily defined doses) were added or updated according to newly included ATC codes
|
||||
* Antibiotic selectors
|
||||
* They now also work in R-3.0 and R-3.1, supporting every version of R since 2013 like the rest of the package
|
||||
* Added more selectors for antibiotic classes: `aminopenicillins()`, `antifungals()`, `antimycobacterials()`, `lincosamides()`, `lipoglycopeptides()`, `polymyxins()`, `quinolones()`, `streptogramins()`, `trimethoprims()` and `ureidopenicillins()`
|
||||
* Added specific selectors for certain types for treatment: `administrable_per_os()` and `administrable_iv()`, which are based on available Defined Daily Doses (DDDs), as defined by the WHOCC. These are ideal for e.g. analysing pathogens in primary care where IV treatment is not an option. They can be combined with other AB selectors, e.g. to select penicillins that are only administrable per os (i.e., orally):
|
||||
```r
|
||||
example_isolates[, penicillins() & administrable_per_os()] # base R
|
||||
example_isolates %>% select(penicillins() & administrable_per_os()) # dplyr
|
||||
```
|
||||
* Added the selector `ab_selector()`, which accepts a filter to be used internally on the `antibiotics` data set, yielding great flexibility on drug properties, such as selecting antibiotic columns with an oral DDD of at least 1 gram:
|
||||
```r
|
||||
example_isolates[, ab_selector(oral_ddd > 1 & oral_units == "g")] # base R
|
||||
example_isolates %>% select(ab_selector(oral_ddd > 1 & oral_units == "g")) # dplyr
|
||||
```
|
||||
* Fix for using selectors multiple times in one call (e.g., using them in `dplyr::filter()` and immediately after in `dplyr::select()`)
|
||||
* Added argument `only_treatable`, which defaults to `TRUE` and will exclude drugs that are only for laboratory tests and not for treating patients (such as imipenem/EDTA and gentamicin-high)
|
||||
* Fixed the Gram stain (`mo_gramstain()`) determination of the taxonomic class Negativicutes within the phylum of Firmicutes - they were considered Gram-positives because of their phylum but are actually Gram-negative. This impacts 137 taxonomic species, genera and families, such as *Negativicoccus* and *Veillonella*.
|
||||
* Dramatic speed improvement for `first_isolate()`
|
||||
* Fix to prevent introducing `NA`s for old MO codes when running `as.mo()` on them
|
||||
* Added more informative error messages when any of the `proportion_*()` and `count_*()` functions fail
|
||||
* When printing a tibble with any old MO code, a warning will be thrown that old codes should be updated using `as.mo()`
|
||||
* Improved automatic column selector when `col_*` arguments are left blank, e.g. in `first_isolate()`
|
||||
* The right input types for `random_mic()`, `random_disk()` and `random_rsi()` are now enforced
|
||||
* `as.rsi()` has an improved algorithm and can now also correct for textual input (such as "Susceptible", "Resistant") in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish
|
||||
* `as.mic()` has an improved algorithm
|
||||
* When warnings are thrown because of too few isolates in any `count_*()`, `proportion_*()` function (or `resistant()` or `susceptible()`), the `dplyr` group will be shown, if available
|
||||
* Fix for legends created with `scale_rsi_colours()` when using `ggplot2` v3.3.4 or higher (this is ggplot2 bug 4511, soon to be fixed)
|
||||
* Fix for minor translation errors
|
||||
* Fix for the MIC interpretation of *Morganellaceae* (such as *Morganella* and *Proteus*) when using the EUCAST 2021 guideline
|
||||
* Improved algorithm for generating random MICs with `random_mic()`
|
||||
* Improved plot legends for MICs and disk diffusion values
|
||||
* Improved speed of `as.ab()` and all `ab_*()` functions
|
||||
* Added `fortify()` extensions for plotting methods
|
||||
* `NA` values of the classes `<mic>`, `<disk>` and `<rsi>` are now exported objects of this package, e.g. `NA_mic_` is an `NA` of class `mic` (just like the base R `NA_character_` is an `NA` of class `character`)
|
||||
* The `proportion_df()`, `count_df()` and `rsi_df()` functions now return with the additional S3 class 'rsi_df' so they can be extended by other packages
|
||||
* The `mdro()` function now returns `NA` for all rows that have no test results
|
||||
* The `species_id` column in the `microorganisms` data set now only contains LPSN record numbers. For this reason, this column is now numeric instead of a character, and `mo_url()` has been updated to reflect this change.
|
||||
* Fixed a small bug in the functions `get_episode()` and `is_new_episode()`
|
||||
* `get_episode()` and `is_new_episode()` can now cope with `NA`s
|
||||
|
||||
### Other
|
||||
* This package is now being maintained by two epidemiologists and a data scientist from two different non-profit healthcare organisations. All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.
|
||||
|
||||
|
||||
# AMR 1.7.1
|
||||
|
||||
### Breaking change
|
||||
* Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using `as.rsi()`)
|
||||
* All antibiotic class selectors (such as `carbapenems()`, `aminoglycosides()`) can now be used for filtering as well, making all their accompanying `filter_*()` functions redundant (such as `filter_carbapenems()`, `filter_aminoglycosides()`). These functions are now deprecated and will be removed in a next release. Examples of how the selectors can be used for filtering:
|
||||
```r
|
||||
# select columns with results for carbapenems
|
||||
@@ -21,6 +88,7 @@
|
||||
```
|
||||
|
||||
### New
|
||||
* Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using `as.rsi()`)
|
||||
* Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()`
|
||||
* Function `italicise_taxonomy()` to make taxonomic names within a string italic, with support for markdown and ANSI
|
||||
* Support for all four methods to determine first isolates as summarised by Hindler *et al.* (doi: [10.1086/511864](https://doi.org/10.1086/511864)): isolate-based, patient-based, episode-based and phenotype-based. The last method is now the default.
|
||||
@@ -72,7 +140,7 @@
|
||||
* All unit tests are now processed by the `tinytest` package, instead of the `testthat` package. The `testthat` package unfortunately requires tons of dependencies that are also heavy and only usable for recent R versions, disallowing developers to test a package under any R 3.* version. On the contrary, the `tinytest` package is very lightweight and dependency-free.
|
||||
|
||||
|
||||
# `AMR` 1.6.0
|
||||
# AMR 1.6.0
|
||||
|
||||
### New
|
||||
* Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the `eucast_rules()` function and in `as.rsi()` to interpret MIC and disk diffusion values. This is now the default guideline in this package.
|
||||
@@ -166,7 +234,7 @@
|
||||
* Loading the package (i.e., `library(AMR)`) now is ~50 times faster than before, in costs of package size (which increased by ~3 MB)
|
||||
|
||||
|
||||
# `AMR` 1.5.0
|
||||
# AMR 1.5.0
|
||||
|
||||
### New
|
||||
* Functions `get_episode()` and `is_new_episode()` to determine (patient) episodes which are not necessarily based on microorganisms. The `get_episode()` function returns the index number of the episode per group, while the `is_new_episode()` function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode. They also support `dplyr`s grouping (i.e. using `group_by()`):
|
||||
@@ -243,7 +311,7 @@
|
||||
* Added CodeFactor as a continuous code review to this package: <https://www.codefactor.io/repository/github/msberends/amr/>
|
||||
* Added Dr. Rogier Schade as contributor
|
||||
|
||||
# `AMR` 1.4.0
|
||||
# AMR 1.4.0
|
||||
|
||||
### New
|
||||
* Support for 'EUCAST Expert Rules' / 'EUCAST Intrinsic Resistance and Unusual Phenotypes' version 3.2 of May 2020. With this addition to the previously implemented version 3.1 of 2016, the `eucast_rules()` function can now correct for more than 180 different antibiotics and the `mdro()` function can determine multidrug resistance based on more than 150 different antibiotics. All previously implemented versions of the EUCAST rules are now maintained and kept available in this package. The `eucast_rules()` function consequently gained the arguments `version_breakpoints` (at the moment defaults to v10.0, 2020) and `version_expertrules` (at the moment defaults to v3.2, 2020). The `example_isolates` data set now also reflects the change from v3.1 to v3.2. The `mdro()` function now accepts `guideline == "EUCAST3.1"` and `guideline == "EUCAST3.2"`.
|
||||
@@ -315,7 +383,7 @@
|
||||
* Removed unnecessary references to the `base` package
|
||||
* Added packages that could be useful for some functions to the `Suggests` field of the `DESCRIPTION` file
|
||||
|
||||
# `AMR` 1.3.0
|
||||
# AMR 1.3.0
|
||||
|
||||
### New
|
||||
* Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally
|
||||
@@ -368,7 +436,7 @@
|
||||
### Other
|
||||
* Moved primary location of this project from GitLab to [GitHub](https://github.com/msberends/AMR), giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI.
|
||||
|
||||
# `AMR` 1.2.0
|
||||
# AMR 1.2.0
|
||||
|
||||
### Breaking
|
||||
* Removed code dependency on all other R packages, making this package fully independent of the development process of others. This is a major code change, but will probably not be noticeable by most users.
|
||||
@@ -406,7 +474,7 @@
|
||||
* Removed previously deprecated function `p.symbol()` - it was replaced with `p_symbol()`
|
||||
* Removed function `read.4d()`, that was only useful for reading data from an old test database.
|
||||
|
||||
# `AMR` 1.1.0
|
||||
# AMR 1.1.0
|
||||
|
||||
### New
|
||||
* Support for easy principal component analysis for AMR, using the new `pca()` function
|
||||
@@ -428,7 +496,7 @@
|
||||
* Support for the upcoming `dplyr` version 1.0.0
|
||||
* More robust assigning for classes `rsi` and `mic`
|
||||
|
||||
# `AMR` 1.0.1
|
||||
# AMR 1.0.1
|
||||
|
||||
### Changed
|
||||
* Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline
|
||||
@@ -444,13 +512,13 @@
|
||||
* Added `uti` (as abbreviation of urinary tract infections) as argument to `as.rsi()`, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs
|
||||
* Info printing in functions `eucast_rules()`, `first_isolate()`, `mdro()` and `resistance_predict()` will now at default only print when R is in an interactive mode (i.e. not in RMarkdown)
|
||||
|
||||
# `AMR` 1.0.0
|
||||
# AMR 1.0.0
|
||||
|
||||
This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.
|
||||
|
||||
### New
|
||||
* Support for the newest [EUCAST Clinical Breakpoint Tables v.10.0](https://www.eucast.org/clinical_breakpoints/), valid from 1 January 2020. This affects translation of MIC and disk zones using `as.rsi()` and inferred resistance and susceptibility using `eucast_rules()`.
|
||||
* The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt>. This **allows for machine reading these guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file [can be found here](https://github.com/msberends/AMR/blob/master/data-raw/read_EUCAST.R).
|
||||
* The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt>. This **allows for machine reading these guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file [can be found here](https://github.com/msberends/AMR/blob/main/data-raw/read_EUCAST.R).
|
||||
* Support for LOINC and SNOMED codes
|
||||
* Support for LOINC codes in the `antibiotics` data set. Use `ab_loinc()` to retrieve LOINC codes, or use a LOINC code for input in any `ab_*` function:
|
||||
```r
|
||||
@@ -492,7 +560,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
|
||||
* Full support for the upcoming R 4.0
|
||||
* Removed unnecessary `AMR::` calls
|
||||
|
||||
# `AMR` 0.9.0
|
||||
# AMR 0.9.0
|
||||
|
||||
### Breaking
|
||||
* Adopted Adeolu *et al.* (2016), [PMID 27620848](https:/pubmed.ncbi.nlm.nih.gov/27620848/) for the `microorganisms` data set, which means that the new order Enterobacterales now consists of a part of the existing family Enterobacteriaceae, but that this family has been split into other families as well (like *Morganellaceae* and *Yersiniaceae*). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations with `mdro()` will now use the Enterobacterales order for all guidelines before 2016 that were dependent on the Enterobacteriaceae family.
|
||||
@@ -558,7 +626,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
|
||||
* Change dependency on `clean` to `cleaner`, as this package was renamed accordingly upon CRAN request
|
||||
* Added Dr. Sofia Ny as contributor
|
||||
|
||||
# `AMR` 0.8.0
|
||||
# AMR 0.8.0
|
||||
|
||||
### Breaking
|
||||
* Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new argument `include_unknown`:
|
||||
@@ -687,7 +755,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
|
||||
* Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors
|
||||
* Cleaned the coding style of every single syntax line in this package with the help of the `lintr` package
|
||||
|
||||
# `AMR` 0.7.1
|
||||
# AMR 0.7.1
|
||||
|
||||
#### New
|
||||
* Function `rsi_df()` to transform a `data.frame` to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions `count_df()` and `portion_df()` to immediately show resistance percentages and number of available isolates:
|
||||
@@ -748,7 +816,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
|
||||
#### Other
|
||||
* Fixed a note thrown by CRAN tests
|
||||
|
||||
# `AMR` 0.7.0
|
||||
# AMR 0.7.0
|
||||
|
||||
#### New
|
||||
* Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use `as.rsi()` on an MIC value (created with `as.mic()`), a disk diffusion value (created with the new `as.disk()`) or on a complete date set containing columns with MIC or disk diffusion values.
|
||||
@@ -767,7 +835,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
|
||||
* All references to antibiotics in our package now use EARS-Net codes, like `AMX` for amoxicillin
|
||||
* Functions `atc_certe`, `ab_umcg` and `atc_trivial_nl` have been removed
|
||||
* All `atc_*` functions are superseded by `ab_*` functions
|
||||
* All output will be translated by using an included translation file which [can be viewed here](https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv)
|
||||
* All output will be translated by using an included translation file which [can be viewed here](https://github.com/msberends/AMR/blob/main/data-raw/translations.tsv)
|
||||
* Improvements to plotting AMR results with `ggplot_rsi()`:
|
||||
* New argument `colours` to set the bar colours
|
||||
* New arguments `title`, `subtitle`, `caption`, `x.title` and `y.title` to set titles and axis descriptions
|
||||
@@ -791,7 +859,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
|
||||
freq(age) %>%
|
||||
boxplot()
|
||||
```
|
||||
* Removed all hardcoded EUCAST rules and replaced them with a new reference file which [can be viewed here](https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv)
|
||||
* Removed all hardcoded EUCAST rules and replaced them with a new reference file which [can be viewed here](https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv)
|
||||
* Added ceftazidim intrinsic resistance to *Streptococci*
|
||||
* Changed default settings for `age_groups()`, to let groups of fives and tens end with 100+ instead of 120+
|
||||
* Fix for `freq()` for when all values are `NA`
|
||||
@@ -806,13 +874,13 @@ This software is now out of beta and considered stable. Nonetheless, this packag
|
||||
#### Other
|
||||
* Support for R 3.6.0 and later by providing support for [staged install](https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html)
|
||||
|
||||
# `AMR` 0.6.1
|
||||
# AMR 0.6.1
|
||||
|
||||
#### Changed
|
||||
* Fixed a critical bug when using `eucast_rules()` with `verbose = TRUE`
|
||||
* Coercion of microbial IDs are now written to the package namespace instead of the user's home folder, to comply with the CRAN policy
|
||||
|
||||
# `AMR` 0.6.0
|
||||
# AMR 0.6.0
|
||||
|
||||
**New website!**
|
||||
|
||||
@@ -1005,7 +1073,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
|
||||
#### Other
|
||||
* Updated licence text to emphasise GPL 2.0 and that this is an R package.
|
||||
|
||||
# `AMR` 0.5.0
|
||||
# AMR 0.5.0
|
||||
|
||||
#### New
|
||||
* Repository moved to GitLab
|
||||
@@ -1088,7 +1156,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
|
||||
* Updated vignettes to comply with README
|
||||
|
||||
|
||||
# `AMR` 0.4.0
|
||||
# AMR 0.4.0
|
||||
|
||||
#### New
|
||||
* The data set `microorganisms` now contains **all microbial taxonomic data from ITIS** (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via https://itis.gov. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set `microorganisms.old` contains all previously known taxonomic names from those kingdoms.
|
||||
@@ -1199,7 +1267,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
|
||||
#### Other
|
||||
* More unit tests to ensure better integrity of functions
|
||||
|
||||
# `AMR` 0.3.0
|
||||
# AMR 0.3.0
|
||||
|
||||
#### New
|
||||
* **BREAKING**: `rsi_df` was removed in favour of new functions `portion_R`, `portion_IR`, `portion_I`, `portion_SI` and `portion_S` to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old `rsi` function. The old function still works, but is deprecated.
|
||||
@@ -1269,7 +1337,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
|
||||
* Windows: https://ci.appveyor.com/project/msberends/amr
|
||||
* Added thesis advisors to DESCRIPTION file
|
||||
|
||||
# `AMR` 0.2.0
|
||||
# AMR 0.2.0
|
||||
|
||||
#### New
|
||||
* Full support for Windows, Linux and macOS
|
||||
@@ -1302,9 +1370,9 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
|
||||
* Added [ORCID](https://orcid.org) of authors to DESCRIPTION file
|
||||
* Added unit testing with the `testthat` package
|
||||
* Added build tests for Linux and macOS using Travis CI (https://travis-ci.org/msberends/AMR)
|
||||
* Added line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/master/R)
|
||||
* Added line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/main/R)
|
||||
|
||||
# `AMR` 0.1.1
|
||||
# AMR 0.1.1
|
||||
|
||||
* `EUCAST_rules` applies for amoxicillin even if ampicillin is missing
|
||||
* Edited column names to comply with GLIMS, the laboratory information system
|
||||
@@ -1312,6 +1380,6 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
|
||||
* Renamed 'Daily Defined Dose' to 'Defined Daily Dose'
|
||||
* Added barplots for `rsi` and `mic` classes
|
||||
|
||||
# `AMR` 0.1.0
|
||||
# AMR 0.1.0
|
||||
|
||||
* First submission to CRAN.
|
||||
|
||||
+180
-132
@@ -53,15 +53,87 @@ pm_left_join <- function(x, y, by = NULL, suffix = c(".x", ".y")) {
|
||||
merged
|
||||
}
|
||||
|
||||
quick_case_when <- function(...) {
|
||||
vectors <- list(...)
|
||||
split <- lapply(vectors, function(x) unlist(strsplit(paste(deparse(x), collapse = ""), "~", fixed = TRUE)))
|
||||
for (i in seq_len(length(vectors))) {
|
||||
if (eval(parse(text = split[[i]][1]), envir = parent.frame())) {
|
||||
return(eval(parse(text = split[[i]][2]), envir = parent.frame()))
|
||||
# support where() like tidyverse:
|
||||
# adapted from https://github.com/nathaneastwood/poorman/blob/52eb6947e0b4430cd588976ed8820013eddf955f/R/where.R#L17-L32
|
||||
where <- function(fn) {
|
||||
if (!is.function(fn)) {
|
||||
stop(pm_deparse_var(fn), " is not a valid predicate function.")
|
||||
}
|
||||
preds <- unlist(lapply(
|
||||
pm_select_env$.data,
|
||||
function(x, fn) {
|
||||
do.call("fn", list(x))
|
||||
},
|
||||
fn
|
||||
))
|
||||
if (!is.logical(preds)) stop("`where()` must be used with functions that return `TRUE` or `FALSE`.")
|
||||
data_cols <- pm_select_env$get_colnames()
|
||||
cols <- data_cols[preds]
|
||||
which(data_cols %in% cols)
|
||||
}
|
||||
|
||||
# copied and slightly rewritten from poorman under same license (2021-10-15)
|
||||
quick_case_when <- function (...) {
|
||||
fs <- list(...)
|
||||
lapply(fs, function(x) if (class(x) != "formula")
|
||||
stop("`case_when()` requires formula inputs."))
|
||||
n <- length(fs)
|
||||
if (n == 0L)
|
||||
stop("No cases provided.")
|
||||
|
||||
validate_case_when_length <- function (query, value, fs) {
|
||||
lhs_lengths <- lengths(query)
|
||||
rhs_lengths <- lengths(value)
|
||||
all_lengths <- unique(c(lhs_lengths, rhs_lengths))
|
||||
if (length(all_lengths) <= 1L)
|
||||
return(all_lengths[[1L]])
|
||||
non_atomic_lengths <- all_lengths[all_lengths != 1L]
|
||||
len <- non_atomic_lengths[[1L]]
|
||||
if (length(non_atomic_lengths) == 1L)
|
||||
return(len)
|
||||
inconsistent_lengths <- non_atomic_lengths[-1L]
|
||||
lhs_problems <- lhs_lengths %in% inconsistent_lengths
|
||||
rhs_problems <- rhs_lengths %in% inconsistent_lengths
|
||||
problems <- lhs_problems | rhs_problems
|
||||
if (any(problems)) {
|
||||
stop("The following formulas must be length ", len, " or 1, not ",
|
||||
paste(inconsistent_lengths, collapse = ", "), ".\n ",
|
||||
paste(fs[problems], collapse = "\n "),
|
||||
call. = FALSE)
|
||||
}
|
||||
}
|
||||
return(NA)
|
||||
|
||||
replace_with <- function (x, i, val, arg_name) {
|
||||
if (is.null(val))
|
||||
return(x)
|
||||
i[is.na(i)] <- FALSE
|
||||
if (length(val) == 1L) {
|
||||
x[i] <- val
|
||||
}
|
||||
else {
|
||||
x[i] <- val[i]
|
||||
}
|
||||
x
|
||||
}
|
||||
|
||||
query <- vector("list", n)
|
||||
value <- vector("list", n)
|
||||
default_env <- parent.frame()
|
||||
for (i in seq_len(n)) {
|
||||
query[[i]] <- eval(fs[[i]][[2]], envir = default_env)
|
||||
value[[i]] <- eval(fs[[i]][[3]], envir = default_env)
|
||||
if (!is.logical(query[[i]]))
|
||||
stop(fs[[i]][[2]], " does not return a `logical` vector.")
|
||||
}
|
||||
m <- validate_case_when_length(query, value, fs)
|
||||
out <- value[[1]][rep(NA_integer_, m)]
|
||||
replaced <- rep(FALSE, m)
|
||||
for (i in seq_len(n)) {
|
||||
out <- replace_with(out, query[[i]] & !replaced, value[[i]],
|
||||
NULL)
|
||||
replaced <- replaced | (query[[i]] & !is.na(query[[i]]))
|
||||
}
|
||||
out
|
||||
}
|
||||
|
||||
# No export, no Rd
|
||||
@@ -135,7 +207,6 @@ check_dataset_integrity <- function() {
|
||||
" the AMR package from working correctly: ",
|
||||
vector_and(overwritten, quotes = "'"),
|
||||
".\nPlease rename your object", plural[3], ".", call = FALSE)
|
||||
remember_thrown_message("dataset_overwritten")
|
||||
}
|
||||
}
|
||||
# check if other packages did not overwrite our data sets
|
||||
@@ -170,65 +241,73 @@ search_type_in_df <- function(x, type, info = TRUE) {
|
||||
|
||||
# remove attributes from other packages
|
||||
x <- as.data.frame(x, stringsAsFactors = FALSE)
|
||||
colnames(x) <- trimws(colnames(x))
|
||||
colnames_formatted <- tolower(generalise_antibiotic_name(colnames(x)))
|
||||
|
||||
# -- mo
|
||||
if (type == "mo") {
|
||||
if (any(vapply(FUN.VALUE = logical(1), x, is.mo))) {
|
||||
found <- sort(colnames(x)[vapply(FUN.VALUE = logical(1), x, is.mo)])[1]
|
||||
} else if ("mo" %in% colnames(x) &
|
||||
suppressWarnings(
|
||||
all(x$mo %in% c(NA, microorganisms$mo)))) {
|
||||
# take first <mo> column
|
||||
found <- colnames(x)[vapply(FUN.VALUE = logical(1), x, is.mo)]
|
||||
} else if ("mo" %in% colnames_formatted &
|
||||
suppressWarnings(all(x$mo %in% c(NA, microorganisms$mo)))) {
|
||||
found <- "mo"
|
||||
} else if (any(colnames(x) %like% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$")) {
|
||||
found <- sort(colnames(x)[colnames(x) %like% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$"])[1]
|
||||
} else if (any(colnames(x) %like% "^(microorganism|organism|bacteria|ba[ck]terie)")) {
|
||||
found <- sort(colnames(x)[colnames(x) %like% "^(microorganism|organism|bacteria|ba[ck]terie)"])[1]
|
||||
} else if (any(colnames(x) %like% "species")) {
|
||||
found <- sort(colnames(x)[colnames(x) %like% "species"])[1]
|
||||
} else if (any(colnames_formatted %like_case% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$")) {
|
||||
found <- sort(colnames(x)[colnames_formatted %like_case% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$"])
|
||||
} else if (any(colnames_formatted %like_case% "^(microorganism|organism|bacteria|ba[ck]terie)")) {
|
||||
found <- sort(colnames(x)[colnames_formatted %like_case% "^(microorganism|organism|bacteria|ba[ck]terie)"])
|
||||
} else if (any(colnames_formatted %like_case% "species")) {
|
||||
found <- sort(colnames(x)[colnames_formatted %like_case% "species"])
|
||||
}
|
||||
|
||||
}
|
||||
# -- key antibiotics
|
||||
if (type %in% c("keyantibiotics", "keyantimicrobials")) {
|
||||
if (any(colnames(x) %like% "^key.*(ab|antibiotics|antimicrobials)")) {
|
||||
found <- sort(colnames(x)[colnames(x) %like% "^key.*(ab|antibiotics|antimicrobials)"])[1]
|
||||
if (any(colnames_formatted %like_case% "^key.*(ab|antibiotics|antimicrobials)")) {
|
||||
found <- sort(colnames(x)[colnames_formatted %like_case% "^key.*(ab|antibiotics|antimicrobials)"])
|
||||
}
|
||||
}
|
||||
# -- date
|
||||
if (type == "date") {
|
||||
if (any(colnames(x) %like% "^(specimen date|specimen_date|spec_date)")) {
|
||||
if (any(colnames_formatted %like_case% "^(specimen date|specimen_date|spec_date)")) {
|
||||
# WHONET support
|
||||
found <- sort(colnames(x)[colnames(x) %like% "^(specimen date|specimen_date|spec_date)"])[1]
|
||||
found <- sort(colnames(x)[colnames_formatted %like_case% "^(specimen date|specimen_date|spec_date)"])
|
||||
if (!any(class(pm_pull(x, found)) %in% c("Date", "POSIXct"))) {
|
||||
stop(font_red(paste0("Found column '", font_bold(found), "' to be used as input for `col_", type,
|
||||
"`, but this column contains no valid dates. Transform its values to valid dates first.")),
|
||||
call. = FALSE)
|
||||
}
|
||||
|
||||
} else if (any(vapply(FUN.VALUE = logical(1), x, function(x) inherits(x, c("Date", "POSIXct"))))) {
|
||||
found <- sort(colnames(x)[vapply(FUN.VALUE = logical(1), x, function(x) inherits(x, c("Date", "POSIXct")))])[1]
|
||||
# take first <Date> column
|
||||
found <- colnames(x)[vapply(FUN.VALUE = logical(1), x, function(x) inherits(x, c("Date", "POSIXct")))]
|
||||
}
|
||||
}
|
||||
# -- patient id
|
||||
if (type == "patient_id") {
|
||||
if (any(colnames(x) %like% "^(identification |patient|patid)")) {
|
||||
found <- sort(colnames(x)[colnames(x) %like% "^(identification |patient|patid)"])[1]
|
||||
crit1 <- colnames_formatted %like_case% "^(patient|patid)"
|
||||
if (any(crit1)) {
|
||||
found <- colnames(x)[crit1]
|
||||
} else {
|
||||
crit2 <- colnames_formatted %like_case% "(identification |patient|pat.*id)"
|
||||
if (any(crit2)) {
|
||||
found <- colnames(x)[crit2]
|
||||
}
|
||||
}
|
||||
}
|
||||
# -- specimen
|
||||
if (type == "specimen") {
|
||||
if (any(colnames(x) %like% "(specimen type|spec_type)")) {
|
||||
found <- sort(colnames(x)[colnames(x) %like% "(specimen type|spec_type)"])[1]
|
||||
} else if (any(colnames(x) %like% "^(specimen)")) {
|
||||
found <- sort(colnames(x)[colnames(x) %like% "^(specimen)"])[1]
|
||||
if (any(colnames_formatted %like_case% "(specimen type|spec_type)")) {
|
||||
found <- sort(colnames(x)[colnames_formatted %like_case% "(specimen type|spec_type)"])
|
||||
} else if (any(colnames_formatted %like_case% "^(specimen)")) {
|
||||
found <- sort(colnames(x)[colnames_formatted %like_case% "^(specimen)"])
|
||||
}
|
||||
}
|
||||
# -- UTI (urinary tract infection)
|
||||
if (type == "uti") {
|
||||
if (any(colnames(x) == "uti")) {
|
||||
found <- colnames(x)[colnames(x) == "uti"][1]
|
||||
} else if (any(colnames(x) %like% "(urine|urinary)")) {
|
||||
found <- sort(colnames(x)[colnames(x) %like% "(urine|urinary)"])[1]
|
||||
if (any(colnames_formatted == "uti")) {
|
||||
found <- colnames(x)[colnames_formatted == "uti"]
|
||||
} else if (any(colnames_formatted %like_case% "(urine|urinary)")) {
|
||||
found <- sort(colnames(x)[colnames_formatted %like_case% "(urine|urinary)"])
|
||||
}
|
||||
if (!is.null(found)) {
|
||||
# this column should contain logicals
|
||||
@@ -241,14 +320,15 @@ search_type_in_df <- function(x, type, info = TRUE) {
|
||||
}
|
||||
}
|
||||
|
||||
found <- found[1]
|
||||
|
||||
if (!is.null(found) & info == TRUE) {
|
||||
if (message_not_thrown_before(fn = paste0("search_", type))) {
|
||||
msg <- paste0("Using column '", font_bold(found), "' as input for `col_", type, "`.")
|
||||
if (type %in% c("keyantibiotics", "specimen")) {
|
||||
if (type %in% c("keyantibiotics", "keyantimicrobials", "specimen")) {
|
||||
msg <- paste(msg, "Use", font_bold(paste0("col_", type), "= FALSE"), "to prevent this.")
|
||||
}
|
||||
message_(msg)
|
||||
remember_thrown_message(fn = paste0("search_", type))
|
||||
}
|
||||
}
|
||||
found
|
||||
@@ -288,12 +368,15 @@ stop_ifnot_installed <- function(package) {
|
||||
return(invisible())
|
||||
}
|
||||
|
||||
pkg_is_available <- function(pkg, also_load = TRUE) {
|
||||
pkg_is_available <- function(pkg, also_load = TRUE, min_version = NULL) {
|
||||
if (also_load == TRUE) {
|
||||
out <- suppressWarnings(require(pkg, character.only = TRUE, warn.conflicts = FALSE, quietly = TRUE))
|
||||
out <- suppressWarnings(require(pkg, character.only = TRUE, warn.conflicts = FALSE))
|
||||
} else {
|
||||
out <- requireNamespace(pkg, quietly = TRUE)
|
||||
}
|
||||
if (!is.null(min_version)) {
|
||||
out <- out && utils::packageVersion(pkg) >= min_version
|
||||
}
|
||||
isTRUE(out)
|
||||
}
|
||||
|
||||
@@ -390,6 +473,9 @@ word_wrap <- function(...,
|
||||
# format backticks
|
||||
msg <- gsub("(`.+?`)", font_grey_bg("\\1"), msg)
|
||||
|
||||
# clean introduced whitespace between fullstops
|
||||
msg <- gsub("[.] +[.]", "..", msg)
|
||||
|
||||
msg
|
||||
}
|
||||
|
||||
@@ -506,12 +592,12 @@ dataset_UTF8_to_ASCII <- function(df) {
|
||||
|
||||
# for eucast_rules() and mdro(), creates markdown output with URLs and names
|
||||
create_eucast_ab_documentation <- function() {
|
||||
x <- trimws(unique(toupper(unlist(strsplit(eucast_rules_file$then_change_these_antibiotics, ",")))))
|
||||
x <- trimws(unique(toupper(unlist(strsplit(EUCAST_RULES_DF$then_change_these_antibiotics, ",")))))
|
||||
ab <- character()
|
||||
for (val in x) {
|
||||
if (val %in% ls(envir = asNamespace("AMR"))) {
|
||||
if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) {
|
||||
# antibiotic group names, as defined in data-raw/_internals.R, such as `CARBAPENEMS`
|
||||
val <- eval(parse(text = val), envir = asNamespace("AMR"))
|
||||
val <- eval(parse(text = paste0("AB_", val)), envir = asNamespace("AMR"))
|
||||
} else if (val %in% AB_lookup$ab) {
|
||||
# separate drugs, such as `AMX`
|
||||
val <- as.ab(val)
|
||||
@@ -521,7 +607,7 @@ create_eucast_ab_documentation <- function() {
|
||||
ab <- c(ab, val)
|
||||
}
|
||||
ab <- unique(ab)
|
||||
atcs <- ab_atc(ab)
|
||||
atcs <- ab_atc(ab, only_first = TRUE)
|
||||
# only keep ABx with an ATC code:
|
||||
ab <- ab[!is.na(atcs)]
|
||||
ab_names <- ab_name(ab, language = NULL, tolower = TRUE)
|
||||
@@ -533,7 +619,7 @@ create_eucast_ab_documentation <- function() {
|
||||
out
|
||||
}
|
||||
|
||||
vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, last_sep = " or ") {
|
||||
vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE, last_sep = " or ") {
|
||||
# makes unique and sorts, and this also removed NAs
|
||||
v <- unique(v)
|
||||
if (isTRUE(sort)) {
|
||||
@@ -549,6 +635,9 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, last_sep =
|
||||
} else {
|
||||
quotes <- quotes[1L]
|
||||
}
|
||||
if (isTRUE(initial_captital)) {
|
||||
v[1] <- gsub("^([a-z])", "\\U\\1", v[1], perl = TRUE)
|
||||
}
|
||||
if (length(v) == 1) {
|
||||
return(paste0(quotes, v, quotes))
|
||||
}
|
||||
@@ -561,8 +650,9 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, last_sep =
|
||||
last_sep, paste0(quotes, v[length(v)], quotes))
|
||||
}
|
||||
|
||||
vector_and <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE) {
|
||||
vector_or(v = v, quotes = quotes, reverse = reverse, sort = sort, last_sep = " and ")
|
||||
vector_and <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE) {
|
||||
vector_or(v = v, quotes = quotes, reverse = reverse, sort = sort,
|
||||
initial_captital = initial_captital, last_sep = " and ")
|
||||
}
|
||||
|
||||
format_class <- function(class, plural = FALSE) {
|
||||
@@ -696,7 +786,7 @@ meet_criteria <- function(object,
|
||||
ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1,
|
||||
"be a finite number",
|
||||
"all be finite numbers"),
|
||||
" (i.e., not be infinite)",
|
||||
" (i.e. not be infinite)",
|
||||
call = call_depth)
|
||||
}
|
||||
if (!is.null(contains_column_class)) {
|
||||
@@ -714,11 +804,6 @@ meet_criteria <- function(object,
|
||||
}
|
||||
|
||||
get_current_data <- function(arg_name, call) {
|
||||
# check if retrieved before, then get it from package environment
|
||||
if (identical(unique_call_id(entire_session = FALSE), pkg_env$get_current_data.call)) {
|
||||
return(pkg_env$get_current_data.out)
|
||||
}
|
||||
|
||||
# try dplyr::cur_data_all() first to support dplyr groups
|
||||
# only useful for e.g. dplyr::filter(), dplyr::mutate() and dplyr::summarise()
|
||||
# not useful (throws error) with e.g. dplyr::select() - but that will be caught later in this function
|
||||
@@ -726,72 +811,32 @@ get_current_data <- function(arg_name, call) {
|
||||
if (!is.null(cur_data_all)) {
|
||||
out <- tryCatch(cur_data_all(), error = function(e) NULL)
|
||||
if (is.data.frame(out)) {
|
||||
out <- structure(out, type = "dplyr_cur_data_all")
|
||||
pkg_env$get_current_data.call <- unique_call_id(entire_session = FALSE)
|
||||
pkg_env$get_current_data.out <- out
|
||||
return(out)
|
||||
}
|
||||
}
|
||||
|
||||
if (getRversion() < "3.2") {
|
||||
# R-3.0 and R-3.1 do not have an `x` element in the call stack, rendering this function useless
|
||||
if (is.na(arg_name)) {
|
||||
# like in carbapenems() etc.
|
||||
warning_("this function can only be used in R >= 3.2", call = call)
|
||||
return(data.frame())
|
||||
} else {
|
||||
# mimic a default R error, e.g. for example_isolates[which(mo_name() %like% "^ent"), ]
|
||||
stop_("argument `", arg_name, "` is missing with no default", call = call)
|
||||
return(structure(out, type = "dplyr_cur_data_all"))
|
||||
}
|
||||
}
|
||||
|
||||
# try a (base R) method, by going over the complete system call stack with sys.frames()
|
||||
not_set <- TRUE
|
||||
source <- "base_R"
|
||||
frms <- lapply(sys.frames(), function(el) {
|
||||
if (not_set == TRUE && ".Generic" %in% names(el)) {
|
||||
if (tryCatch(".data" %in% names(el) && is.data.frame(el$`.data`), error = function(e) FALSE)) {
|
||||
# - - - -
|
||||
# dplyr
|
||||
# - - - -
|
||||
# an element `.data` will be in the system call stack when using dplyr::select()
|
||||
# [but not when using dplyr::filter(), dplyr::mutate() or dplyr::summarise()]
|
||||
not_set <<- FALSE
|
||||
source <<- "dplyr_selector"
|
||||
el$`.data`
|
||||
} else if (tryCatch(any(c("x", "xx") %in% names(el)), error = function(e) FALSE)) {
|
||||
# - - - -
|
||||
# base R
|
||||
# - - - -
|
||||
# an element `x` will be in this environment for only cols, e.g. `example_isolates[, carbapenems()]`
|
||||
# an element `xx` will be in this environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
|
||||
if (tryCatch(is.data.frame(el$xx), error = function(e) FALSE)) {
|
||||
not_set <<- FALSE
|
||||
el$xx
|
||||
} else if (tryCatch(is.data.frame(el$x))) {
|
||||
not_set <<- FALSE
|
||||
el$x
|
||||
} else {
|
||||
NULL
|
||||
}
|
||||
} else {
|
||||
NULL
|
||||
# try a manual (base R) method, by going over all underlying environments with sys.frames()
|
||||
for (env in sys.frames()) {
|
||||
if (!is.null(env$`.Generic`)) {
|
||||
# don't check `".Generic" %in% names(env)`, because in R < 3.2, `names(env)` is always NULL
|
||||
|
||||
if (!is.null(env$`.data`) && is.data.frame(env$`.data`)) {
|
||||
# an element `.data` will be in the environment when using `dplyr::select()`
|
||||
# (but not when using `dplyr::filter()`, `dplyr::mutate()` or `dplyr::summarise()`)
|
||||
return(structure(env$`.data`, type = "dplyr_selector"))
|
||||
|
||||
} else if (!is.null(env$xx) && is.data.frame(env$xx)) {
|
||||
# an element `xx` will be in the environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
|
||||
return(structure(env$xx, type = "base_R"))
|
||||
|
||||
} else if (!is.null(env$x) && is.data.frame(env$x)) {
|
||||
# an element `x` will be in the environment for only cols, e.g. `example_isolates[, carbapenems()]`
|
||||
return(structure(env$x, type = "base_R"))
|
||||
}
|
||||
} else {
|
||||
NULL
|
||||
}
|
||||
})
|
||||
|
||||
# lookup the matched frame and return its value: a data.frame
|
||||
vars_df <- tryCatch(frms[[which(!vapply(FUN.VALUE = logical(1), frms, is.null))]], error = function(e) NULL)
|
||||
if (is.data.frame(vars_df)) {
|
||||
out <- structure(vars_df, type = source)
|
||||
pkg_env$get_current_data.call <- unique_call_id(entire_session = FALSE)
|
||||
pkg_env$get_current_data.out <- out
|
||||
return(out)
|
||||
}
|
||||
|
||||
# nothing worked, so:
|
||||
# no data.frame found, so an error must be returned:
|
||||
if (is.na(arg_name)) {
|
||||
if (isTRUE(is.numeric(call))) {
|
||||
fn <- as.character(sys.call(call + 1)[1])
|
||||
@@ -803,10 +848,11 @@ get_current_data <- function(arg_name, call) {
|
||||
} else {
|
||||
examples <- ""
|
||||
}
|
||||
stop_("this function must be used inside valid dplyr selection verbs or inside a data.frame call",
|
||||
stop_("this function must be used inside a `dplyr` verb or `data.frame` call",
|
||||
examples,
|
||||
call = call)
|
||||
} else {
|
||||
# mimic a base R error that the argument is missing
|
||||
stop_("argument `", arg_name, "` is missing with no default", call = call)
|
||||
}
|
||||
}
|
||||
@@ -821,19 +867,19 @@ get_current_column <- function() {
|
||||
}
|
||||
}
|
||||
|
||||
# cur_column() doesn't always work (only allowed for conditions set by dplyr), but it's probably still possible:
|
||||
frms <- lapply(sys.frames(), function(el) {
|
||||
if ("i" %in% names(el)) {
|
||||
if ("tibble_vars" %in% names(el)) {
|
||||
# cur_column() doesn't always work (only allowed for certain conditions set by dplyr), but it's probably still possible:
|
||||
frms <- lapply(sys.frames(), function(env) {
|
||||
if (!is.null(env$i)) {
|
||||
if (!is.null(env$tibble_vars)) {
|
||||
# for mutate_if()
|
||||
el$tibble_vars[el$i]
|
||||
env$tibble_vars[env$i]
|
||||
} else {
|
||||
# for mutate(across())
|
||||
df <- tryCatch(get_current_data(NA, 0), error = function(e) NULL)
|
||||
if (is.data.frame(df)) {
|
||||
colnames(df)[el$i]
|
||||
colnames(df)[env$i]
|
||||
} else {
|
||||
el$i
|
||||
env$i
|
||||
}
|
||||
}
|
||||
} else {
|
||||
@@ -851,7 +897,7 @@ get_current_column <- function() {
|
||||
}
|
||||
|
||||
is_null_or_grouped_tbl <- function(x) {
|
||||
# attribute "grouped_df" might change at one point, so only set in one place; here.
|
||||
# class "grouped_df" might change at one point, so only set in one place; here.
|
||||
is.null(x) || inherits(x, "grouped_df")
|
||||
}
|
||||
|
||||
@@ -860,7 +906,7 @@ unique_call_id <- function(entire_session = FALSE) {
|
||||
c(envir = "session",
|
||||
call = "session")
|
||||
} else {
|
||||
# combination of environment ID (like "0x7fed4ee8c848")
|
||||
# combination of environment ID (such as "0x7fed4ee8c848")
|
||||
# and highest system call
|
||||
call <- paste0(deparse(sys.calls()[[1]]), collapse = "")
|
||||
if (!interactive() || call %like% "run_test_dir|test_all|tinytest|test_package|testthat") {
|
||||
@@ -872,16 +918,18 @@ unique_call_id <- function(entire_session = FALSE) {
|
||||
}
|
||||
}
|
||||
|
||||
remember_thrown_message <- function(fn, entire_session = FALSE) {
|
||||
# this is to prevent that messages/notes will be printed for every dplyr group
|
||||
# e.g. this would show a msg 4 times: example_isolates %>% group_by(hospital_id) %>% filter(mo_is_gram_negative())
|
||||
assign(x = paste0("thrown_msg.", fn),
|
||||
value = unique_call_id(entire_session = entire_session),
|
||||
envir = pkg_env)
|
||||
}
|
||||
|
||||
message_not_thrown_before <- function(fn, entire_session = FALSE) {
|
||||
is.null(pkg_env[[paste0("thrown_msg.", fn)]]) || !identical(pkg_env[[paste0("thrown_msg.", fn)]], unique_call_id(entire_session))
|
||||
# this is to prevent that messages/notes will be printed for every dplyr group or more than once per session
|
||||
# e.g. this would show a msg 4 times: example_isolates %>% group_by(hospital_id) %>% filter(mo_is_gram_negative())
|
||||
not_thrown_before <- is.null(pkg_env[[paste0("thrown_msg.", fn)]]) || !identical(pkg_env[[paste0("thrown_msg.", fn)]],
|
||||
unique_call_id(entire_session = entire_session))
|
||||
if (isTRUE(not_thrown_before)) {
|
||||
# message was not thrown before - remember this so on the next run it will return FALSE:
|
||||
assign(x = paste0("thrown_msg.", fn),
|
||||
value = unique_call_id(entire_session = entire_session),
|
||||
envir = pkg_env)
|
||||
}
|
||||
not_thrown_before
|
||||
}
|
||||
|
||||
has_colour <- function() {
|
||||
@@ -976,12 +1024,12 @@ font_grey <- function(..., collapse = " ") {
|
||||
try_colour(..., before = "\033[38;5;249m", after = "\033[39m", collapse = collapse)
|
||||
}
|
||||
font_grey_bg <- function(..., collapse = " ") {
|
||||
if (tryCatch(rstudioapi::getThemeInfo()$dark == TRUE, error = function(e) FALSE)) {
|
||||
if (tryCatch(import_fn("getThemeInfo", "rstudioapi", error_on_fail = FALSE)()$dark, error = function(e) FALSE)) {
|
||||
# similar to HTML #444444
|
||||
try_colour(..., before = "\033[48;5;238m", after = "\033[49m", collapse = collapse)
|
||||
} else {
|
||||
# similar to HTML #eeeeee
|
||||
try_colour(..., before = "\033[48;5;254m", after = "\033[49m", collapse = collapse)
|
||||
# similar to HTML #f0f0f0
|
||||
try_colour(..., before = "\033[48;5;255m", after = "\033[49m", collapse = collapse)
|
||||
}
|
||||
}
|
||||
font_green_bg <- function(..., collapse = " ") {
|
||||
|
||||
@@ -33,7 +33,7 @@
|
||||
#' @param ... arguments passed on to internal functions
|
||||
#' @rdname as.ab
|
||||
#' @inheritSection WHOCC WHOCC
|
||||
#' @details All entries in the [antibiotics] data set have three different identifiers: a human readable EARS-Net code (column `ab`, used by ECDC and WHONET), an ATC code (column `atc`, used by WHO), and a CID code (column `cid`, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem.
|
||||
#' @details All entries in the [antibiotics] data set have three different identifiers: a human readable EARS-Net code (column `ab`, used by ECDC and WHONET), an ATC code (column `atc`, used by WHO), and a CID code (column `cid`, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem. Not that some drugs contain multiple ATC codes.
|
||||
#'
|
||||
#' All these properties will be searched for the user input. The [as.ab()] can correct for different forms of misspelling:
|
||||
#'
|
||||
@@ -101,6 +101,11 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
|
||||
if (is.ab(x)) {
|
||||
return(x)
|
||||
}
|
||||
if (all(x %in% c(AB_lookup$ab, NA))) {
|
||||
# all valid AB codes, but not yet right class
|
||||
return(set_clean_class(x,
|
||||
new_class = c("ab", "character")))
|
||||
}
|
||||
|
||||
initial_search <- is.null(list(...)$initial_search)
|
||||
already_regex <- isTRUE(list(...)$already_regex)
|
||||
@@ -110,28 +115,12 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
|
||||
x <- toupper(x)
|
||||
x_nonNA <- x[!is.na(x)]
|
||||
|
||||
if (all(x_nonNA %in% antibiotics$ab, na.rm = TRUE)) {
|
||||
# all valid AB codes, but not yet right class
|
||||
return(set_clean_class(x,
|
||||
new_class = c("ab", "character")))
|
||||
}
|
||||
if (all(x_nonNA %in% toupper(antibiotics$name), na.rm = TRUE)) {
|
||||
# all valid AB names
|
||||
out <- antibiotics$ab[match(x, toupper(antibiotics$name))]
|
||||
out[is.na(x)] <- NA_character_
|
||||
return(out)
|
||||
}
|
||||
if (all(x_nonNA %in% antibiotics$atc, na.rm = TRUE)) {
|
||||
# all valid ATC codes
|
||||
out <- antibiotics$ab[match(x, antibiotics$atc)]
|
||||
out[is.na(x)] <- NA_character_
|
||||
return(out)
|
||||
}
|
||||
|
||||
# remove diacritics
|
||||
x <- iconv(x, from = "UTF-8", to = "ASCII//TRANSLIT")
|
||||
x <- gsub('"', "", x, fixed = TRUE)
|
||||
x <- gsub("(specimen|specimen date|specimen_date|spec_date|^dates?$)", "", x, ignore.case = TRUE, perl = TRUE)
|
||||
x <- gsub("(specimen|specimen date|specimen_date|spec_date|gender|^dates?$)", "", x, ignore.case = TRUE, perl = TRUE)
|
||||
# penicillin is a special case: we call it so, but then mean benzylpenicillin
|
||||
x[x %like_case% "^PENICILLIN" & x %unlike_case% "[ /+-]"] <- "benzylpenicillin"
|
||||
x_bak_clean <- x
|
||||
if (already_regex == FALSE) {
|
||||
x_bak_clean <- generalise_antibiotic_name(x_bak_clean)
|
||||
@@ -155,13 +144,29 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
|
||||
found[1L]
|
||||
}
|
||||
|
||||
if (initial_search == TRUE) {
|
||||
progress <- progress_ticker(n = length(x), n_min = 25, print = info) # start if n >= 25
|
||||
# Fill in names, AB codes, CID codes and ATC codes directly (`x` is already clean and uppercase)
|
||||
known_names <- x %in% AB_lookup$generalised_name
|
||||
x_new[known_names] <- AB_lookup$ab[match(x[known_names], AB_lookup$generalised_name)]
|
||||
known_codes_ab <- x %in% AB_lookup$ab
|
||||
known_codes_atc <- vapply(FUN.VALUE = logical(1), x, function(x_) x_ %in% unlist(AB_lookup$atc), USE.NAMES = FALSE)
|
||||
known_codes_cid <- x %in% AB_lookup$cid
|
||||
x_new[known_codes_ab] <- AB_lookup$ab[match(x[known_codes_ab], AB_lookup$ab)]
|
||||
x_new[known_codes_atc] <- AB_lookup$ab[vapply(FUN.VALUE = integer(1),
|
||||
x[known_codes_atc],
|
||||
function(x_) which(vapply(FUN.VALUE = logical(1),
|
||||
AB_lookup$atc,
|
||||
function(atc) x_ %in% atc)),
|
||||
USE.NAMES = FALSE)]
|
||||
x_new[known_codes_cid] <- AB_lookup$ab[match(x[known_codes_cid], AB_lookup$cid)]
|
||||
already_known <- known_names | known_codes_ab | known_codes_atc | known_codes_cid
|
||||
|
||||
if (initial_search == TRUE & sum(already_known) < length(x)) {
|
||||
progress <- progress_ticker(n = sum(!already_known), n_min = 25, print = info) # start if n >= 25
|
||||
on.exit(close(progress))
|
||||
}
|
||||
|
||||
for (i in seq_len(length(x))) {
|
||||
|
||||
for (i in which(!already_known)) {
|
||||
|
||||
if (initial_search == TRUE) {
|
||||
progress$tick()
|
||||
}
|
||||
@@ -189,34 +194,6 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
|
||||
next
|
||||
}
|
||||
|
||||
# exact name
|
||||
found <- antibiotics[which(AB_lookup$generalised_name == x[i]), ]$ab
|
||||
if (length(found) > 0) {
|
||||
x_new[i] <- found[1L]
|
||||
next
|
||||
}
|
||||
|
||||
# exact AB code
|
||||
found <- antibiotics[which(antibiotics$ab == x[i]), ]$ab
|
||||
if (length(found) > 0) {
|
||||
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
|
||||
next
|
||||
}
|
||||
|
||||
# exact ATC code
|
||||
found <- antibiotics[which(antibiotics$atc == x[i]), ]$ab
|
||||
if (length(found) > 0) {
|
||||
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
|
||||
next
|
||||
}
|
||||
|
||||
# exact CID code
|
||||
found <- antibiotics[which(antibiotics$cid == x[i]), ]$ab
|
||||
if (length(found) > 0) {
|
||||
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
|
||||
next
|
||||
}
|
||||
|
||||
# exact LOINC code
|
||||
loinc_found <- unlist(lapply(AB_lookup$generalised_loinc,
|
||||
function(s) x[i] %in% s))
|
||||
@@ -252,6 +229,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
|
||||
}
|
||||
x_spelling <- x[i]
|
||||
if (already_regex == FALSE) {
|
||||
|
||||
x_spelling <- gsub("[IY]+", "[IY]+", x_spelling, perl = TRUE)
|
||||
x_spelling <- gsub("(C|K|Q|QU|S|Z|X|KS)+", "(C|K|Q|QU|S|Z|X|KS)+", x_spelling, perl = TRUE)
|
||||
x_spelling <- gsub("(PH|F|V)+", "(PH|F|V)+", x_spelling, perl = TRUE)
|
||||
@@ -296,7 +274,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
|
||||
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
|
||||
next
|
||||
}
|
||||
|
||||
|
||||
# INITIAL SEARCH - More uncertain results ----
|
||||
|
||||
if (initial_search == TRUE && fast_mode == FALSE) {
|
||||
@@ -325,9 +303,9 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
|
||||
function(y) {
|
||||
for (i in seq_len(length(y))) {
|
||||
for (lang in LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED != "en"]) {
|
||||
y[i] <- ifelse(tolower(y[i]) %in% tolower(translations_file[, lang, drop = TRUE]),
|
||||
translations_file[which(tolower(translations_file[, lang, drop = TRUE]) == tolower(y[i]) &
|
||||
!isFALSE(translations_file$fixed)), "pattern"],
|
||||
y[i] <- ifelse(tolower(y[i]) %in% tolower(TRANSLATIONS[, lang, drop = TRUE]),
|
||||
TRANSLATIONS[which(tolower(TRANSLATIONS[, lang, drop = TRUE]) == tolower(y[i]) &
|
||||
!isFALSE(TRANSLATIONS$fixed)), "pattern"],
|
||||
y[i])
|
||||
}
|
||||
}
|
||||
@@ -461,14 +439,14 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
|
||||
x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
|
||||
}
|
||||
|
||||
if (initial_search == TRUE) {
|
||||
if (initial_search == TRUE & sum(already_known) < length(x)) {
|
||||
close(progress)
|
||||
}
|
||||
|
||||
# take failed ATC codes apart from rest
|
||||
x_unknown_ATCs <- x_unknown[x_unknown %like% "[A-Z][0-9][0-9][A-Z][A-Z][0-9][0-9]"]
|
||||
x_unknown <- x_unknown[!x_unknown %in% x_unknown_ATCs]
|
||||
if (length(x_unknown_ATCs) > 0) {
|
||||
if (length(x_unknown_ATCs) > 0 & fast_mode == FALSE) {
|
||||
warning_("These ATC codes are not (yet) in the antibiotics data set: ",
|
||||
vector_and(x_unknown_ATCs), ".",
|
||||
call = FALSE)
|
||||
@@ -479,11 +457,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
|
||||
vector_and(x_unknown), ".",
|
||||
call = FALSE)
|
||||
}
|
||||
|
||||
x_result <- data.frame(x = x_bak_clean, stringsAsFactors = FALSE) %pm>%
|
||||
pm_left_join(data.frame(x = x, x_new = x_new, stringsAsFactors = FALSE), by = "x") %pm>%
|
||||
pm_pull(x_new)
|
||||
|
||||
|
||||
x_result <- x_new[match(x_bak_clean, x)]
|
||||
if (length(x_result) == 0) {
|
||||
x_result <- NA_character_
|
||||
}
|
||||
@@ -580,6 +555,15 @@ unique.ab <- function(x, incomparables = FALSE, ...) {
|
||||
y
|
||||
}
|
||||
|
||||
#' @method rep ab
|
||||
#' @export
|
||||
#' @noRd
|
||||
rep.ab <- function(x, ...) {
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(x)
|
||||
y
|
||||
}
|
||||
|
||||
generalise_antibiotic_name <- function(x) {
|
||||
x <- toupper(x)
|
||||
# remove suffices
|
||||
|
||||
+451
-181
@@ -23,22 +23,32 @@
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Antibiotic Class Selectors
|
||||
#' Antibiotic Selectors
|
||||
#'
|
||||
#' These functions help to filter and select columns with antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(getRversion() < "3.2", paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
|
||||
#' These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group, without the need to define the columns or antibiotic abbreviations. In short, if you have a column name that resembles an antimicrobial agent, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "CZO" and "J01DB04" will all be picked up by [cephalosporins()].
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param ab_class an antimicrobial class, such as `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value.
|
||||
#' @param ab_class an antimicrobial class or a part of it, such as `"carba"` and `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value.
|
||||
#' @param filter an [expression] to be evaluated in the [antibiotics] data set, such as `name %like% "trim"`
|
||||
#' @param only_rsi_columns a [logical] to indicate whether only columns of class `<rsi>` must be selected (defaults to `FALSE`), see [as.rsi()]
|
||||
#' @details \strong{\Sexpr{ifelse(getRversion() < "3.2", paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
|
||||
#' @param only_treatable a [logical] to indicate whether agents that are only for laboratory tests should be excluded (defaults to `TRUE`), such as gentamicin-high (`GEH`) and imipenem/EDTA (`IPE`)
|
||||
#' @param ... ignored, only in place to allow future extensions
|
||||
#' @details
|
||||
#' These functions can be used in data set calls for selecting columns and filtering rows. They are heavily inspired by the [Tidyverse selection helpers][tidyselect::language] such as [`everything()`][tidyselect::everything()], but also work in base \R and not only in `dplyr` verbs. Nonetheless, they are very convenient to use with `dplyr` functions such as [`select()`][dplyr::select()], [`filter()`][dplyr::filter()] and [`summarise()`][dplyr::summarise()], see *Examples*.
|
||||
#'
|
||||
#' All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the [antibiotics] data set. This means that a selector such as [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
|
||||
#'
|
||||
#' These functions can be used in data set calls for selecting columns and filtering rows, see *Examples*. They support base R, but work more convenient in dplyr functions such as [`select()`][dplyr::select()], [`filter()`][dplyr::filter()] and [`summarise()`][dplyr::summarise()].
|
||||
#' The [ab_class()] function can be used to filter/select on a manually defined antibiotic class. It searches for results in the [antibiotics] data set within the columns `group`, `atc_group1` and `atc_group2`.
|
||||
#'
|
||||
#' All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) in the [antibiotics] data set. This means that a selector like e.g. [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
|
||||
#' The [ab_selector()] function can be used to internally filter the [antibiotics] data set on any results, see *Examples*. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.
|
||||
#'
|
||||
#' The group of betalactams consists of all carbapenems, cephalosporins and penicillins.
|
||||
#' The [administrable_per_os()] and [administrable_iv()] functions also rely on the [antibiotics] data set - antibiotic columns will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the [antibiotics] data set.
|
||||
#'
|
||||
#' @section Full list of supported (antibiotic) classes:
|
||||
#'
|
||||
#' `r paste0(" * ", na.omit(sapply(DEFINED_AB_GROUPS, function(ab) ifelse(tolower(gsub("^AB_", "", ab)) %in% ls(envir = asNamespace("AMR")), paste0("[", tolower(gsub("^AB_", "", ab)), "()] can select: \\cr ", vector_and(paste0(ab_name(eval(parse(text = ab), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), " (", eval(parse(text = ab), envir = asNamespace("AMR")), ")"), quotes = FALSE, sort = TRUE)), character(0)), USE.NAMES = FALSE)), "\n", collapse = "")`
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @name antibiotic_class_selectors
|
||||
#' @return (internally) a [character] vector of column names, with additional class `"ab_selector"`
|
||||
#' @export
|
||||
#' @inheritSection AMR Reference Data Publicly Available
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
@@ -46,7 +56,7 @@
|
||||
#' # `example_isolates` is a data set available in the AMR package.
|
||||
#' # See ?example_isolates.
|
||||
#'
|
||||
#' # Base R ------------------------------------------------------------------
|
||||
#' # base R ------------------------------------------------------------------
|
||||
#'
|
||||
#' # select columns 'IPM' (imipenem) and 'MEM' (meropenem)
|
||||
#' example_isolates[, carbapenems()]
|
||||
@@ -54,6 +64,9 @@
|
||||
#' # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
|
||||
#' example_isolates[, c("mo", aminoglycosides())]
|
||||
#'
|
||||
#' # select only antibiotic columns with DDDs for oral treatment
|
||||
#' example_isolates[, administrable_per_os()]
|
||||
#'
|
||||
#' # filter using any() or all()
|
||||
#' example_isolates[any(carbapenems() == "R"), ]
|
||||
#' subset(example_isolates, any(carbapenems() == "R"))
|
||||
@@ -68,6 +81,17 @@
|
||||
#' # filter + select in one go: get penicillins in carbapenems-resistant strains
|
||||
#' example_isolates[any(carbapenems() == "R"), penicillins()]
|
||||
#'
|
||||
#' # You can combine selectors with '&' to be more specific. For example,
|
||||
#' # penicillins() would select benzylpenicillin ('peni G') and
|
||||
#' # administrable_per_os() would select erythromycin. Yet, when combined these
|
||||
#' # drugs are both omitted since benzylpenicillin is not administrable per os
|
||||
#' # and erythromycin is not a penicillin:
|
||||
#' example_isolates[, penicillins() & administrable_per_os()]
|
||||
#'
|
||||
#' # ab_selector() applies a filter in the `antibiotics` data set and is thus very
|
||||
#' # flexible. For instance, to select antibiotic columns with an oral DDD of at
|
||||
#' # least 1 gram:
|
||||
#' example_isolates[, ab_selector(oral_ddd > 1 & oral_units == "g")]
|
||||
#'
|
||||
#' # dplyr -------------------------------------------------------------------
|
||||
#' \donttest{
|
||||
@@ -77,6 +101,16 @@
|
||||
#' example_isolates %>%
|
||||
#' group_by(hospital_id) %>%
|
||||
#' summarise(across(aminoglycosides(), resistance))
|
||||
#'
|
||||
#' # You can combine selectors with '&' to be more specific:
|
||||
#' example_isolates %>%
|
||||
#' select(penicillins() & administrable_per_os())
|
||||
#'
|
||||
#' # get susceptibility for antibiotics whose name contains "trim":
|
||||
#' example_isolates %>%
|
||||
#' filter(first_isolate()) %>%
|
||||
#' group_by(hospital_id) %>%
|
||||
#' summarise(across(ab_selector(name %like% "trim"), susceptibility))
|
||||
#'
|
||||
#' # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
|
||||
#' example_isolates %>%
|
||||
@@ -104,7 +138,6 @@
|
||||
#' example_isolates %>%
|
||||
#' select(mo, ab_class("mycobact"))
|
||||
#'
|
||||
#'
|
||||
#' # get bug/drug combinations for only macrolides in Gram-positives:
|
||||
#' example_isolates %>%
|
||||
#' filter(mo_is_gram_positive()) %>%
|
||||
@@ -112,178 +145,379 @@
|
||||
#' bug_drug_combinations() %>%
|
||||
#' format()
|
||||
#'
|
||||
#'
|
||||
#' data.frame(some_column = "some_value",
|
||||
#' J01CA01 = "S") %>% # ATC code of ampicillin
|
||||
#' select(penicillins()) # only the 'J01CA01' column will be selected
|
||||
#'
|
||||
#'
|
||||
#' # with dplyr 1.0.0 and higher (that adds 'across()'), this is all equal:
|
||||
#' # (though the row names on the first are more correct)
|
||||
#' example_isolates[carbapenems() == "R", ]
|
||||
#' example_isolates %>% filter(carbapenems() == "R")
|
||||
#' example_isolates %>% filter(across(carbapenems(), ~.x == "R"))
|
||||
#' }
|
||||
#' }
|
||||
ab_class <- function(ab_class,
|
||||
only_rsi_columns = FALSE) {
|
||||
ab_selector(ab_class, function_name = "ab_class", only_rsi_columns = only_rsi_columns)
|
||||
only_rsi_columns = FALSE,
|
||||
only_treatable = TRUE,
|
||||
...) {
|
||||
meet_criteria(ab_class, allow_class = "character", has_length = 1, allow_NULL = TRUE)
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec(NULL, only_rsi_columns = only_rsi_columns, ab_class_args = ab_class, only_treatable = only_treatable)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
aminoglycosides <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("aminoglycoside", function_name = "aminoglycosides", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
betalactams <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("carbapenem|cephalosporin|penicillin", function_name = "betalactams", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
carbapenems <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("carbapenem", function_name = "carbapenems", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
cephalosporins <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("cephalosporin", function_name = "cephalosporins", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
cephalosporins_1st <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("cephalosporins.*1", function_name = "cephalosporins_1st", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
cephalosporins_2nd <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("cephalosporins.*2", function_name = "cephalosporins_2nd", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
cephalosporins_3rd <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("cephalosporins.*3", function_name = "cephalosporins_3rd", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
cephalosporins_4th <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("cephalosporins.*4", function_name = "cephalosporins_4th", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
cephalosporins_5th <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("cephalosporins.*5", function_name = "cephalosporins_5th", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
fluoroquinolones <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("fluoroquinolone", function_name = "fluoroquinolones", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
glycopeptides <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("glycopeptide", function_name = "glycopeptides", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
macrolides <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("macrolide", function_name = "macrolides", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
oxazolidinones <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("oxazolidinone", function_name = "oxazolidinones", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
penicillins <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("penicillin", function_name = "penicillins", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
tetracyclines <- function(only_rsi_columns = FALSE) {
|
||||
ab_selector("tetracycline", function_name = "tetracyclines", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
ab_selector <- function(ab_class,
|
||||
function_name,
|
||||
only_rsi_columns) {
|
||||
meet_criteria(ab_class, allow_class = "character", has_length = 1, .call_depth = 1)
|
||||
meet_criteria(function_name, allow_class = "character", has_length = 1, .call_depth = 1)
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1, .call_depth = 1)
|
||||
ab_selector <- function(filter,
|
||||
only_rsi_columns = FALSE,
|
||||
only_treatable = TRUE,
|
||||
...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
|
||||
|
||||
if (getRversion() < "3.2") {
|
||||
warning_("antibiotic class selectors such as ", function_name,
|
||||
"() require R version 3.2 or later - you have ", R.version.string,
|
||||
call = FALSE)
|
||||
return(NULL)
|
||||
}
|
||||
|
||||
# to improve speed, get_current_data() and get_column_abx() only run once when e.g. in a select or group call
|
||||
# get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
|
||||
# but it only takes a couple of milliseconds
|
||||
vars_df <- get_current_data(arg_name = NA, call = -2)
|
||||
# to improve speed, get_column_abx() will only run once when e.g. in a select or group call
|
||||
ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE)
|
||||
call <- substitute(filter)
|
||||
agents <- tryCatch(AMR::antibiotics[which(eval(call, envir = AMR::antibiotics)), "ab", drop = TRUE],
|
||||
error = function(e) stop_(e$message, call = -5))
|
||||
agents <- ab_in_data[ab_in_data %in% agents]
|
||||
message_agent_names(function_name = "ab_selector",
|
||||
agents = agents,
|
||||
ab_group = NULL,
|
||||
examples = "",
|
||||
call = call)
|
||||
structure(unname(agents),
|
||||
class = c("ab_selector", "character"))
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
administrable_per_os <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
# get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
|
||||
# but it only takes a couple of milliseconds
|
||||
vars_df <- get_current_data(arg_name = NA, call = -2)
|
||||
# to improve speed, get_column_abx() will only run once when e.g. in a select or group call
|
||||
ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE)
|
||||
agents_all <- antibiotics[which(!is.na(antibiotics$oral_ddd)), "ab", drop = TRUE]
|
||||
agents <- antibiotics[which(antibiotics$ab %in% ab_in_data & !is.na(antibiotics$oral_ddd)), "ab", drop = TRUE]
|
||||
agents <- ab_in_data[ab_in_data %in% agents]
|
||||
message_agent_names(function_name = "administrable_per_os",
|
||||
agents = agents,
|
||||
ab_group = "administrable_per_os",
|
||||
examples = paste0(" (such as ",
|
||||
vector_or(ab_name(sample(agents_all,
|
||||
size = min(5, length(agents_all)),
|
||||
replace = FALSE),
|
||||
tolower = TRUE,
|
||||
language = NULL),
|
||||
quotes = FALSE),
|
||||
")"))
|
||||
structure(unname(agents),
|
||||
class = c("ab_selector", "character"))
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
administrable_iv <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
# get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
|
||||
# but it only takes a couple of milliseconds
|
||||
vars_df <- get_current_data(arg_name = NA, call = -2)
|
||||
# to improve speed, get_column_abx() will only run once when e.g. in a select or group call
|
||||
ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE)
|
||||
agents_all <- antibiotics[which(!is.na(antibiotics$iv_ddd)), "ab", drop = TRUE]
|
||||
agents <- antibiotics[which(antibiotics$ab %in% ab_in_data & !is.na(antibiotics$iv_ddd)), "ab", drop = TRUE]
|
||||
agents <- ab_in_data[ab_in_data %in% agents]
|
||||
message_agent_names(function_name = "administrable_iv",
|
||||
agents = agents,
|
||||
ab_group = "administrable_iv",
|
||||
examples = "")
|
||||
structure(unname(agents),
|
||||
class = c("ab_selector", "character"))
|
||||
}
|
||||
|
||||
# nolint start
|
||||
# #' @rdname antibiotic_class_selectors
|
||||
# #' @export
|
||||
# not_intrinsic_resistant <- function(mo, ..., only_rsi_columns = FALSE, ...) {
|
||||
# meet_criteria(mo, allow_class = c("mo", "data.frame", "list", "character", "numeric", "integer", "factor"), has_length = 1, allow_NA = FALSE)
|
||||
# meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
#
|
||||
# x <- as.mo(mo, ...)
|
||||
# wont_work <- intrinsic_resistant[which(intrinsic_resistant$microorganism == mo_name(x, language = NULL)),
|
||||
# "antibiotic",
|
||||
# drop = TRUE]
|
||||
#
|
||||
# # get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
|
||||
# # but it only takes a couple of milliseconds
|
||||
# vars_df <- get_current_data(arg_name = NA, call = -2)
|
||||
# # to improve speed, get_column_abx() will only run once when e.g. in a select or group call
|
||||
# ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE)
|
||||
#
|
||||
# agents <- ab_in_data[!names(ab_in_data) %in% as.character(as.ab(wont_work))]
|
||||
#
|
||||
# # show used version number once per session (pkg_env will reload every session)
|
||||
# if (message_not_thrown_before("intrinsic_resistant_version.ab", entire_session = TRUE)) {
|
||||
# message_("Determining intrinsic resistance based on ",
|
||||
# format_eucast_version_nr(3.2, markdown = FALSE), ". ",
|
||||
# font_red("This note will be shown once per session."))
|
||||
# }
|
||||
#
|
||||
# message_agent_names(function_name = "not_intrinsic_resistant",
|
||||
# agents = ab_in_data,
|
||||
# ab_group = NULL,
|
||||
# examples = "",
|
||||
# call = mo_name(x, language = NULL))
|
||||
#
|
||||
# agents
|
||||
# }
|
||||
# nolint end
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
aminoglycosides <- function(only_rsi_columns = FALSE, only_treatable = TRUE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("aminoglycosides", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
aminopenicillins <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("aminopenicillins", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
antifungals <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("antifungals", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
antimycobacterials <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("antimycobacterials", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
betalactams <- function(only_rsi_columns = FALSE, only_treatable = TRUE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("betalactams", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
carbapenems <- function(only_rsi_columns = FALSE, only_treatable = TRUE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("carbapenems", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
cephalosporins <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("cephalosporins", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
cephalosporins_1st <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("cephalosporins_1st", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
cephalosporins_2nd <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("cephalosporins_2nd", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
cephalosporins_3rd <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("cephalosporins_3rd", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
cephalosporins_4th <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("cephalosporins_4th", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
cephalosporins_5th <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("cephalosporins_5th", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
fluoroquinolones <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("fluoroquinolones", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
glycopeptides <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("glycopeptides", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
lincosamides <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("lincosamides", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
lipoglycopeptides <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("lipoglycopeptides", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
macrolides <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("macrolides", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
oxazolidinones <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("oxazolidinones", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
penicillins <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("penicillins", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
polymyxins <- function(only_rsi_columns = FALSE, only_treatable = TRUE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("polymyxins", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
streptogramins <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("streptogramins", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
quinolones <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("quinolones", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
tetracyclines <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("tetracyclines", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
trimethoprims <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("trimethoprims", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @export
|
||||
ureidopenicillins <- function(only_rsi_columns = FALSE, ...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
ab_select_exec("ureidopenicillins", only_rsi_columns = only_rsi_columns)
|
||||
}
|
||||
|
||||
ab_select_exec <- function(function_name,
|
||||
only_rsi_columns = FALSE,
|
||||
only_treatable = FALSE,
|
||||
ab_class_args = NULL) {
|
||||
# get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
|
||||
# but it only takes a couple of milliseconds
|
||||
vars_df <- get_current_data(arg_name = NA, call = -3)
|
||||
# to improve speed, get_column_abx() will only run once when e.g. in a select or group call
|
||||
ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE)
|
||||
|
||||
# untreatable drugs
|
||||
untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate"), "ab", drop = TRUE]
|
||||
if (only_treatable == TRUE & any(untreatable %in% names(ab_in_data))) {
|
||||
if (message_not_thrown_before(paste0("ab_class.untreatable.", function_name), entire_session = TRUE)) {
|
||||
warning_("Some agents in `", function_name, "()` were ignored since they cannot be used for treating patients: ",
|
||||
vector_and(ab_name(names(ab_in_data)[names(ab_in_data) %in% untreatable],
|
||||
language = NULL,
|
||||
tolower = TRUE),
|
||||
quotes = FALSE,
|
||||
sort = TRUE), ". They can be included using `", function_name, "(only_treatable = FALSE)`. ",
|
||||
"This warning will be shown once per session.",
|
||||
call = FALSE)
|
||||
}
|
||||
ab_in_data <- ab_in_data[!names(ab_in_data) %in% untreatable]
|
||||
}
|
||||
|
||||
if (length(ab_in_data) == 0) {
|
||||
message_("No antimicrobial agents found.")
|
||||
message_("No antimicrobial agents found in the data.")
|
||||
return(NULL)
|
||||
}
|
||||
|
||||
ab_reference <- subset(antibiotics,
|
||||
group %like% ab_class |
|
||||
atc_group1 %like% ab_class |
|
||||
atc_group2 %like% ab_class)
|
||||
ab_group <- find_ab_group(ab_class)
|
||||
if (ab_group == "") {
|
||||
ab_group <- paste0("'", ab_class, "'")
|
||||
examples <- ""
|
||||
if (is.null(ab_class_args)) {
|
||||
# their upper case equivalent are vectors with class <ab>, created in data-raw/_internals.R
|
||||
# carbapenems() gets its codes from AMR:::AB_CARBAPENEMS
|
||||
abx <- get(paste0("AB_", toupper(function_name)), envir = asNamespace("AMR"))
|
||||
ab_group <- function_name
|
||||
examples <- paste0(" (such as ", vector_or(ab_name(sample(abx, size = min(2, length(abx)), replace = FALSE),
|
||||
tolower = TRUE,
|
||||
language = NULL),
|
||||
quotes = FALSE), ")")
|
||||
} else {
|
||||
examples <- paste0(" (such as ", find_ab_names(ab_class, 2), ")")
|
||||
}
|
||||
# get the columns with a group names in the chosen ab class
|
||||
agents <- ab_in_data[names(ab_in_data) %in% ab_reference$ab]
|
||||
|
||||
if (message_not_thrown_before(function_name)) {
|
||||
if (length(agents) == 0) {
|
||||
message_("No antimicrobial agents of class ", ab_group, " found", examples, ".")
|
||||
} else {
|
||||
agents_formatted <- paste0("'", font_bold(agents, collapse = NULL), "'")
|
||||
agents_names <- ab_name(names(agents), tolower = TRUE, language = NULL)
|
||||
need_name <- tolower(gsub("[^a-zA-Z]", "", agents)) != tolower(gsub("[^a-zA-Z]", "", agents_names))
|
||||
agents_formatted[need_name] <- paste0(agents_formatted[need_name],
|
||||
" (", agents_names[need_name], ")")
|
||||
message_("For `", function_name, "(", ifelse(function_name == "ab_class", paste0("\"", ab_class, "\""), ""), ")` using ",
|
||||
ifelse(length(agents) == 1, "column: ", "columns: "),
|
||||
vector_and(agents_formatted, quotes = FALSE))
|
||||
}
|
||||
remember_thrown_message(function_name)
|
||||
# this for the 'manual' ab_class() function
|
||||
abx <- subset(AB_lookup,
|
||||
group %like% ab_class_args |
|
||||
atc_group1 %like% ab_class_args |
|
||||
atc_group2 %like% ab_class_args)$ab
|
||||
ab_group <- find_ab_group(ab_class_args)
|
||||
function_name <- "ab_class"
|
||||
examples <- paste0(" (such as ", find_ab_names(ab_class_args, 2), ")")
|
||||
}
|
||||
|
||||
if (!is.null(attributes(vars_df)$type) &&
|
||||
attributes(vars_df)$type %in% c("dplyr_cur_data_all", "base_R") &&
|
||||
!any(as.character(sys.calls()) %like% paste0("(across|if_any|if_all)\\((c\\()?[a-z(), ]*", function_name))) {
|
||||
structure(unname(agents),
|
||||
class = c("ab_selector", "character"))
|
||||
} else {
|
||||
# don't return with "ab_selector" class if method is a dplyr selector,
|
||||
# dplyr::select() will complain:
|
||||
# > Subscript has the wrong type `ab_selector`.
|
||||
# > It must be numeric or character.
|
||||
unname(agents)
|
||||
}
|
||||
# get the columns with a group names in the chosen ab class
|
||||
agents <- ab_in_data[names(ab_in_data) %in% abx]
|
||||
|
||||
message_agent_names(function_name = function_name,
|
||||
agents = agents,
|
||||
ab_group = ab_group,
|
||||
examples = examples,
|
||||
ab_class_args = ab_class_args)
|
||||
|
||||
structure(unname(agents),
|
||||
class = c("ab_selector", "character"))
|
||||
}
|
||||
|
||||
#' @method c ab_selector
|
||||
@@ -321,7 +555,6 @@ all_any_ab_selector <- function(type, ..., na.rm = TRUE) {
|
||||
#' @export
|
||||
#' @noRd
|
||||
all.ab_selector <- function(..., na.rm = FALSE) {
|
||||
# this is all() for
|
||||
all_any_ab_selector("all", ..., na.rm = na.rm)
|
||||
}
|
||||
|
||||
@@ -367,7 +600,6 @@ any.ab_selector_any_all <- function(..., na.rm = FALSE) {
|
||||
`==.ab_selector` <- function(e1, e2) {
|
||||
calls <- as.character(match.call())
|
||||
fn_name <- calls[2]
|
||||
# keep only the ... in c(...)
|
||||
fn_name <- gsub("^(c\\()(.*)(\\))$", "\\2", fn_name)
|
||||
if (is_any(fn_name)) {
|
||||
type <- "any"
|
||||
@@ -390,7 +622,6 @@ any.ab_selector_any_all <- function(..., na.rm = FALSE) {
|
||||
`!=.ab_selector` <- function(e1, e2) {
|
||||
calls <- as.character(match.call())
|
||||
fn_name <- calls[2]
|
||||
# keep only the ... in c(...)
|
||||
fn_name <- gsub("^(c\\()(.*)(\\))$", "\\2", fn_name)
|
||||
if (is_any(fn_name)) {
|
||||
type <- "any"
|
||||
@@ -410,6 +641,25 @@ any.ab_selector_any_all <- function(..., na.rm = FALSE) {
|
||||
class = c("ab_selector_any_all", "logical"))
|
||||
}
|
||||
|
||||
#' @method & ab_selector
|
||||
#' @export
|
||||
#' @noRd
|
||||
`&.ab_selector` <- function(e1, e2) {
|
||||
# this is only required for base R, since tidyselect has already implemented this
|
||||
# e.g., for: example_isolates[, penicillins() & administrable_per_os()]
|
||||
structure(intersect(unclass(e1), unclass(e2)),
|
||||
class = c("ab_selector", "character"))
|
||||
}
|
||||
#' @method | ab_selector
|
||||
#' @export
|
||||
#' @noRd
|
||||
`|.ab_selector` <- function(e1, e2) {
|
||||
# this is only required for base R, since tidyselect has already implemented this
|
||||
# e.g., for: example_isolates[, penicillins() | administrable_per_os()]
|
||||
structure(union(unclass(e1), unclass(e2)),
|
||||
class = c("ab_selector", "character"))
|
||||
}
|
||||
|
||||
is_any <- function(el1) {
|
||||
syscall <- paste0(trimws(deparse(sys.calls()[[1]])), collapse = " ")
|
||||
el1 <- gsub("(.*),.*", "\\1", el1)
|
||||
@@ -421,30 +671,17 @@ is_all <- function(el1) {
|
||||
syscall %like% paste0("[^_a-zA-Z0-9]all\\(", "(c\\()?", el1)
|
||||
}
|
||||
|
||||
|
||||
find_ab_group <- function(ab_class) {
|
||||
ab_class[ab_class == "carbapenem|cephalosporin|penicillin"] <- "betalactam"
|
||||
ab_class <- gsub("[^a-zA-Z0-9]", ".*", ab_class)
|
||||
ifelse(ab_class %in% c("aminoglycoside",
|
||||
"betalactam",
|
||||
"carbapenem",
|
||||
"cephalosporin",
|
||||
"fluoroquinolone",
|
||||
"glycopeptide",
|
||||
"macrolide",
|
||||
"oxazolidinone",
|
||||
"tetracycline"),
|
||||
paste0(ab_class, "s"),
|
||||
antibiotics %pm>%
|
||||
subset(group %like% ab_class |
|
||||
atc_group1 %like% ab_class |
|
||||
atc_group2 %like% ab_class) %pm>%
|
||||
pm_pull(group) %pm>%
|
||||
unique() %pm>%
|
||||
tolower() %pm>%
|
||||
sort() %pm>%
|
||||
paste(collapse = "/")
|
||||
)
|
||||
find_ab_group <- function(ab_class_args) {
|
||||
ab_class_args <- gsub("[^a-zA-Z0-9]", ".*", ab_class_args)
|
||||
AB_lookup %pm>%
|
||||
subset(group %like% ab_class_args |
|
||||
atc_group1 %like% ab_class_args |
|
||||
atc_group2 %like% ab_class_args) %pm>%
|
||||
pm_pull(group) %pm>%
|
||||
unique() %pm>%
|
||||
tolower() %pm>%
|
||||
sort() %pm>%
|
||||
paste(collapse = "/")
|
||||
}
|
||||
|
||||
find_ab_names <- function(ab_group, n = 3) {
|
||||
@@ -462,8 +699,41 @@ find_ab_names <- function(ab_group, n = 3) {
|
||||
antibiotics$atc_group2 %like% ab_group) &
|
||||
antibiotics$ab %unlike% "[0-9]$"), ]$name
|
||||
}
|
||||
if (length(drugs) == 0) {
|
||||
return("??")
|
||||
}
|
||||
vector_or(ab_name(sample(drugs, size = min(n, length(drugs)), replace = FALSE),
|
||||
tolower = TRUE,
|
||||
language = NULL),
|
||||
quotes = FALSE)
|
||||
}
|
||||
|
||||
message_agent_names <- function(function_name, agents, ab_group = NULL, examples = "", ab_class_args = NULL, call = NULL) {
|
||||
if (message_not_thrown_before(paste0(function_name, ".", paste(sort(agents), collapse = "|")))) {
|
||||
if (length(agents) == 0) {
|
||||
if (is.null(ab_group)) {
|
||||
message_("For `", function_name, "()` no antimicrobial agents found", examples, ".")
|
||||
} else if (ab_group == "administrable_per_os") {
|
||||
message_("No orally administrable agents found", examples, ".")
|
||||
} else if (ab_group == "administrable_iv") {
|
||||
message_("No IV administrable agents found", examples, ".")
|
||||
} else {
|
||||
message_("No antimicrobial agents of class '", ab_group, "' found", examples, ".")
|
||||
}
|
||||
} else {
|
||||
agents_formatted <- paste0("'", font_bold(agents, collapse = NULL), "'")
|
||||
agents_names <- ab_name(names(agents), tolower = TRUE, language = NULL)
|
||||
need_name <- generalise_antibiotic_name(agents) != generalise_antibiotic_name(agents_names)
|
||||
agents_formatted[need_name] <- paste0(agents_formatted[need_name], " (", agents_names[need_name], ")")
|
||||
message_("For `", function_name, "(",
|
||||
ifelse(function_name == "ab_class",
|
||||
paste0("\"", ab_class_args, "\""),
|
||||
ifelse(!is.null(call),
|
||||
paste0(deparse(call), collapse = " "),
|
||||
"")),
|
||||
")` using ",
|
||||
ifelse(length(agents) == 1, "column ", "columns "),
|
||||
vector_and(agents_formatted, quotes = FALSE, sort = FALSE))
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
+221
-47
@@ -29,22 +29,27 @@
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param x any (vector of) text that can be coerced to a valid antibiotic code with [as.ab()]
|
||||
#' @param tolower a [logical] to indicate whether the first [character] of every output should be transformed to a lower case [character]. This will lead to e.g. "polymyxin B" and not "polymyxin b".
|
||||
#' @param property one of the column names of one of the [antibiotics] data set
|
||||
#' @param property one of the column names of one of the [antibiotics] data set: `vector_or(colnames(antibiotics), sort = FALSE)`.
|
||||
#' @param language language of the returned text, defaults to system language (see [get_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation.
|
||||
#' @param administration way of administration, either `"oral"` or `"iv"`
|
||||
#' @param units a [logical] to indicate whether the units instead of the DDDs itself must be returned, see *Examples*
|
||||
#' @param open browse the URL using [utils::browseURL()]
|
||||
#' @param ... other arguments passed on to [as.ab()]
|
||||
#' @param ... in case of [set_ab_names()] and `data` is a [data.frame]: variables to select (supports tidy selection like `AMX:VAN`), otherwise other arguments passed on to [as.ab()]
|
||||
#' @param data a [data.frame] of which the columns need to be renamed, or a [character] vector of column names
|
||||
#' @param snake_case a [logical] to indicate whether the names should be in so-called [snake case](https://en.wikipedia.org/wiki/Snake_case): in lower case and all spaces/slashes replaced with an underscore (`_`)
|
||||
#' @param only_first a [logical] to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)
|
||||
#' @details All output [will be translated][translate] where possible.
|
||||
#'
|
||||
#' The function [ab_url()] will return the direct URL to the official WHO website. A warning will be returned if the required ATC code is not available.
|
||||
#'
|
||||
#' The function [set_ab_names()] is a special column renaming function for [data.frame]s. It renames columns names that resemble antimicrobial drugs. It always makes sure that the new column names are unique. If `property = "atc"` is set, preference is given to ATC codes from the J-group.
|
||||
#' @inheritSection as.ab Source
|
||||
#' @rdname ab_property
|
||||
#' @name ab_property
|
||||
#' @return
|
||||
#' - An [integer] in case of [ab_cid()]
|
||||
#' - A named [list] in case of [ab_info()] and multiple [ab_synonyms()]/[ab_tradenames()]
|
||||
#' - A named [list] in case of [ab_info()] and multiple [ab_atc()]/[ab_synonyms()]/[ab_tradenames()]
|
||||
#' - A [double] in case of [ab_ddd()]
|
||||
#' - A [data.frame] in case of [set_ab_names()]
|
||||
#' - A [character] in all other cases
|
||||
#' @export
|
||||
#' @seealso [antibiotics]
|
||||
@@ -53,7 +58,7 @@
|
||||
#' @examples
|
||||
#' # all properties:
|
||||
#' ab_name("AMX") # "Amoxicillin"
|
||||
#' ab_atc("AMX") # J01CA04 (ATC code from the WHO)
|
||||
#' ab_atc("AMX") # "J01CA04" (ATC code from the WHO)
|
||||
#' ab_cid("AMX") # 33613 (Compound ID from PubChem)
|
||||
#' ab_synonyms("AMX") # a list with brand names of amoxicillin
|
||||
#' ab_tradenames("AMX") # same
|
||||
@@ -68,10 +73,10 @@
|
||||
#' tolower = TRUE) # "amoxicillin/clavulanic acid" "polymyxin B"
|
||||
#'
|
||||
#' # defined daily doses (DDD)
|
||||
#' ab_ddd("AMX", "oral") # 1
|
||||
#' ab_ddd("AMX", "oral", units = TRUE) # "g"
|
||||
#' ab_ddd("AMX", "iv") # 1
|
||||
#' ab_ddd("AMX", "iv", units = TRUE) # "g"
|
||||
#' ab_ddd("AMX", "oral") # 1.5
|
||||
#' ab_ddd_units("AMX", "oral") # "g"
|
||||
#' ab_ddd("AMX", "iv") # 3
|
||||
#' ab_ddd_units("AMX", "iv") # "g"
|
||||
#'
|
||||
#' ab_info("AMX") # all properties as a list
|
||||
#'
|
||||
@@ -88,6 +93,33 @@
|
||||
#' ab_atc("cephtriaxone")
|
||||
#' ab_atc("cephthriaxone")
|
||||
#' ab_atc("seephthriaaksone")
|
||||
#'
|
||||
#' # use set_ab_names() for renaming columns
|
||||
#' colnames(example_isolates)
|
||||
#' colnames(set_ab_names(example_isolates))
|
||||
#' colnames(set_ab_names(example_isolates, NIT:VAN))
|
||||
#' \donttest{
|
||||
#' if (require("dplyr")) {
|
||||
#' example_isolates %>%
|
||||
#' set_ab_names()
|
||||
#'
|
||||
#' # this does the same:
|
||||
#' example_isolates %>%
|
||||
#' rename_with(set_ab_names)
|
||||
#'
|
||||
#' # set_ab_names() works with any AB property:
|
||||
#' example_isolates %>%
|
||||
#' set_ab_names(property = "atc")
|
||||
#'
|
||||
#' example_isolates %>%
|
||||
#' set_ab_names(where(is.rsi)) %>%
|
||||
#' colnames()
|
||||
#'
|
||||
#' example_isolates %>%
|
||||
#' set_ab_names(NIT:VAN) %>%
|
||||
#' colnames()
|
||||
#' }
|
||||
#' }
|
||||
ab_name <- function(x, language = get_locale(), tolower = FALSE, ...) {
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@@ -102,14 +134,6 @@ ab_name <- function(x, language = get_locale(), tolower = FALSE, ...) {
|
||||
x
|
||||
}
|
||||
|
||||
#' @rdname ab_property
|
||||
#' @aliases ATC
|
||||
#' @export
|
||||
ab_atc <- function(x, ...) {
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
ab_validate(x = x, property = "atc", ...)
|
||||
}
|
||||
|
||||
#' @rdname ab_property
|
||||
#' @export
|
||||
ab_cid <- function(x, ...) {
|
||||
@@ -145,6 +169,36 @@ ab_group <- function(x, language = get_locale(), ...) {
|
||||
translate_AMR(ab_validate(x = x, property = "group", ...), language = language, only_affect_ab_names = TRUE)
|
||||
}
|
||||
|
||||
#' @rdname ab_property
|
||||
#' @aliases ATC
|
||||
#' @export
|
||||
ab_atc <- function(x, only_first = FALSE, ...) {
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(only_first, allow_class = "logical", has_length = 1)
|
||||
|
||||
atcs <- ab_validate(x = x, property = "atc", ...)
|
||||
|
||||
if (only_first == TRUE) {
|
||||
atcs <- vapply(FUN.VALUE = character(1),
|
||||
# get only the first ATC code
|
||||
atcs,
|
||||
function(x) {
|
||||
# try to get the J-group
|
||||
if (any(x %like% "^J")) {
|
||||
x[x %like% "^J"][1L]
|
||||
} else {
|
||||
as.character(x[1L])
|
||||
}
|
||||
})
|
||||
} else if (length(atcs) == 1) {
|
||||
atcs <- unname(unlist(atcs))
|
||||
} else {
|
||||
names(atcs) <- x
|
||||
}
|
||||
|
||||
atcs
|
||||
}
|
||||
|
||||
#' @rdname ab_property
|
||||
#' @export
|
||||
ab_atc_group1 <- function(x, language = get_locale(), ...) {
|
||||
@@ -176,18 +230,48 @@ ab_loinc <- function(x, ...) {
|
||||
|
||||
#' @rdname ab_property
|
||||
#' @export
|
||||
ab_ddd <- function(x, administration = "oral", units = FALSE, ...) {
|
||||
ab_ddd <- function(x, administration = "oral", ...) {
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1)
|
||||
meet_criteria(units, allow_class = "logical", has_length = 1)
|
||||
|
||||
|
||||
x <- as.ab(x, ...)
|
||||
ddd_prop <- administration
|
||||
if (units == TRUE) {
|
||||
# old behaviour
|
||||
units <- list(...)$units
|
||||
if (!is.null(units) && isTRUE(units)) {
|
||||
if (message_not_thrown_before("ab_ddd", entire_session = TRUE)) {
|
||||
warning_("Using `ab_ddd(..., units = TRUE)` is deprecated, use `ab_ddd_units()` to retrieve units instead. ",
|
||||
"This warning will be shown once per session.", call = FALSE)
|
||||
}
|
||||
ddd_prop <- paste0(ddd_prop, "_units")
|
||||
} else {
|
||||
ddd_prop <- paste0(ddd_prop, "_ddd")
|
||||
}
|
||||
ab_validate(x = x, property = ddd_prop, ...)
|
||||
out <- ab_validate(x = x, property = ddd_prop)
|
||||
|
||||
if (any(ab_name(x, language = NULL) %like% "/" & is.na(out))) {
|
||||
warning_("DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package. ",
|
||||
"Please refer to the WHOCC website:\n",
|
||||
"www.whocc.no/ddd/list_of_ddds_combined_products/", call = FALSE)
|
||||
}
|
||||
out
|
||||
}
|
||||
|
||||
#' @rdname ab_property
|
||||
#' @export
|
||||
ab_ddd_units <- function(x, administration = "oral", ...) {
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1)
|
||||
|
||||
x <- as.ab(x, ...)
|
||||
if (any(ab_name(x, language = NULL) %like% "/")) {
|
||||
warning_("DDDs of combined products are available for different dose combinations and not (yet) part of the AMR package. ",
|
||||
"Please refer to the WHOCC website:\n",
|
||||
"www.whocc.no/ddd/list_of_ddds_combined_products/", call = FALSE)
|
||||
}
|
||||
|
||||
ddd_prop <- paste0(administration, "_units")
|
||||
ab_validate(x = x, property = ddd_prop)
|
||||
}
|
||||
|
||||
#' @rdname ab_property
|
||||
@@ -198,17 +282,18 @@ ab_info <- function(x, language = get_locale(), ...) {
|
||||
|
||||
x <- as.ab(x, ...)
|
||||
list(ab = as.character(x),
|
||||
atc = ab_atc(x),
|
||||
cid = ab_cid(x),
|
||||
name = ab_name(x, language = language),
|
||||
group = ab_group(x, language = language),
|
||||
atc_group1 = ab_atc_group1(x, language = language),
|
||||
atc_group2 = ab_atc_group2(x, language = language),
|
||||
tradenames = ab_tradenames(x),
|
||||
ddd = list(oral = list(amount = ab_ddd(x, administration = "oral", units = FALSE),
|
||||
units = ab_ddd(x, administration = "oral", units = TRUE)),
|
||||
iv = list(amount = ab_ddd(x, administration = "iv", units = FALSE),
|
||||
units = ab_ddd(x, administration = "iv", units = TRUE))))
|
||||
cid = ab_cid(x),
|
||||
name = ab_name(x, language = language),
|
||||
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),
|
||||
tradenames = ab_tradenames(x),
|
||||
loinc = ab_loinc(x),
|
||||
ddd = list(oral = list(amount = ab_ddd(x, administration = "oral"),
|
||||
units = ab_ddd_units(x, administration = "oral")),
|
||||
iv = list(amount = ab_ddd(x, administration = "iv"),
|
||||
units = ab_ddd_units(x, administration = "iv"))))
|
||||
}
|
||||
|
||||
|
||||
@@ -218,12 +303,13 @@ ab_url <- function(x, open = FALSE, ...) {
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(open, allow_class = "logical", has_length = 1)
|
||||
|
||||
ab <- as.ab(x = x, ... = ...)
|
||||
u <- paste0("https://www.whocc.no/atc_ddd_index/?code=", ab_atc(ab), "&showdescription=no")
|
||||
u[is.na(ab_atc(ab))] <- NA_character_
|
||||
ab <- as.ab(x = x, ...)
|
||||
atcs <- ab_atc(ab, only_first = TRUE)
|
||||
u <- paste0("https://www.whocc.no/atc_ddd_index/?code=", atcs, "&showdescription=no")
|
||||
u[is.na(atcs)] <- NA_character_
|
||||
names(u) <- ab_name(ab)
|
||||
|
||||
NAs <- ab_name(ab, tolower = TRUE, language = NULL)[!is.na(ab) & is.na(ab_atc(ab))]
|
||||
NAs <- ab_name(ab, tolower = TRUE, language = NULL)[!is.na(ab) & is.na(atcs)]
|
||||
if (length(NAs) > 0) {
|
||||
warning_("No ATC code available for ", vector_and(NAs, quotes = FALSE), ".")
|
||||
}
|
||||
@@ -248,20 +334,108 @@ ab_property <- function(x, property = "name", language = get_locale(), ...) {
|
||||
translate_AMR(ab_validate(x = x, property = property, ...), language = language)
|
||||
}
|
||||
|
||||
#' @rdname ab_property
|
||||
#' @aliases ATC
|
||||
#' @export
|
||||
set_ab_names <- function(data, ..., property = "name", language = get_locale(), snake_case = NULL) {
|
||||
meet_criteria(data, allow_class = c("data.frame", "character"))
|
||||
meet_criteria(property, is_in = colnames(antibiotics), has_length = 1, ignore.case = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(snake_case, allow_class = "logical", has_length = 1, allow_NULL = TRUE)
|
||||
|
||||
x_deparsed <- deparse(substitute(data))
|
||||
if (length(x_deparsed) > 1 || any(x_deparsed %unlike% "[a-z]+")) {
|
||||
x_deparsed <- "your_data"
|
||||
}
|
||||
|
||||
property <- tolower(property)
|
||||
if (is.null(snake_case)) {
|
||||
snake_case <- property == "name"
|
||||
}
|
||||
|
||||
if (is.data.frame(data)) {
|
||||
if (tryCatch(length(list(...)) > 0, error = function(e) TRUE)) {
|
||||
df <- pm_select(data, ...)
|
||||
} else {
|
||||
df <- data
|
||||
}
|
||||
vars <- get_column_abx(df, info = FALSE, only_rsi_columns = FALSE, sort = FALSE)
|
||||
if (length(vars) == 0) {
|
||||
message_("No columns with antibiotic results found for `set_ab_names()`, leaving names unchanged.")
|
||||
return(data)
|
||||
}
|
||||
} else {
|
||||
# quickly get antibiotic codes
|
||||
vars_ab <- as.ab(data, fast_mode = TRUE)
|
||||
vars <- data[!is.na(vars_ab)]
|
||||
}
|
||||
x <- vapply(FUN.VALUE = character(1),
|
||||
ab_property(vars, property = property, language = language),
|
||||
function(x) {
|
||||
if (property == "atc") {
|
||||
# try to get the J-group
|
||||
if (any(x %like% "^J")) {
|
||||
x[x %like% "^J"][1L]
|
||||
} else {
|
||||
as.character(x[1L])
|
||||
}
|
||||
} else {
|
||||
as.character(x[1L])
|
||||
}
|
||||
},
|
||||
USE.NAMES = FALSE)
|
||||
if (any(x %in% c("", NA))) {
|
||||
warning_("No ", property, " found for column(s): ", vector_and(vars[x %in% c("", NA)], sort = FALSE), call = FALSE)
|
||||
x[x %in% c("", NA)] <- vars[x %in% c("", NA)]
|
||||
}
|
||||
|
||||
if (snake_case == TRUE) {
|
||||
x <- tolower(gsub("[^a-zA-Z0-9]+", "_", x))
|
||||
}
|
||||
|
||||
if (any(duplicated(x))) {
|
||||
# very hacky way of adding the index to each duplicate
|
||||
# so "Amoxicillin", "Amoxicillin", "Amoxicillin"
|
||||
# will be "Amoxicillin", "Amoxicillin_2", "Amoxicillin_3"
|
||||
invisible(lapply(unique(x),
|
||||
function(u) {
|
||||
dups <- which(x == u)
|
||||
if (length(dups) > 1) {
|
||||
# there are duplicates
|
||||
dup_add_int <- dups[2:length(dups)]
|
||||
x[dup_add_int] <<- paste0(x[dup_add_int], "_", c(2:length(dups)))
|
||||
}
|
||||
}))
|
||||
}
|
||||
if (is.data.frame(data)) {
|
||||
colnames(data)[colnames(data) %in% vars] <- x
|
||||
data
|
||||
} else {
|
||||
data[which(!is.na(vars_ab))] <- x
|
||||
data
|
||||
}
|
||||
}
|
||||
|
||||
ab_validate <- function(x, property, ...) {
|
||||
|
||||
check_dataset_integrity()
|
||||
|
||||
# try to catch an error when inputting an invalid argument
|
||||
# so the 'call.' can be set to FALSE
|
||||
tryCatch(x[1L] %in% antibiotics[1, property],
|
||||
error = function(e) stop(e$message, call. = FALSE))
|
||||
x_bak <- x
|
||||
if (!all(x %in% antibiotics[, property])) {
|
||||
x <- data.frame(ab = as.ab(x, ...), stringsAsFactors = FALSE) %pm>%
|
||||
pm_left_join(antibiotics, by = "ab") %pm>%
|
||||
pm_pull(property)
|
||||
if (tryCatch(all(x[!is.na(x)] %in% AB_lookup$ab), error = function(e) FALSE)) {
|
||||
# special case for ab_* functions where class is already <ab>
|
||||
x <- AB_lookup[match(x, AB_lookup$ab), property, drop = TRUE]
|
||||
|
||||
} else {
|
||||
# try to catch an error when inputting an invalid argument
|
||||
# so the 'call.' can be set to FALSE
|
||||
tryCatch(x[1L] %in% antibiotics[1, property],
|
||||
error = function(e) stop(e$message, call. = FALSE))
|
||||
|
||||
if (!all(x %in% AB_lookup[, property])) {
|
||||
x <- as.ab(x, ...)
|
||||
x <- AB_lookup[match(x, AB_lookup$ab), property, drop = TRUE]
|
||||
}
|
||||
}
|
||||
|
||||
if (property == "ab") {
|
||||
return(set_clean_class(x, new_class = c("ab", "character")))
|
||||
} else if (property == "cid") {
|
||||
@@ -269,7 +443,7 @@ ab_validate <- function(x, property, ...) {
|
||||
} else if (property %like% "ddd") {
|
||||
return(as.double(x))
|
||||
} else {
|
||||
x[is.na(x) & !is.na(x_bak)] <- NA
|
||||
x[is.na(x)] <- NA
|
||||
return(x)
|
||||
}
|
||||
}
|
||||
|
||||
@@ -61,7 +61,7 @@
|
||||
#' Matthijs S. Berends \cr
|
||||
#' m.s.berends \[at\] umcg \[dot\] nl \cr
|
||||
#' University of Groningen
|
||||
#' Department of Medical Microbiology and Infection Prevention
|
||||
#' Department of Medical Microbiology and Infection Prevention \cr
|
||||
#' University Medical Center Groningen \cr
|
||||
#' Post Office Box 30001 \cr
|
||||
#' 9700 RB Groningen \cr
|
||||
|
||||
+46
-27
@@ -25,9 +25,9 @@
|
||||
|
||||
#' Get ATC Properties from WHOCC Website
|
||||
#'
|
||||
#' Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic), such as the name, defined daily dose (DDD) or standard unit.
|
||||
#' Gets data from the WHOCC website to determine properties of an Anatomical Therapeutic Chemical (ATC) (e.g. an antibiotic), such as the name, defined daily dose (DDD) or standard unit.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param atc_code a [character] or [character] vector with ATC code(s) of antibiotic(s)
|
||||
#' @param atc_code a [character] (vector) with ATC code(s) of antibiotics, will be coerced with [as.ab()] and [ab_atc()] internally if not a valid ATC code
|
||||
#' @param property property of an ATC code. Valid values are `"ATC"`, `"Name"`, `"DDD"`, `"U"` (`"unit"`), `"Adm.R"`, `"Note"` and `groups`. For this last option, all hierarchical groups of an ATC code will be returned, see *Examples*.
|
||||
#' @param administration type of administration when using `property = "Adm.R"`, see *Details*
|
||||
#' @param url url of website of the WHOCC. The sign `%s` can be used as a placeholder for ATC codes.
|
||||
@@ -68,6 +68,7 @@
|
||||
#' if (requireNamespace("curl") && requireNamespace("rvest") && requireNamespace("xml2")) {
|
||||
#' # oral DDD (Defined Daily Dose) of amoxicillin
|
||||
#' atc_online_property("J01CA04", "DDD", "O")
|
||||
#' atc_online_ddd(ab_atc("amox"))
|
||||
#'
|
||||
#' # parenteral DDD (Defined Daily Dose) of amoxicillin
|
||||
#' atc_online_property("J01CA04", "DDD", "P")
|
||||
@@ -81,7 +82,7 @@ atc_online_property <- function(atc_code,
|
||||
url = "https://www.whocc.no/atc_ddd_index/?code=%s&showdescription=no",
|
||||
url_vet = "https://www.whocc.no/atcvet/atcvet_index/?code=%s&showdescription=no") {
|
||||
meet_criteria(atc_code, allow_class = "character")
|
||||
meet_criteria(property, allow_class = "character", has_length = 1, is_in = c("ATC", "Name", "DDD", "U", "Adm.R", "Note", "groups"), ignore.case = TRUE)
|
||||
meet_criteria(property, allow_class = "character", has_length = 1, is_in = c("ATC", "Name", "DDD", "U", "unit", "Adm.R", "Note", "groups"), ignore.case = TRUE)
|
||||
meet_criteria(administration, allow_class = "character", has_length = 1)
|
||||
meet_criteria(url, allow_class = "character", has_length = 1, looks_like = "https?://")
|
||||
meet_criteria(url_vet, allow_class = "character", has_length = 1, looks_like = "https?://")
|
||||
@@ -97,8 +98,8 @@ atc_online_property <- function(atc_code,
|
||||
|
||||
check_dataset_integrity()
|
||||
|
||||
if (!all(atc_code %in% antibiotics)) {
|
||||
atc_code <- as.character(ab_atc(atc_code))
|
||||
if (!all(atc_code %in% unlist(antibiotics$atc))) {
|
||||
atc_code <- as.character(ab_atc(atc_code, only_first = TRUE))
|
||||
}
|
||||
|
||||
if (!has_internet()) {
|
||||
@@ -108,12 +109,11 @@ atc_online_property <- function(atc_code,
|
||||
return(rep(NA, length(atc_code)))
|
||||
}
|
||||
|
||||
# also allow unit as property
|
||||
if (property %like% "unit") {
|
||||
property <- "U"
|
||||
}
|
||||
|
||||
property <- tolower(property)
|
||||
# also allow unit as property
|
||||
if (property == "unit") {
|
||||
property <- "u"
|
||||
}
|
||||
if (property == "ddd") {
|
||||
returnvalue <- rep(NA_real_, length(atc_code))
|
||||
} else if (property == "groups") {
|
||||
@@ -138,15 +138,21 @@ atc_online_property <- function(atc_code,
|
||||
atc_url <- sub("%s", atc_code[i], atc_url, fixed = TRUE)
|
||||
|
||||
if (property == "groups") {
|
||||
tbl <- read_html(atc_url) %pm>%
|
||||
html_node("#content") %pm>%
|
||||
html_children() %pm>%
|
||||
html_node("a")
|
||||
out <- tryCatch(
|
||||
read_html(atc_url) %pm>%
|
||||
html_node("#content") %pm>%
|
||||
html_children() %pm>%
|
||||
html_node("a"),
|
||||
error = function(e) NULL)
|
||||
if (is.null(out)) {
|
||||
message_("Connection to ", atc_url, " failed.")
|
||||
return(rep(NA, length(atc_code)))
|
||||
}
|
||||
|
||||
# get URLS of items
|
||||
hrefs <- tbl %pm>% html_attr("href")
|
||||
hrefs <- out %pm>% html_attr("href")
|
||||
# get text of items
|
||||
texts <- tbl %pm>% html_text()
|
||||
texts <- out %pm>% html_text()
|
||||
# select only text items where URL like "code="
|
||||
texts <- texts[grepl("?code=", tolower(hrefs), fixed = TRUE)]
|
||||
# last one is antibiotics, skip it
|
||||
@@ -154,15 +160,21 @@ atc_online_property <- function(atc_code,
|
||||
returnvalue <- c(list(texts), returnvalue)
|
||||
|
||||
} else {
|
||||
tbl <- read_html(atc_url) %pm>%
|
||||
html_nodes("table") %pm>%
|
||||
html_table(header = TRUE) %pm>%
|
||||
as.data.frame(stringsAsFactors = FALSE)
|
||||
out <- tryCatch(
|
||||
read_html(atc_url) %pm>%
|
||||
html_nodes("table") %pm>%
|
||||
html_table(header = TRUE) %pm>%
|
||||
as.data.frame(stringsAsFactors = FALSE),
|
||||
error = function(e) NULL)
|
||||
if (is.null(out)) {
|
||||
message_("Connection to ", atc_url, " failed.")
|
||||
return(rep(NA, length(atc_code)))
|
||||
}
|
||||
|
||||
# case insensitive column names
|
||||
colnames(tbl) <- gsub("^atc.*", "atc", tolower(colnames(tbl)))
|
||||
colnames(out) <- gsub("^atc.*", "atc", tolower(colnames(out)))
|
||||
|
||||
if (length(tbl) == 0) {
|
||||
if (length(out) == 0) {
|
||||
warning_("ATC not found: ", atc_code[i], ". Please check ", atc_url, ".", call = FALSE)
|
||||
returnvalue[i] <- NA
|
||||
next
|
||||
@@ -170,15 +182,15 @@ atc_online_property <- function(atc_code,
|
||||
|
||||
if (property %in% c("atc", "name")) {
|
||||
# ATC and name are only in first row
|
||||
returnvalue[i] <- tbl[1, property]
|
||||
returnvalue[i] <- out[1, property]
|
||||
} else {
|
||||
if (!"adm.r" %in% colnames(tbl) | is.na(tbl[1, "adm.r"])) {
|
||||
if (!"adm.r" %in% colnames(out) | is.na(out[1, "adm.r"])) {
|
||||
returnvalue[i] <- NA
|
||||
next
|
||||
} else {
|
||||
for (j in seq_len(nrow(tbl))) {
|
||||
if (tbl[j, "adm.r"] == administration) {
|
||||
returnvalue[i] <- tbl[j, property]
|
||||
for (j in seq_len(nrow(out))) {
|
||||
if (out[j, "adm.r"] == administration) {
|
||||
returnvalue[i] <- out[j, property]
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -206,3 +218,10 @@ atc_online_ddd <- function(atc_code, ...) {
|
||||
meet_criteria(atc_code, allow_class = "character")
|
||||
atc_online_property(atc_code = atc_code, property = "ddd", ...)
|
||||
}
|
||||
|
||||
#' @rdname atc_online
|
||||
#' @export
|
||||
atc_online_ddd_units <- function(atc_code, ...) {
|
||||
meet_criteria(atc_code, allow_class = "character")
|
||||
atc_online_property(atc_code = atc_code, property = "unit", ...)
|
||||
}
|
||||
|
||||
@@ -25,7 +25,7 @@
|
||||
|
||||
#' Determine Bug-Drug Combinations
|
||||
#'
|
||||
#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use [format()] on the result to prettify it to a publicable/printable format, see *Examples*.
|
||||
#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use [format()] on the result to prettify it to a publishable/printable format, see *Examples*.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @inheritParams eucast_rules
|
||||
#' @param combine_IR a [logical] to indicate whether values R and I should be summed
|
||||
@@ -81,7 +81,7 @@ bug_drug_combinations <- function(x,
|
||||
unique_mo <- sort(unique(x[, col_mo, drop = TRUE]))
|
||||
|
||||
# select only groups and antibiotics
|
||||
if (inherits(x.bak, "grouped_df")) {
|
||||
if (is_null_or_grouped_tbl(x.bak)) {
|
||||
data_has_groups <- TRUE
|
||||
groups <- setdiff(names(attributes(x.bak)$groups), ".rows")
|
||||
x <- x[, c(groups, col_mo, colnames(x)[vapply(FUN.VALUE = logical(1), x, is.rsi)]), drop = FALSE]
|
||||
@@ -113,7 +113,7 @@ bug_drug_combinations <- function(x,
|
||||
data.frame(S = m["S", ], I = m["I", ], R = m["R", ], stringsAsFactors = FALSE)
|
||||
})
|
||||
merged <- do.call(rbind, pivot)
|
||||
out_group <- data.frame(mo = unique_mo[i],
|
||||
out_group <- data.frame(mo = rep(unique_mo[i], NROW(merged)),
|
||||
ab = rownames(merged),
|
||||
S = merged$S,
|
||||
I = merged$I,
|
||||
@@ -218,7 +218,7 @@ format.bug_drug_combinations <- function(x,
|
||||
ab_txt[i] <- gsub("group", ab_group(ab[i], language = language), ab_txt[i])
|
||||
ab_txt[i] <- gsub("atc_group1", ab_atc_group1(ab[i], language = language), ab_txt[i])
|
||||
ab_txt[i] <- gsub("atc_group2", ab_atc_group2(ab[i], language = language), ab_txt[i])
|
||||
ab_txt[i] <- gsub("atc", ab_atc(ab[i]), ab_txt[i])
|
||||
ab_txt[i] <- gsub("atc", ab_atc(ab[i], only_first = TRUE), ab_txt[i])
|
||||
ab_txt[i] <- gsub("name", ab_name(ab[i], language = language), ab_txt[i])
|
||||
ab_txt[i]
|
||||
}
|
||||
|
||||
@@ -41,7 +41,7 @@ format_included_data_number <- function(data) {
|
||||
|
||||
#' The Catalogue of Life
|
||||
#'
|
||||
#' This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life.
|
||||
#' This package contains the complete taxonomic tree (last updated: `r CATALOGUE_OF_LIFE$yearmonth_LPSN`) of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (CoL), supplemented with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN).
|
||||
#' @section Catalogue of Life:
|
||||
#' \if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
|
||||
#' This package contains the complete taxonomic tree of almost all microorganisms (`r format_included_data_number(microorganisms)` species) from the authoritative and comprehensive Catalogue of Life (CoL, <http://www.catalogueoflife.org>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, [lpsn.dsmz.de](https://lpsn.dsmz.de)). This supplementation is needed until the [CoL+ project](https://github.com/CatalogueOfLife/general) is finished, which we await.
|
||||
@@ -58,7 +58,7 @@ format_included_data_number <- function(data) {
|
||||
#'
|
||||
#' The Catalogue of Life (<http://www.catalogueoflife.org>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.9 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.
|
||||
#'
|
||||
#' The syntax used to transform the original data to a cleansed \R format, can be found here: <https://github.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R>.
|
||||
#' The syntax used to transform the original data to a cleansed \R format, can be found here: <https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R>.
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
#' @name catalogue_of_life
|
||||
#' @rdname catalogue_of_life
|
||||
@@ -141,5 +141,5 @@ print.catalogue_of_life_version <- function(x, ...) {
|
||||
" Number of included bacterial species: ", format(x$LPSN$n, big.mark = ","), "\n\n",
|
||||
"=> Total number of species included: ", format(x$total_included$n_total_species, big.mark = ","), "\n",
|
||||
"=> Total number of synonyms included: ", format(x$total_included$n_total_synonyms, big.mark = ","), "\n\n",
|
||||
"See for more info ?microorganisms and ?catalogue_of_life.\n"))
|
||||
"See for more info ", font_grey_bg("`?microorganisms`"), " and ", font_grey_bg("`?catalogue_of_life`"), ".\n"))
|
||||
}
|
||||
|
||||
@@ -82,6 +82,12 @@
|
||||
#' n1 = count_all(CIP), # the actual total; sum of all three
|
||||
#' n2 = n_rsi(CIP), # same - analogous to n_distinct
|
||||
#' total = n()) # NOT the number of tested isolates!
|
||||
#'
|
||||
#' # Number of available isolates for a whole antibiotic class
|
||||
#' # (i.e., in this data set columns GEN, TOB, AMK, KAN)
|
||||
#' example_isolates %>%
|
||||
#' group_by(hospital_id) %>%
|
||||
#' summarise(across(aminoglycosides(), n_rsi))
|
||||
#'
|
||||
#' # Count co-resistance between amoxicillin/clav acid and gentamicin,
|
||||
#' # so we can see that combination therapy does a lot more than mono therapy.
|
||||
@@ -108,81 +114,95 @@
|
||||
#' }
|
||||
#' }
|
||||
count_resistant <- function(..., only_all_tested = FALSE) {
|
||||
rsi_calc(...,
|
||||
ab_result = "R",
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = TRUE)
|
||||
tryCatch(
|
||||
rsi_calc(...,
|
||||
ab_result = "R",
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = TRUE),
|
||||
error = function(e) stop_(e$message, call = -5))
|
||||
}
|
||||
|
||||
#' @rdname count
|
||||
#' @export
|
||||
count_susceptible <- function(..., only_all_tested = FALSE) {
|
||||
rsi_calc(...,
|
||||
ab_result = c("S", "I"),
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = TRUE)
|
||||
tryCatch(
|
||||
rsi_calc(...,
|
||||
ab_result = c("S", "I"),
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = TRUE),
|
||||
error = function(e) stop_(e$message, call = -5))
|
||||
}
|
||||
|
||||
#' @rdname count
|
||||
#' @export
|
||||
count_R <- function(..., only_all_tested = FALSE) {
|
||||
rsi_calc(...,
|
||||
ab_result = "R",
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = TRUE)
|
||||
tryCatch(
|
||||
rsi_calc(...,
|
||||
ab_result = "R",
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = TRUE),
|
||||
error = function(e) stop_(e$message, call = -5))
|
||||
}
|
||||
|
||||
#' @rdname count
|
||||
#' @export
|
||||
count_IR <- function(..., only_all_tested = FALSE) {
|
||||
if (message_not_thrown_before("count_IR")) {
|
||||
warning_("Using count_IR() is discouraged; use count_resistant() instead to not consider \"I\" being resistant.", call = FALSE)
|
||||
remember_thrown_message("count_IR")
|
||||
if (message_not_thrown_before("count_IR", entire_session = TRUE)) {
|
||||
message_("Using `count_IR()` is discouraged; use `count_resistant()` instead to not consider \"I\" being resistant. This note will be shown once for this session.", as_note = FALSE)
|
||||
}
|
||||
rsi_calc(...,
|
||||
ab_result = c("I", "R"),
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = TRUE)
|
||||
tryCatch(
|
||||
rsi_calc(...,
|
||||
ab_result = c("I", "R"),
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = TRUE),
|
||||
error = function(e) stop_(e$message, call = -5))
|
||||
}
|
||||
|
||||
#' @rdname count
|
||||
#' @export
|
||||
count_I <- function(..., only_all_tested = FALSE) {
|
||||
rsi_calc(...,
|
||||
ab_result = "I",
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = TRUE)
|
||||
tryCatch(
|
||||
rsi_calc(...,
|
||||
ab_result = "I",
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = TRUE),
|
||||
error = function(e) stop_(e$message, call = -5))
|
||||
}
|
||||
|
||||
#' @rdname count
|
||||
#' @export
|
||||
count_SI <- function(..., only_all_tested = FALSE) {
|
||||
rsi_calc(...,
|
||||
ab_result = c("S", "I"),
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = TRUE)
|
||||
tryCatch(
|
||||
rsi_calc(...,
|
||||
ab_result = c("S", "I"),
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = TRUE),
|
||||
error = function(e) stop_(e$message, call = -5))
|
||||
}
|
||||
|
||||
#' @rdname count
|
||||
#' @export
|
||||
count_S <- function(..., only_all_tested = FALSE) {
|
||||
if (message_not_thrown_before("count_S")) {
|
||||
warning_("Using count_S() is discouraged; use count_susceptible() instead to also consider \"I\" being susceptible.", call = FALSE)
|
||||
remember_thrown_message("count_S")
|
||||
if (message_not_thrown_before("count_S", entire_session = TRUE)) {
|
||||
message_("Using `count_S()` is discouraged; use `count_susceptible()` instead to also consider \"I\" being susceptible. This note will be shown once for this session.", as_note = FALSE)
|
||||
}
|
||||
rsi_calc(...,
|
||||
ab_result = "S",
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = TRUE)
|
||||
tryCatch(
|
||||
rsi_calc(...,
|
||||
ab_result = "S",
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = TRUE),
|
||||
error = function(e) stop_(e$message, call = -5))
|
||||
}
|
||||
|
||||
#' @rdname count
|
||||
#' @export
|
||||
count_all <- function(..., only_all_tested = FALSE) {
|
||||
rsi_calc(...,
|
||||
ab_result = c("S", "I", "R"),
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = TRUE)
|
||||
tryCatch(
|
||||
rsi_calc(...,
|
||||
ab_result = c("S", "I", "R"),
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = TRUE),
|
||||
error = function(e) stop_(e$message, call = -5))
|
||||
}
|
||||
|
||||
#' @rdname count
|
||||
@@ -196,11 +216,13 @@ count_df <- function(data,
|
||||
language = get_locale(),
|
||||
combine_SI = TRUE,
|
||||
combine_IR = FALSE) {
|
||||
rsi_calc_df(type = "count",
|
||||
data = data,
|
||||
translate_ab = translate_ab,
|
||||
language = language,
|
||||
combine_SI = combine_SI,
|
||||
combine_IR = combine_IR,
|
||||
combine_SI_missing = missing(combine_SI))
|
||||
tryCatch(
|
||||
rsi_calc_df(type = "count",
|
||||
data = data,
|
||||
translate_ab = translate_ab,
|
||||
language = language,
|
||||
combine_SI = combine_SI,
|
||||
combine_IR = combine_IR,
|
||||
combine_SI_missing = missing(combine_SI)),
|
||||
error = function(e) stop_(e$message, call = -5))
|
||||
}
|
||||
|
||||
@@ -26,7 +26,7 @@
|
||||
#' Define Custom EUCAST Rules
|
||||
#'
|
||||
#' Define custom EUCAST rules for your organisation or specific analysis and use the output of this function in [eucast_rules()].
|
||||
#' @inheritSection lifecycle Maturing Lifecycle
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param ... rules in formula notation, see *Examples*
|
||||
#' @details
|
||||
#' Some organisations have their own adoption of EUCAST rules. This function can be used to define custom EUCAST rules to be used in the [eucast_rules()] function.
|
||||
@@ -89,9 +89,9 @@
|
||||
#'
|
||||
#' ### Usage of antibiotic group names
|
||||
#'
|
||||
#' It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part *after* the tilde. In above examples, the antibiotic group `aminopenicillins` is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the antibiotic agents that will be matched when running the rule.
|
||||
#' It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part *after* the tilde. In above examples, the antibiotic group `aminopenicillins` is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the agents that will be matched when running the rule.
|
||||
#'
|
||||
#' `r paste0(" * ", sapply(DEFINED_AB_GROUPS, function(x) paste0("``", tolower(x), "``\\cr(", paste0(sort(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE)), collapse = ", "), ")"), USE.NAMES = FALSE), "\n", collapse = "")`
|
||||
#' `r paste0(" * ", sapply(DEFINED_AB_GROUPS, function(x) paste0("``", tolower(gsub("^AB_", "", x)), "``\\cr(", vector_and(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), quotes = FALSE), ")"), USE.NAMES = FALSE), "\n", collapse = "")`
|
||||
#' @returns A [list] containing the custom rules
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
#' @export
|
||||
@@ -140,12 +140,12 @@ custom_eucast_rules <- function(...) {
|
||||
stop_ifnot(deparse(result) %like% "==",
|
||||
"the result of rule ", i, " (the part after the `~`) must contain `==`, such as in `... ~ ampicillin == \"R\"`, see `?custom_eucast_rules`")
|
||||
result_group <- as.character(result)[[2]]
|
||||
if (paste0(toupper(result_group), "S") %in% DEFINED_AB_GROUPS) {
|
||||
if (paste0("AB_", toupper(result_group), "S") %in% DEFINED_AB_GROUPS) {
|
||||
# support for e.g. 'aminopenicillin' if user meant 'aminopenicillins'
|
||||
result_group <- paste0(result_group, "s")
|
||||
}
|
||||
if (toupper(result_group) %in% DEFINED_AB_GROUPS) {
|
||||
result_group <- eval(parse(text = toupper(result_group)), envir = asNamespace("AMR"))
|
||||
if (paste0("AB_", toupper(result_group)) %in% DEFINED_AB_GROUPS) {
|
||||
result_group <- eval(parse(text = paste0("AB_", toupper(result_group))), envir = asNamespace("AMR"))
|
||||
} else {
|
||||
result_group <- tryCatch(
|
||||
suppressWarnings(as.ab(result_group,
|
||||
@@ -157,7 +157,7 @@ custom_eucast_rules <- function(...) {
|
||||
stop_if(any(is.na(result_group)),
|
||||
"this result of rule ", i, " could not be translated to a single antimicrobial agent/group: \"",
|
||||
as.character(result)[[2]], "\".\n\nThe input can be a name or code of an antimicrobial agent, or be one of: ",
|
||||
vector_or(tolower(DEFINED_AB_GROUPS), quotes = FALSE), ".")
|
||||
vector_or(tolower(gsub("AB_", "", DEFINED_AB_GROUPS)), quotes = FALSE), ".")
|
||||
result_value <- as.character(result)[[3]]
|
||||
result_value[result_value == "NA"] <- NA
|
||||
stop_ifnot(result_value %in% c("R", "S", "I", NA),
|
||||
|
||||
@@ -23,28 +23,28 @@
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Data Sets with `r format(nrow(antibiotics) + nrow(antivirals), big.mark = ",")` Antimicrobials
|
||||
#' Data Sets with `r format(nrow(antibiotics) + nrow(antivirals), big.mark = ",")` Antimicrobial Drugs
|
||||
#'
|
||||
#' Two data sets containing all antibiotics/antimycotics and antivirals. Use [as.ab()] or one of the [`ab_*`][ab_property()] functions to retrieve values from the [antibiotics] data set. Three identifiers are included in this data set: an antibiotic ID (`ab`, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (`atc`) as defined by the WHO, and a Compound ID (`cid`) as found in PubChem. Other properties in this data set are derived from one or more of these codes.
|
||||
#' Two data sets containing all antibiotics/antimycotics and antivirals. Use [as.ab()] or one of the [`ab_*`][ab_property()] functions to retrieve values from the [antibiotics] data set. Three identifiers are included in this data set: an antibiotic ID (`ab`, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (`atc`) as defined by the WHO, and a Compound ID (`cid`) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.
|
||||
#' @format
|
||||
#' ## For the [antibiotics] data set: a [data.frame] with `r nrow(antibiotics)` observations and `r ncol(antibiotics)` variables:
|
||||
#' - `ab`\cr Antibiotic ID as used in this package (such as `AMC`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
|
||||
#' - `atc`\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like `J01CR02`
|
||||
#' - `cid`\cr Compound ID as found in PubChem
|
||||
#' - `name`\cr Official name as used by WHONET/EARS-Net or the WHO
|
||||
#' - `group`\cr A short and concise group name, based on WHONET and WHOCC definitions
|
||||
#' - `atc`\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like `J01CR02`
|
||||
#' - `atc_group1`\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like `"Macrolides, lincosamides and streptogramins"`
|
||||
#' - `atc_group2`\cr Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like `"Macrolides"`
|
||||
#' - `abbr`\cr List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)
|
||||
#' - `synonyms`\cr Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID
|
||||
#' - `oral_ddd`\cr Defined Daily Dose (DDD), oral treatment
|
||||
#' - `oral_ddd`\cr Defined Daily Dose (DDD), oral treatment, currently available for `r sum(!is.na(antibiotics$oral_ddd))` drugs
|
||||
#' - `oral_units`\cr Units of `oral_ddd`
|
||||
#' - `iv_ddd`\cr Defined Daily Dose (DDD), parenteral treatment
|
||||
#' - `iv_ddd`\cr Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for `r sum(!is.na(antibiotics$iv_ddd))` drugs
|
||||
#' - `iv_units`\cr Units of `iv_ddd`
|
||||
#' - `loinc`\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use [ab_loinc()] to retrieve them quickly, see [ab_property()].
|
||||
#'
|
||||
#' ## For the [antivirals] data set: a [data.frame] with `r nrow(antivirals)` observations and `r ncol(antivirals)` variables:
|
||||
#' - `atc`\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC
|
||||
#' - `atc`\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC
|
||||
#' - `cid`\cr Compound ID as found in PubChem
|
||||
#' - `name`\cr Official name as used by WHONET/EARS-Net or the WHO
|
||||
#' - `atc_group`\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC
|
||||
@@ -55,18 +55,18 @@
|
||||
#' - `iv_units`\cr Units of `iv_ddd`
|
||||
#' @details Properties that are based on an ATC code are only available when an ATC is available. These properties are: `atc_group1`, `atc_group2`, `oral_ddd`, `oral_units`, `iv_ddd` and `iv_units`.
|
||||
#'
|
||||
#' Synonyms (i.e. trade names) are derived from the Compound ID (`cid`) and consequently only available where a CID is available.
|
||||
#' Synonyms (i.e. trade names) were derived from the Compound ID (`cid`) and consequently only available where a CID is available.
|
||||
#'
|
||||
#' ## Direct download
|
||||
#' These data sets are available as 'flat files' for use even without \R - you can find the files here:
|
||||
#'
|
||||
#' * <https://github.com/msberends/AMR/raw/master/data-raw/antibiotics.txt>
|
||||
#' * <https://github.com/msberends/AMR/raw/master/data-raw/antivirals.txt>
|
||||
#' * <https://github.com/msberends/AMR/raw/main/data-raw/antibiotics.txt>
|
||||
#' * <https://github.com/msberends/AMR/raw/main/data-raw/antivirals.txt>
|
||||
#'
|
||||
#' Files in \R format (with preserved data structure) can be found here:
|
||||
#'
|
||||
#' * <https://github.com/msberends/AMR/raw/master/data/antibiotics.rda>
|
||||
#' * <https://github.com/msberends/AMR/raw/master/data/antivirals.rda>
|
||||
#' * <https://github.com/msberends/AMR/raw/main/data/antibiotics.rda>
|
||||
#' * <https://github.com/msberends/AMR/raw/main/data/antivirals.rda>
|
||||
#' @source World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <https://www.whocc.no/atc_ddd_index/>
|
||||
#'
|
||||
#' WHONET 2019 software: <http://www.whonet.org/software.html>
|
||||
@@ -83,7 +83,7 @@
|
||||
|
||||
#' Data Set with `r format(nrow(microorganisms), big.mark = ",")` Microorganisms
|
||||
#'
|
||||
#' A data set containing the microbial taxonomy, last updated in `r CATALOGUE_OF_LIFE$yearmonth_LPSN`, of six kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using [as.mo()].
|
||||
#' A data set containing the full microbial taxonomy (**last updated: `r CATALOGUE_OF_LIFE$yearmonth_LPSN`**) of `r nr2char(length(unique(microorganisms$kingdom[!microorganisms$kingdom %like% "unknown"])))` kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using [as.mo()].
|
||||
#' @inheritSection catalogue_of_life Catalogue of Life
|
||||
#' @format A [data.frame] with `r format(nrow(microorganisms), big.mark = ",")` observations and `r ncol(microorganisms)` variables:
|
||||
#' - `mo`\cr ID of microorganism as used by this package
|
||||
@@ -105,20 +105,21 @@
|
||||
#'
|
||||
#' - 11 entries of *Streptococcus* (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)
|
||||
#' - 2 entries of *Staphylococcus* (coagulase-negative (CoNS) and coagulase-positive (CoPS))
|
||||
#' - 3 entries of *Trichomonas* (*Trichomonas vaginalis*, and its family and genus)
|
||||
#' - 1 entry of *Candida* (*Candida krusei*), that is not (yet) in the Catalogue of Life
|
||||
#' - 1 entry of *Blastocystis* (*Blastocystis hominis*), although it officially does not exist (Noel *et al.* 2005, PMID 15634993)
|
||||
#' - 3 entries of *Trichomonas* (*T. vaginalis*, and its family and genus)
|
||||
#' - 1 entry of *Candida* (*C. krusei*), that is not (yet) in the Catalogue of Life
|
||||
#' - 1 entry of *Blastocystis* (*B. hominis*), although it officially does not exist (Noel *et al.* 2005, PMID 15634993)
|
||||
#' - 1 entry of *Moraxella* (*M. catarrhalis*), which was formally named *Branhamella catarrhalis* (Catlin, 1970) though this change was never accepted within the field of clinical microbiology
|
||||
#' - 5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)
|
||||
#' - 6 families under the Enterobacterales order, according to Adeolu *et al.* (2016, PMID 27620848), that are not (yet) in the Catalogue of Life
|
||||
#'
|
||||
#' ## Direct download
|
||||
#' This data set is available as 'flat file' for use even without \R - you can find the file here:
|
||||
#'
|
||||
#' * <https://github.com/msberends/AMR/raw/master/data-raw/microorganisms.txt>
|
||||
#' * <https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt>
|
||||
#'
|
||||
#' The file in \R format (with preserved data structure) can be found here:
|
||||
#'
|
||||
#' * <https://github.com/msberends/AMR/raw/master/data/microorganisms.rda>
|
||||
#' * <https://github.com/msberends/AMR/raw/main/data/microorganisms.rda>
|
||||
#' @section About the Records from LPSN (see *Source*):
|
||||
#' The List of Prokaryotic names with Standing in Nomenclature (LPSN) provides comprehensive information on the nomenclature of prokaryotes. LPSN is a free to use service founded by Jean P. Euzeby in 1997 and later on maintained by Aidan C. Parte.
|
||||
#'
|
||||
@@ -251,7 +252,7 @@
|
||||
#' - `breakpoint_S`\cr Lowest MIC value or highest number of millimetres that leads to "S"
|
||||
#' - `breakpoint_R`\cr Highest MIC value or lowest number of millimetres that leads to "R"
|
||||
#' - `uti`\cr A [logical] value (`TRUE`/`FALSE`) to indicate whether the rule applies to a urinary tract infection (UTI)
|
||||
#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt>. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically.
|
||||
#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt>. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically.
|
||||
#' @inheritSection AMR Reference Data Publicly Available
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
#' @seealso [intrinsic_resistant]
|
||||
@@ -263,7 +264,7 @@
|
||||
#' @format A [data.frame] with `r format(nrow(intrinsic_resistant), big.mark = ",")` observations and `r ncol(intrinsic_resistant)` variables:
|
||||
#' - `microorganism`\cr Name of the microorganism
|
||||
#' - `antibiotic`\cr Name of the antibiotic drug
|
||||
#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt>. This file **allows for machine reading EUCAST guidelines about intrinsic resistance**, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.
|
||||
#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/main/data-raw/intrinsic_resistant.txt>. This file **allows for machine reading EUCAST guidelines about intrinsic resistance**, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.
|
||||
#'
|
||||
#' This data set is based on `r format_eucast_version_nr(3.2)`.
|
||||
#' @inheritSection AMR Reference Data Publicly Available
|
||||
|
||||
+2
-470
@@ -26,477 +26,9 @@
|
||||
#' Deprecated Functions
|
||||
#'
|
||||
#' These functions are so-called '[Deprecated]'. **They will be removed in a future release.** Using the functions will give a warning with the name of the function it has been replaced by (if there is one).
|
||||
#' @details All antibiotic class selectors (such as [carbapenems()], [aminoglycosides()]) can now be used for filtering as well, making all their accompanying `filter_*()` functions redundant (such as [filter_carbapenems()], [filter_aminoglycosides()]).
|
||||
#' @inheritSection lifecycle Retired Lifecycle
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
#' @keywords internal
|
||||
#' @name AMR-deprecated
|
||||
#' @export
|
||||
p_symbol <- function(p, emptychar = " ") {
|
||||
.Deprecated(package = "AMR", new = "cleaner::p_symbol")
|
||||
|
||||
p <- as.double(p)
|
||||
s <- rep(NA_character_, length(p))
|
||||
|
||||
s[p <= 1] <- emptychar
|
||||
s[p <= 0.100] <- "."
|
||||
s[p <= 0.050] <- "*"
|
||||
s[p <= 0.010] <- "**"
|
||||
s[p <= 0.001] <- "***"
|
||||
|
||||
s
|
||||
}
|
||||
|
||||
#' @name AMR-deprecated
|
||||
#' @export
|
||||
filter_first_weighted_isolate <- function(x = NULL,
|
||||
col_date = NULL,
|
||||
col_patient_id = NULL,
|
||||
col_mo = NULL,
|
||||
...) {
|
||||
|
||||
.Deprecated(old = "filter_first_weighted_isolate()",
|
||||
new = "filter_first_isolate()",
|
||||
package = "AMR")
|
||||
|
||||
if (is_null_or_grouped_tbl(x)) {
|
||||
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
|
||||
# is also fix for using a grouped df as input (a dot as first argument)
|
||||
x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
|
||||
}
|
||||
meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
|
||||
meet_criteria(col_date, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
|
||||
meet_criteria(col_patient_id, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
|
||||
meet_criteria(col_mo, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
|
||||
|
||||
filter_first_isolate(x = x, col_date = col_date, col_patient_id = col_patient_id, col_mo = col_mo, ...)
|
||||
}
|
||||
|
||||
#' @name AMR-deprecated
|
||||
#' @export
|
||||
key_antibiotics <- function(x = NULL,
|
||||
col_mo = NULL,
|
||||
universal_1 = guess_ab_col(x, "amoxicillin"),
|
||||
universal_2 = guess_ab_col(x, "amoxicillin/clavulanic acid"),
|
||||
universal_3 = guess_ab_col(x, "cefuroxime"),
|
||||
universal_4 = guess_ab_col(x, "piperacillin/tazobactam"),
|
||||
universal_5 = guess_ab_col(x, "ciprofloxacin"),
|
||||
universal_6 = guess_ab_col(x, "trimethoprim/sulfamethoxazole"),
|
||||
GramPos_1 = guess_ab_col(x, "vancomycin"),
|
||||
GramPos_2 = guess_ab_col(x, "teicoplanin"),
|
||||
GramPos_3 = guess_ab_col(x, "tetracycline"),
|
||||
GramPos_4 = guess_ab_col(x, "erythromycin"),
|
||||
GramPos_5 = guess_ab_col(x, "oxacillin"),
|
||||
GramPos_6 = guess_ab_col(x, "rifampin"),
|
||||
GramNeg_1 = guess_ab_col(x, "gentamicin"),
|
||||
GramNeg_2 = guess_ab_col(x, "tobramycin"),
|
||||
GramNeg_3 = guess_ab_col(x, "colistin"),
|
||||
GramNeg_4 = guess_ab_col(x, "cefotaxime"),
|
||||
GramNeg_5 = guess_ab_col(x, "ceftazidime"),
|
||||
GramNeg_6 = guess_ab_col(x, "meropenem"),
|
||||
warnings = TRUE,
|
||||
...) {
|
||||
|
||||
.Deprecated(old = "key_antibiotics()",
|
||||
new = "key_antimicrobials()",
|
||||
package = "AMR")
|
||||
|
||||
if (is_null_or_grouped_tbl(x)) {
|
||||
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
|
||||
# is also fix for using a grouped df as input (a dot as first argument)
|
||||
x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
|
||||
}
|
||||
|
||||
key_antimicrobials(x = x,
|
||||
col_mo = col_mo,
|
||||
universal = c(universal_1, universal_2, universal_3, universal_4, universal_5, universal_6),
|
||||
gram_negative = c(GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6),
|
||||
gram_positive = c(GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6),
|
||||
antifungal = NULL,
|
||||
only_rsi_columns = FALSE,
|
||||
...)
|
||||
}
|
||||
|
||||
#' @name AMR-deprecated
|
||||
#' @export
|
||||
key_antibiotics_equal <- function(y,
|
||||
z,
|
||||
type = "keyantimicrobials",
|
||||
ignore_I = TRUE,
|
||||
points_threshold = 2,
|
||||
info = FALSE,
|
||||
na.rm = TRUE,
|
||||
...) {
|
||||
|
||||
.Deprecated(old = "key_antibiotics_equal()",
|
||||
new = "antimicrobials_equal()",
|
||||
package = "AMR")
|
||||
|
||||
antimicrobials_equal(y = y,
|
||||
z = z,
|
||||
type = type,
|
||||
ignore_I = ignore_I,
|
||||
points_threshold = points_threshold,
|
||||
info = info)
|
||||
}
|
||||
|
||||
|
||||
#' @name AMR-deprecated
|
||||
#' @export
|
||||
filter_ab_class <- function(x,
|
||||
ab_class,
|
||||
result = NULL,
|
||||
scope = "any",
|
||||
only_rsi_columns = FALSE,
|
||||
...) {
|
||||
|
||||
.call_depth <- list(...)$`.call_depth`
|
||||
if (is.null(.call_depth)) {
|
||||
.call_depth <- 0
|
||||
}
|
||||
.x_name <- list(...)$`.x_name`
|
||||
if (is.null(.x_name)) {
|
||||
.x_name <- deparse(substitute(x))
|
||||
}
|
||||
.fn <- list(...)$`.fn`
|
||||
if (is.null(.fn)) {
|
||||
.fn <- "filter_ab_class"
|
||||
}
|
||||
.fn_old <- .fn
|
||||
# new way: using the ab selectors
|
||||
.fn <- gsub("filter_", "", .fn, fixed = TRUE)
|
||||
.fn <- gsub("^([1-5][a-z]+)_cephalosporins", "cephalosporins_\\1", .fn)
|
||||
|
||||
if (missing(x) || is_null_or_grouped_tbl(x)) {
|
||||
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
|
||||
# is also fix for using a grouped df as input (a dot as first argument)
|
||||
x <- get_current_data(arg_name = "x", call = -2 - .call_depth)
|
||||
.x_name <- "your_data"
|
||||
}
|
||||
meet_criteria(x, allow_class = "data.frame", .call_depth = .call_depth)
|
||||
meet_criteria(ab_class, allow_class = "character", has_length = 1, .call_depth = .call_depth)
|
||||
if (!is.null(result)) {
|
||||
# make result = "SI" works too:
|
||||
result <- toupper(unlist(strsplit(result, "")))
|
||||
}
|
||||
meet_criteria(result, allow_class = "character", has_length = c(1, 2, 3), is_in = c("S", "I", "R"), allow_NULL = TRUE, .call_depth = .call_depth)
|
||||
meet_criteria(scope, allow_class = "character", has_length = 1, is_in = c("all", "any"), .call_depth = .call_depth)
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1, .call_depth = .call_depth)
|
||||
|
||||
if (is.null(result)) {
|
||||
result <- c("S", "I", "R")
|
||||
}
|
||||
|
||||
# get e.g. carbapenems() from filter_carbapenems()
|
||||
fn <- get(.fn, envir = asNamespace("AMR"))
|
||||
if (scope == "any") {
|
||||
scope_fn <- any
|
||||
} else {
|
||||
scope_fn <- all
|
||||
}
|
||||
|
||||
# be nice here, be VERY extensive about how the AB selectors have taken over this function
|
||||
deprecated_fn <- paste0(.fn, "(", ifelse(.fn == "ab_class", paste0("\"", ab_class, "\""), ""), ")",
|
||||
ifelse(length(result) > 1,
|
||||
paste0(", c(", paste0("\"", result, "\"", collapse = ", "), ")"),
|
||||
ifelse(is.null(result),
|
||||
"",
|
||||
paste0(" == \"", result, "\""))))
|
||||
if (.x_name == ".") {
|
||||
.x_name <- "your_data"
|
||||
}
|
||||
warning_(paste0("`", .fn_old, "()` is deprecated. Use the antibiotic selector `", .fn, "()` instead.\n",
|
||||
"In dplyr:\n",
|
||||
" - ", .x_name, " %>% filter(", scope, "(", deprecated_fn, "))\n",
|
||||
ifelse(length(result) > 1,
|
||||
paste0(" - ", .x_name, " %>% filter(", scope, "(",
|
||||
.fn, "(", ifelse(.fn == "ab_class", paste0("\"", ab_class, "\""), ""), ") == \"R\"))\n"),
|
||||
""),
|
||||
"In base R:\n",
|
||||
" - ", .x_name, "[", scope, "(", deprecated_fn, "), ]\n",
|
||||
ifelse(length(result) > 1,
|
||||
paste0(" - ", .x_name, "[", scope, "(",
|
||||
.fn, "(", ifelse(.fn == "ab_class", paste0("\"", ab_class, "\""), ""), ") == \"R\"), ]\n"),
|
||||
""),
|
||||
" - subset(", .x_name, ", ", scope, "(", deprecated_fn, "))",
|
||||
ifelse(length(result) > 1,
|
||||
paste0("\n - subset(", .x_name, ", ", scope, "(",
|
||||
.fn, "(", ifelse(.fn == "ab_class", paste0("\"", ab_class, "\""), ""), ") == \"R\"))"),
|
||||
"")),
|
||||
call = FALSE)
|
||||
|
||||
if (.fn == "ab_class") {
|
||||
subset(x, scope_fn(fn(ab_class = ab_class), result))
|
||||
} else {
|
||||
subset(x, scope_fn(fn(), result))
|
||||
}
|
||||
}
|
||||
|
||||
#' @name AMR-deprecated
|
||||
#' @export
|
||||
filter_aminoglycosides <- function(x,
|
||||
result = NULL,
|
||||
scope = "any",
|
||||
only_rsi_columns = FALSE,
|
||||
...) {
|
||||
filter_ab_class(x = x,
|
||||
ab_class = "aminoglycoside",
|
||||
result = result,
|
||||
scope = scope,
|
||||
only_rsi_columns = only_rsi_columns,
|
||||
.call_depth = 1,
|
||||
.fn = "filter_aminoglycosides",
|
||||
.x_name = deparse(substitute(x)),
|
||||
...)
|
||||
}
|
||||
|
||||
#' @name AMR-deprecated
|
||||
#' @export
|
||||
filter_betalactams <- function(x,
|
||||
result = NULL,
|
||||
scope = "any",
|
||||
only_rsi_columns = FALSE,
|
||||
...) {
|
||||
filter_ab_class(x = x,
|
||||
ab_class = "carbapenem|cephalosporin|penicillin",
|
||||
result = result,
|
||||
scope = scope,
|
||||
only_rsi_columns = only_rsi_columns,
|
||||
.call_depth = 1,
|
||||
.fn = "filter_betalactams",
|
||||
.x_name = deparse(substitute(x)),
|
||||
...)
|
||||
}
|
||||
#' @name AMR-deprecated
|
||||
#' @export
|
||||
filter_carbapenems <- function(x,
|
||||
result = NULL,
|
||||
scope = "any",
|
||||
only_rsi_columns = FALSE,
|
||||
...) {
|
||||
filter_ab_class(x = x,
|
||||
ab_class = "carbapenem",
|
||||
result = result,
|
||||
scope = scope,
|
||||
only_rsi_columns = only_rsi_columns,
|
||||
.call_depth = 1,
|
||||
.fn = "filter_carbapenems",
|
||||
.x_name = deparse(substitute(x)),
|
||||
...)
|
||||
}
|
||||
|
||||
#' @name AMR-deprecated
|
||||
#' @export
|
||||
filter_cephalosporins <- function(x,
|
||||
result = NULL,
|
||||
scope = "any",
|
||||
only_rsi_columns = FALSE,
|
||||
...) {
|
||||
filter_ab_class(x = x,
|
||||
ab_class = "cephalosporin",
|
||||
result = result,
|
||||
scope = scope,
|
||||
only_rsi_columns = only_rsi_columns,
|
||||
.call_depth = 1,
|
||||
.fn = "filter_cephalosporins",
|
||||
.x_name = deparse(substitute(x)),
|
||||
...)
|
||||
}
|
||||
|
||||
#' @name AMR-deprecated
|
||||
#' @export
|
||||
filter_1st_cephalosporins <- function(x,
|
||||
result = NULL,
|
||||
scope = "any",
|
||||
only_rsi_columns = FALSE,
|
||||
...) {
|
||||
filter_ab_class(x = x,
|
||||
ab_class = "cephalosporins (1st gen.)",
|
||||
result = result,
|
||||
scope = scope,
|
||||
only_rsi_columns = only_rsi_columns,
|
||||
.call_depth = 1,
|
||||
.fn = "filter_1st_cephalosporins",
|
||||
.x_name = deparse(substitute(x)),
|
||||
...)
|
||||
}
|
||||
|
||||
#' @name AMR-deprecated
|
||||
#' @export
|
||||
filter_2nd_cephalosporins <- function(x,
|
||||
result = NULL,
|
||||
scope = "any",
|
||||
only_rsi_columns = FALSE,
|
||||
...) {
|
||||
filter_ab_class(x = x,
|
||||
ab_class = "cephalosporins (2nd gen.)",
|
||||
result = result,
|
||||
scope = scope,
|
||||
only_rsi_columns = only_rsi_columns,
|
||||
.call_depth = 1,
|
||||
.fn = "filter_2nd_cephalosporins",
|
||||
.x_name = deparse(substitute(x)),
|
||||
...)
|
||||
}
|
||||
|
||||
#' @name AMR-deprecated
|
||||
#' @export
|
||||
filter_3rd_cephalosporins <- function(x,
|
||||
result = NULL,
|
||||
scope = "any",
|
||||
only_rsi_columns = FALSE,
|
||||
...) {
|
||||
filter_ab_class(x = x,
|
||||
ab_class = "cephalosporins (3rd gen.)",
|
||||
result = result,
|
||||
scope = scope,
|
||||
only_rsi_columns = only_rsi_columns,
|
||||
.call_depth = 1,
|
||||
.fn = "filter_3rd_cephalosporins",
|
||||
.x_name = deparse(substitute(x)),
|
||||
...)
|
||||
}
|
||||
|
||||
#' @name AMR-deprecated
|
||||
#' @export
|
||||
filter_4th_cephalosporins <- function(x,
|
||||
result = NULL,
|
||||
scope = "any",
|
||||
only_rsi_columns = FALSE,
|
||||
...) {
|
||||
filter_ab_class(x = x,
|
||||
ab_class = "cephalosporins (4th gen.)",
|
||||
result = result,
|
||||
scope = scope,
|
||||
only_rsi_columns = only_rsi_columns,
|
||||
.call_depth = 1,
|
||||
.fn = "filter_4th_cephalosporins",
|
||||
.x_name = deparse(substitute(x)),
|
||||
...)
|
||||
}
|
||||
|
||||
#' @name AMR-deprecated
|
||||
#' @export
|
||||
filter_5th_cephalosporins <- function(x,
|
||||
result = NULL,
|
||||
scope = "any",
|
||||
only_rsi_columns = FALSE,
|
||||
...) {
|
||||
filter_ab_class(x = x,
|
||||
ab_class = "cephalosporins (5th gen.)",
|
||||
result = result,
|
||||
scope = scope,
|
||||
only_rsi_columns = only_rsi_columns,
|
||||
.call_depth = 1,
|
||||
.fn = "filter_5th_cephalosporins",
|
||||
.x_name = deparse(substitute(x)),
|
||||
...)
|
||||
}
|
||||
|
||||
#' @name AMR-deprecated
|
||||
#' @export
|
||||
filter_fluoroquinolones <- function(x,
|
||||
result = NULL,
|
||||
scope = "any",
|
||||
only_rsi_columns = FALSE,
|
||||
...) {
|
||||
filter_ab_class(x = x,
|
||||
ab_class = "fluoroquinolone",
|
||||
result = result,
|
||||
scope = scope,
|
||||
only_rsi_columns = only_rsi_columns,
|
||||
.call_depth = 1,
|
||||
.fn = "filter_fluoroquinolones",
|
||||
.x_name = deparse(substitute(x)),
|
||||
...)
|
||||
}
|
||||
|
||||
#' @name AMR-deprecated
|
||||
#' @export
|
||||
filter_glycopeptides <- function(x,
|
||||
result = NULL,
|
||||
scope = "any",
|
||||
only_rsi_columns = FALSE,
|
||||
...) {
|
||||
filter_ab_class(x = x,
|
||||
ab_class = "glycopeptide",
|
||||
result = result,
|
||||
scope = scope,
|
||||
only_rsi_columns = only_rsi_columns,
|
||||
.call_depth = 1,
|
||||
.fn = "filter_glycopeptides",
|
||||
.x_name = deparse(substitute(x)),
|
||||
...)
|
||||
}
|
||||
|
||||
#' @name AMR-deprecated
|
||||
#' @export
|
||||
filter_macrolides <- function(x,
|
||||
result = NULL,
|
||||
scope = "any",
|
||||
only_rsi_columns = FALSE,
|
||||
...) {
|
||||
filter_ab_class(x = x,
|
||||
ab_class = "macrolide",
|
||||
result = result,
|
||||
scope = scope,
|
||||
only_rsi_columns = only_rsi_columns,
|
||||
.call_depth = 1,
|
||||
.fn = "filter_macrolides",
|
||||
.x_name = deparse(substitute(x)),
|
||||
...)
|
||||
}
|
||||
|
||||
#' @name AMR-deprecated
|
||||
#' @export
|
||||
filter_oxazolidinones <- function(x,
|
||||
result = NULL,
|
||||
scope = "any",
|
||||
only_rsi_columns = FALSE,
|
||||
...) {
|
||||
filter_ab_class(x = x,
|
||||
ab_class = "oxazolidinone",
|
||||
result = result,
|
||||
scope = scope,
|
||||
only_rsi_columns = only_rsi_columns,
|
||||
.call_depth = 1,
|
||||
.fn = "filter_oxazolidinones",
|
||||
.x_name = deparse(substitute(x)),
|
||||
...)
|
||||
}
|
||||
|
||||
#' @name AMR-deprecated
|
||||
#' @export
|
||||
filter_penicillins <- function(x,
|
||||
result = NULL,
|
||||
scope = "any",
|
||||
only_rsi_columns = FALSE,
|
||||
...) {
|
||||
filter_ab_class(x = x,
|
||||
ab_class = "penicillin",
|
||||
result = result,
|
||||
scope = scope,
|
||||
only_rsi_columns = only_rsi_columns,
|
||||
.call_depth = 1,
|
||||
.fn = "filter_penicillins",
|
||||
.x_name = deparse(substitute(x)),
|
||||
...)
|
||||
}
|
||||
|
||||
#' @name AMR-deprecated
|
||||
#' @export
|
||||
filter_tetracyclines <- function(x,
|
||||
result = NULL,
|
||||
scope = "any",
|
||||
only_rsi_columns = FALSE,
|
||||
...) {
|
||||
filter_ab_class(x = x,
|
||||
ab_class = "tetracycline",
|
||||
result = result,
|
||||
scope = scope,
|
||||
only_rsi_columns = only_rsi_columns,
|
||||
.call_depth = 1,
|
||||
.fn = "filter_tetracyclines",
|
||||
.x_name = deparse(substitute(x)),
|
||||
...)
|
||||
}
|
||||
# @export
|
||||
NULL
|
||||
|
||||
@@ -119,6 +119,12 @@ all_valid_disks <- function(x) {
|
||||
!any(is.na(x_disk)) && !all(is.na(x))
|
||||
}
|
||||
|
||||
#' @rdname as.disk
|
||||
#' @details `NA_disk_` is a missing value of the new `<disk>` class.
|
||||
#' @export
|
||||
NA_disk_ <- set_clean_class(as.integer(NA_real_),
|
||||
new_class = c("disk", "integer"))
|
||||
|
||||
#' @rdname as.disk
|
||||
#' @export
|
||||
is.disk <- function(x) {
|
||||
@@ -195,6 +201,15 @@ unique.disk <- function(x, incomparables = FALSE, ...) {
|
||||
y
|
||||
}
|
||||
|
||||
#' @method rep disk
|
||||
#' @export
|
||||
#' @noRd
|
||||
rep.disk <- function(x, ...) {
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(x)
|
||||
y
|
||||
}
|
||||
|
||||
# will be exported using s3_register() in R/zzz.R
|
||||
get_skimmers.disk <- function(column) {
|
||||
skimr::sfl(
|
||||
|
||||
+15
-18
@@ -27,7 +27,7 @@
|
||||
#'
|
||||
#' These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument `episode_days`. This can be used to determine clinical episodes for any epidemiological analysis. The [get_episode()] function returns the index number of the episode per group, while the [is_new_episode()] function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param x vector of dates (class `Date` or `POSIXt`)
|
||||
#' @param x vector of dates (class `Date` or `POSIXt`), will be sorted internally to determine episodes
|
||||
#' @param episode_days required episode length in days, can also be less than a day or `Inf`, see *Details*
|
||||
#' @param ... ignored, only in place to allow future extensions
|
||||
#' @details
|
||||
@@ -105,11 +105,11 @@
|
||||
#' }
|
||||
#' }
|
||||
get_episode <- function(x, episode_days, ...) {
|
||||
meet_criteria(x, allow_class = c("Date", "POSIXt"))
|
||||
meet_criteria(x, allow_class = c("Date", "POSIXt"), allow_NA = TRUE)
|
||||
meet_criteria(episode_days, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = FALSE)
|
||||
|
||||
exec_episode(type = "sequential",
|
||||
x = x,
|
||||
exec_episode(x = x,
|
||||
type = "sequential",
|
||||
episode_days = episode_days,
|
||||
... = ...)
|
||||
}
|
||||
@@ -117,27 +117,27 @@ get_episode <- function(x, episode_days, ...) {
|
||||
#' @rdname get_episode
|
||||
#' @export
|
||||
is_new_episode <- function(x, episode_days, ...) {
|
||||
meet_criteria(x, allow_class = c("Date", "POSIXt"))
|
||||
meet_criteria(x, allow_class = c("Date", "POSIXt"), allow_NA = TRUE)
|
||||
meet_criteria(episode_days, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = FALSE)
|
||||
|
||||
exec_episode(type = "logical",
|
||||
x = x,
|
||||
exec_episode(x = x,
|
||||
type = "logical",
|
||||
episode_days = episode_days,
|
||||
... = ...)
|
||||
}
|
||||
|
||||
exec_episode <- function(type, x, episode_days, ...) {
|
||||
exec_episode <- function(x, type, episode_days, ...) {
|
||||
x <- as.double(as.POSIXct(x)) # as.POSIXct() required for Date classes
|
||||
# since x is now in seconds, get seconds from episode_days as well
|
||||
episode_seconds <- episode_days * 60 * 60 * 24
|
||||
|
||||
if (length(x) == 1) {
|
||||
if (length(x) == 1) { # this will also match 1 NA, which is fine
|
||||
if (type == "logical") {
|
||||
return(TRUE)
|
||||
} else if (type == "sequential") {
|
||||
return(1)
|
||||
}
|
||||
} else if (length(x) == 2) {
|
||||
} else if (length(x) == 2 && !all(is.na(x))) {
|
||||
if (max(x) - min(x) >= episode_seconds) {
|
||||
if (type == "logical") {
|
||||
return(c(TRUE, TRUE))
|
||||
@@ -155,7 +155,7 @@ exec_episode <- function(type, x, episode_days, ...) {
|
||||
|
||||
# I asked on StackOverflow:
|
||||
# https://stackoverflow.com/questions/42122245/filter-one-row-every-year
|
||||
exec <- function(x, episode_seconds) {
|
||||
run_episodes <- function(x, episode_seconds) {
|
||||
indices <- integer()
|
||||
start <- x[1]
|
||||
ind <- 1
|
||||
@@ -181,11 +181,8 @@ exec_episode <- function(type, x, episode_days, ...) {
|
||||
}
|
||||
}
|
||||
|
||||
df <- data.frame(x = x,
|
||||
y = seq_len(length(x))) %pm>%
|
||||
pm_arrange(x)
|
||||
df$new <- exec(df$x, episode_seconds)
|
||||
df %pm>%
|
||||
pm_arrange(y) %pm>%
|
||||
pm_pull(new)
|
||||
ord <- order(x)
|
||||
out <- run_episodes(x[ord], episode_seconds)[order(ord)]
|
||||
out[is.na(x) & ord != 1] <- NA # every NA but the first must remain NA
|
||||
out
|
||||
}
|
||||
|
||||
+13
-27
@@ -23,6 +23,10 @@
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
# ====================================================== #
|
||||
# || Change the EUCAST version numbers in R/globals.R || #
|
||||
# ====================================================== #
|
||||
|
||||
format_eucast_version_nr <- function(version, markdown = TRUE) {
|
||||
# for documentation - adds title, version number, year and url in markdown language
|
||||
lst <- c(EUCAST_VERSION_BREAKPOINTS, EUCAST_VERSION_EXPERT_RULES)
|
||||
@@ -55,7 +59,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
|
||||
#' @param verbose a [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.
|
||||
#' @param version_breakpoints the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either `r vector_or(names(EUCAST_VERSION_BREAKPOINTS), reverse = TRUE)`.
|
||||
#' @param version_expertrules the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either `r vector_or(names(EUCAST_VERSION_EXPERT_RULES), reverse = TRUE)`.
|
||||
#' @param ampc_cephalosporin_resistance a [character] value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to `NA`. Currently only works when `version_expertrules` is `3.2`; '*EUCAST Expert Rules v3.2 on Enterobacterales*' states that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three agents. A value of `NA` (the default) for this argument will remove results for these three agents, while e.g. a value of `"R"` will make the results for these agents resistant. Use `NULL` or `FALSE` to not alter results for these three agents of AmpC de-repressed cephalosporin-resistant mutants. Using `TRUE` is equal to using `"R"`. \cr For *EUCAST Expert Rules* v3.2, this rule applies to: `r vector_and(gsub("[^a-zA-Z ]+", "", unlist(strsplit(eucast_rules_file[which(eucast_rules_file$reference.version == 3.2 & eucast_rules_file$reference.rule %like% "ampc"), "this_value"][1], "|", fixed = TRUE))), quotes = "*")`.
|
||||
#' @param ampc_cephalosporin_resistance a [character] value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to `NA`. Currently only works when `version_expertrules` is `3.2`; '*EUCAST Expert Rules v3.2 on Enterobacterales*' states that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three agents. A value of `NA` (the default) for this argument will remove results for these three agents, while e.g. a value of `"R"` will make the results for these agents resistant. Use `NULL` or `FALSE` to not alter results for these three agents of AmpC de-repressed cephalosporin-resistant mutants. Using `TRUE` is equal to using `"R"`. \cr For *EUCAST Expert Rules* v3.2, this rule applies to: `r vector_and(gsub("[^a-zA-Z ]+", "", unlist(strsplit(EUCAST_RULES_DF[which(EUCAST_RULES_DF$reference.version == 3.2 & EUCAST_RULES_DF$reference.rule %like% "ampc"), "this_value"][1], "|", fixed = TRUE))), quotes = "*")`.
|
||||
#' @param ... column name of an antibiotic, see section *Antibiotics* below
|
||||
#' @param ab any (vector of) text that can be coerced to a valid antibiotic code with [as.ab()]
|
||||
#' @param administration route of administration, either `r vector_or(dosage$administration)`
|
||||
@@ -66,7 +70,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
|
||||
#' **Note:** This function does not translate MIC values to RSI values. Use [as.rsi()] for that. \cr
|
||||
#' **Note:** When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. \cr
|
||||
#'
|
||||
#' The file containing all EUCAST rules is located here: <https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv>. **Note:** Old taxonomic names are replaced with the current taxonomy where applicable. For example, *Ochrobactrum anthropi* was renamed to *Brucella anthropi* in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The file used as input for this `AMR` package contains the taxonomy updated until [`r CATALOGUE_OF_LIFE$yearmonth_LPSN`][catalogue_of_life()].
|
||||
#' The file containing all EUCAST rules is located here: <https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv>. **Note:** Old taxonomic names are replaced with the current taxonomy where applicable. For example, *Ochrobactrum anthropi* was renamed to *Brucella anthropi* in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The file used as input for this `AMR` package contains the taxonomy updated until [`r CATALOGUE_OF_LIFE$yearmonth_LPSN`][catalogue_of_life()].
|
||||
#'
|
||||
#' ## Custom Rules
|
||||
#'
|
||||
@@ -105,6 +109,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
|
||||
#' Leclercq et al. **EUCAST expert rules in antimicrobial susceptibility testing.** *Clin Microbiol Infect.* 2013;19(2):141-60; \doi{https://doi.org/10.1111/j.1469-0691.2011.03703.x}
|
||||
#' - EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf)
|
||||
#' - EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf)
|
||||
#' - EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.3, 2021. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf)
|
||||
#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx)
|
||||
#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx)
|
||||
#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 11.0, 2021. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_11.0_Breakpoint_Tables.xlsx)
|
||||
@@ -159,7 +164,7 @@ eucast_rules <- function(x,
|
||||
rules = getOption("AMR_eucastrules", default = c("breakpoints", "expert")),
|
||||
verbose = FALSE,
|
||||
version_breakpoints = 11.0,
|
||||
version_expertrules = 3.2,
|
||||
version_expertrules = 3.3,
|
||||
ampc_cephalosporin_resistance = NA,
|
||||
only_rsi_columns = FALSE,
|
||||
custom_rules = NULL,
|
||||
@@ -316,25 +321,6 @@ eucast_rules <- function(x,
|
||||
}
|
||||
|
||||
# Some helper functions ---------------------------------------------------
|
||||
get_antibiotic_columns <- function(x, cols_ab) {
|
||||
x <- trimws(unique(toupper(unlist(strsplit(x, ",")))))
|
||||
x_new <- character()
|
||||
for (val in x) {
|
||||
if (val %in% ls(envir = asNamespace("AMR"))) {
|
||||
# antibiotic group names, as defined in data-raw/_internals.R, such as `CARBAPENEMS`
|
||||
val <- eval(parse(text = val), envir = asNamespace("AMR"))
|
||||
} else if (val %in% AB_lookup$ab) {
|
||||
# separate drugs, such as `AMX`
|
||||
val <- as.ab(val)
|
||||
} else {
|
||||
stop_("unknown antimicrobial agent (group) in EUCAST rules file: ", val, call = FALSE)
|
||||
}
|
||||
x_new <- c(x_new, val)
|
||||
}
|
||||
x_new <- unique(x_new)
|
||||
out <- cols_ab[match(x_new, names(cols_ab))]
|
||||
out[!is.na(out)]
|
||||
}
|
||||
get_antibiotic_names <- function(x) {
|
||||
x <- x %pm>%
|
||||
strsplit(",") %pm>%
|
||||
@@ -561,11 +547,11 @@ eucast_rules <- function(x,
|
||||
# Official EUCAST rules ---------------------------------------------------
|
||||
eucast_notification_shown <- FALSE
|
||||
if (!is.null(list(...)$eucast_rules_df)) {
|
||||
# this allows: eucast_rules(x, eucast_rules_df = AMR:::eucast_rules_file %>% filter(is.na(have_these_values)))
|
||||
# this allows: eucast_rules(x, eucast_rules_df = AMR:::EUCAST_RULES_DF %>% filter(is.na(have_these_values)))
|
||||
eucast_rules_df <- list(...)$eucast_rules_df
|
||||
} else {
|
||||
# otherwise internal data file, created in data-raw/_internals.R
|
||||
eucast_rules_df <- eucast_rules_file
|
||||
eucast_rules_df <- EUCAST_RULES_DF
|
||||
}
|
||||
|
||||
# filter on user-set guideline versions ----
|
||||
@@ -580,6 +566,7 @@ eucast_rules <- function(x,
|
||||
(reference.rule_group %like% "expert" & reference.version == version_expertrules))
|
||||
}
|
||||
# filter out AmpC de-repressed cephalosporin-resistant mutants ----
|
||||
# no need to filter on version number here - the rules contain these version number, so are inherently filtered
|
||||
# cefotaxime, ceftriaxone, ceftazidime
|
||||
if (is.null(ampc_cephalosporin_resistance) || isFALSE(ampc_cephalosporin_resistance)) {
|
||||
eucast_rules_df <- subset(eucast_rules_df,
|
||||
@@ -720,7 +707,7 @@ eucast_rules <- function(x,
|
||||
rows <- tryCatch(which(x[, if_mo_property, drop = TRUE] %like% mo_value),
|
||||
error = function(e) integer(0))
|
||||
} else {
|
||||
source_antibiotics <- get_antibiotic_columns(source_antibiotics, cols_ab)
|
||||
source_antibiotics <- get_ab_from_namespace(source_antibiotics, cols_ab)
|
||||
if (length(source_value) == 1 & length(source_antibiotics) > 1) {
|
||||
source_value <- rep(source_value, length(source_antibiotics))
|
||||
}
|
||||
@@ -748,7 +735,7 @@ eucast_rules <- function(x,
|
||||
}
|
||||
}
|
||||
|
||||
cols <- get_antibiotic_columns(target_antibiotics, cols_ab)
|
||||
cols <- get_ab_from_namespace(target_antibiotics, cols_ab)
|
||||
|
||||
# Apply rule on data ------------------------------------------------------
|
||||
# this will return the unique number of changes
|
||||
@@ -1072,7 +1059,6 @@ eucast_dosage <- function(ab, administration = "iv", version_breakpoints = 11.0)
|
||||
message_("Dosages for antimicrobial drugs, as meant for ",
|
||||
format_eucast_version_nr(version_breakpoints, markdown = FALSE), ". ",
|
||||
font_red("This note will be shown once per session."))
|
||||
remember_thrown_message(paste0("eucast_dosage_v", gsub("[^0-9]", "", version_breakpoints)), entire_session = TRUE)
|
||||
}
|
||||
|
||||
ab <- as.ab(ab)
|
||||
|
||||
+47
-51
@@ -23,9 +23,9 @@
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Determine First (Weighted) Isolates
|
||||
#' Determine First Isolates
|
||||
#'
|
||||
#' Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler *et al.* in 2007 (\doi{10.1086/511864}). To determine patient episodes not necessarily based on microorganisms, use [is_new_episode()] that also supports grouping with the `dplyr` package.
|
||||
#' Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler *et al.* in 2007 (\doi{10.1086/511864}). To determine patient episodes not necessarily based on microorganisms, use [is_new_episode()] that also supports grouping with the `dplyr` package.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param x a [data.frame] containing isolates. Can be left blank for automatic determination, see *Examples*.
|
||||
#' @param col_date column name of the result date (or date that is was received on the lab), defaults to the first column with a date class
|
||||
@@ -34,7 +34,7 @@
|
||||
#' @param col_testcode column name of the test codes. Use `col_testcode = NULL` to **not** exclude certain test codes (such as test codes for screening). In that case `testcodes_exclude` will be ignored.
|
||||
#' @param col_specimen column name of the specimen type or group
|
||||
#' @param col_icu column name of the logicals (`TRUE`/`FALSE`) whether a ward or department is an Intensive Care Unit (ICU)
|
||||
#' @param col_keyantimicrobials (only useful when `method = "phenotype-based"`) column name of the key antimicrobials to determine first (weighted) isolates, see [key_antimicrobials()]. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' or 'antimicrobials' (case insensitive). Use `col_keyantimicrobials = FALSE` to prevent this. Can also be the output of [key_antimicrobials()].
|
||||
#' @param col_keyantimicrobials (only useful when `method = "phenotype-based"`) column name of the key antimicrobials to determine first isolates, see [key_antimicrobials()]. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' or 'antimicrobials' (case insensitive). Use `col_keyantimicrobials = FALSE` to prevent this. Can also be the output of [key_antimicrobials()].
|
||||
#' @param episode_days episode in days after which a genus/species combination will be determined as 'first isolate' again. The default of 365 days is based on the guideline by CLSI, see *Source*.
|
||||
#' @param testcodes_exclude a [character] vector with test codes that should be excluded (case-insensitive)
|
||||
#' @param icu_exclude a [logical] to indicate whether ICU isolates should be excluded (rows with value `TRUE` in the column set with `col_icu`)
|
||||
@@ -102,9 +102,9 @@
|
||||
#'
|
||||
#' This is a more reliable method, since it also *weighs* the antibiogram (antimicrobial test results) yielding so-called 'first weighted isolates'. There are two different methods to weigh the antibiogram:
|
||||
#'
|
||||
#' 1. Using `type = "points"` and argument `points_threshold`
|
||||
#' 1. Using `type = "points"` and argument `points_threshold` (default)
|
||||
#'
|
||||
#' This method weighs *all* antimicrobial agents available in the data set. Any difference from I to S or R (or vice versa) counts as 0.5 points, a difference from S to R (or vice versa) counts as 1 point. When the sum of points exceeds `points_threshold`, which defaults to `2`, an isolate will be selected as a first weighted isolate.
|
||||
#' This method weighs *all* antimicrobial agents available in the data set. Any difference from I to S or R (or vice versa) counts as `0.5` points, a difference from S to R (or vice versa) counts as `1` point. When the sum of points exceeds `points_threshold`, which defaults to `2`, an isolate will be selected as a first weighted isolate.
|
||||
#'
|
||||
#' All antimicrobials are internally selected using the [all_antimicrobials()] function. The output of this function does not need to be passed to the [first_isolate()] function.
|
||||
#'
|
||||
@@ -131,11 +131,8 @@
|
||||
#' # `example_isolates` is a data set available in the AMR package.
|
||||
#' # See ?example_isolates.
|
||||
#'
|
||||
#' example_isolates[first_isolate(example_isolates), ]
|
||||
#' \donttest{
|
||||
#' # faster way, only works in R 3.2 and later:
|
||||
#' example_isolates[first_isolate(), ]
|
||||
#'
|
||||
#' \donttest{
|
||||
#' # get all first Gram-negatives
|
||||
#' example_isolates[which(first_isolate() & mo_is_gram_negative()), ]
|
||||
#'
|
||||
@@ -221,7 +218,7 @@ first_isolate <- function(x = NULL,
|
||||
meet_criteria(col_icu, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
|
||||
# method
|
||||
method <- coerce_method(method)
|
||||
meet_criteria(method, allow_class = "character", has_length = 1, is_in = c("phenotype-based", "episode-based", "patient-based", "isolate-based", "p", "e", "i"))
|
||||
meet_criteria(method, allow_class = "character", has_length = 1, is_in = c("phenotype-based", "episode-based", "patient-based", "isolate-based"))
|
||||
# key antimicrobials
|
||||
if (length(col_keyantimicrobials) > 1) {
|
||||
meet_criteria(col_keyantimicrobials, allow_class = "character", has_length = nrow(x))
|
||||
@@ -241,7 +238,7 @@ first_isolate <- function(x = NULL,
|
||||
meet_criteria(testcodes_exclude, allow_class = "character", allow_NULL = TRUE)
|
||||
meet_criteria(icu_exclude, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(specimen_group, allow_class = "character", has_length = 1, allow_NULL = TRUE)
|
||||
meet_criteria(type, allow_class = "character", has_length = 1)
|
||||
meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("points", "keyantimicrobials"))
|
||||
meet_criteria(ignore_I, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(points_threshold, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
|
||||
meet_criteria(info, allow_class = "logical", has_length = 1)
|
||||
@@ -253,21 +250,21 @@ first_isolate <- function(x = NULL,
|
||||
|
||||
any_col_contains_rsi <- any(vapply(FUN.VALUE = logical(1),
|
||||
X = x,
|
||||
FUN = function(x) any(as.character(x) %in% c("R", "S", "I"), na.rm = TRUE),
|
||||
# check only first 10,000 rows
|
||||
FUN = function(x) any(as.character(x[1:10000]) %in% c("R", "S", "I"), na.rm = TRUE),
|
||||
USE.NAMES = FALSE))
|
||||
if (method == "phenotype-based" & !any_col_contains_rsi) {
|
||||
method <- "episode-based"
|
||||
}
|
||||
if (info == TRUE & message_not_thrown_before("first_isolate.method")) {
|
||||
message_(paste0("Determining first isolates using the '", font_bold(method), "' method",
|
||||
message_(paste0("Determining first isolates ",
|
||||
ifelse(method %in% c("episode-based", "phenotype-based"),
|
||||
ifelse(is.infinite(episode_days),
|
||||
" without a specified episode length",
|
||||
paste(" and an episode length of", episode_days, "days")),
|
||||
"without a specified episode length",
|
||||
paste("using an episode length of", episode_days, "days")),
|
||||
"")),
|
||||
as_note = FALSE,
|
||||
add_fn = font_black)
|
||||
remember_thrown_message("first_isolate.method")
|
||||
}
|
||||
|
||||
# try to find columns based on type
|
||||
@@ -364,10 +361,9 @@ first_isolate <- function(x = NULL,
|
||||
}
|
||||
# remove testcodes
|
||||
if (!is.null(testcodes_exclude) & info == TRUE & message_not_thrown_before("first_isolate.excludingtestcodes")) {
|
||||
message_("Excluding test codes: ", toString(paste0("'", testcodes_exclude, "'")),
|
||||
message_("Excluding test codes: ", vector_and(testcodes_exclude, quotes = TRUE),
|
||||
add_fn = font_black,
|
||||
as_note = FALSE)
|
||||
remember_thrown_message("first_isolate.excludingtestcodes")
|
||||
}
|
||||
|
||||
if (is.null(col_specimen)) {
|
||||
@@ -381,7 +377,6 @@ first_isolate <- function(x = NULL,
|
||||
message_("Excluding other than specimen group '", specimen_group, "'",
|
||||
add_fn = font_black,
|
||||
as_note = FALSE)
|
||||
remember_thrown_message("first_isolate.excludingspecimen")
|
||||
}
|
||||
}
|
||||
if (!is.null(col_keyantimicrobials)) {
|
||||
@@ -449,20 +444,7 @@ first_isolate <- function(x = NULL,
|
||||
!is.na(x$newvar_mo)), , drop = FALSE])
|
||||
|
||||
# Analysis of first isolate ----
|
||||
x$other_pat_or_mo <- ifelse(x$newvar_patient_id == pm_lag(x$newvar_patient_id) &
|
||||
x$newvar_genus_species == pm_lag(x$newvar_genus_species),
|
||||
FALSE,
|
||||
TRUE)
|
||||
x$episode_group <- paste(x$newvar_patient_id, x$newvar_genus_species)
|
||||
x$more_than_episode_ago <- unlist(lapply(split(x$newvar_date,
|
||||
x$episode_group),
|
||||
is_new_episode,
|
||||
episode_days = episode_days),
|
||||
use.names = FALSE)
|
||||
|
||||
weighted.notice <- ""
|
||||
if (!is.null(col_keyantimicrobials)) {
|
||||
weighted.notice <- "weighted "
|
||||
if (info == TRUE & message_not_thrown_before("first_isolate.type")) {
|
||||
if (type == "keyantimicrobials") {
|
||||
message_("Basing inclusion on key antimicrobials, ",
|
||||
@@ -477,25 +459,39 @@ first_isolate <- function(x = NULL,
|
||||
add_fn = font_black,
|
||||
as_note = FALSE)
|
||||
}
|
||||
remember_thrown_message("first_isolate.type")
|
||||
}
|
||||
type_param <- type
|
||||
|
||||
}
|
||||
|
||||
x$other_pat_or_mo <- ifelse(x$newvar_patient_id == pm_lag(x$newvar_patient_id) &
|
||||
x$newvar_genus_species == pm_lag(x$newvar_genus_species),
|
||||
FALSE,
|
||||
TRUE)
|
||||
|
||||
x$episode_group <- paste(x$newvar_patient_id, x$newvar_genus_species)
|
||||
x$more_than_episode_ago <- unlist(lapply(split(x$newvar_date,
|
||||
x$episode_group),
|
||||
exec_episode, # this will skip meet_criteria() in is_new_episode(), saving time
|
||||
type = "logical",
|
||||
episode_days = episode_days),
|
||||
use.names = FALSE)
|
||||
|
||||
if (!is.null(col_keyantimicrobials)) {
|
||||
# with key antibiotics
|
||||
x$other_key_ab <- !antimicrobials_equal(y = x$newvar_key_ab,
|
||||
z = pm_lag(x$newvar_key_ab),
|
||||
type = type_param,
|
||||
type = type,
|
||||
ignore_I = ignore_I,
|
||||
points_threshold = points_threshold)
|
||||
# with key antibiotics
|
||||
x$newvar_first_isolate <- pm_if_else(x$newvar_row_index_sorted >= row.start &
|
||||
x$newvar_row_index_sorted <= row.end &
|
||||
x$newvar_genus_species != "" &
|
||||
(x$other_pat_or_mo | x$more_than_episode_ago | x$other_key_ab),
|
||||
TRUE,
|
||||
FALSE)
|
||||
|
||||
} else {
|
||||
# no key antibiotics
|
||||
x1 <<- x$other_pat_or_mo
|
||||
x2 <<- x$more_than_episode_ago
|
||||
x$newvar_first_isolate <- pm_if_else(x$newvar_row_index_sorted >= row.start &
|
||||
x$newvar_row_index_sorted <= row.end &
|
||||
x$newvar_genus_species != "" &
|
||||
@@ -575,7 +571,7 @@ first_isolate <- function(x = NULL,
|
||||
}
|
||||
|
||||
# arrange back according to original sorting again
|
||||
x <- x[order(x$newvar_row_index), ]
|
||||
x <- x[order(x$newvar_row_index), , drop = FALSE]
|
||||
rownames(x) <- NULL
|
||||
|
||||
if (info == TRUE) {
|
||||
@@ -590,16 +586,16 @@ first_isolate <- function(x = NULL,
|
||||
}
|
||||
# mark up number of found
|
||||
n_found <- format(n_found, big.mark = big.mark, decimal.mark = decimal.mark)
|
||||
if (p_found_total != p_found_scope) {
|
||||
msg_txt <- paste0("=> Found ",
|
||||
font_bold(paste0(n_found, " first ", weighted.notice, "isolates")),
|
||||
" (", method, ", ", p_found_scope, " within scope and ", p_found_total, " of total where a microbial ID was available)")
|
||||
} else {
|
||||
msg_txt <- paste0("=> Found ",
|
||||
font_bold(paste0(n_found, " first ", weighted.notice, "isolates")),
|
||||
" (", method, ", ", p_found_total, " of total where a microbial ID was available)")
|
||||
}
|
||||
message_(msg_txt, add_fn = font_black, as_note = FALSE)
|
||||
message_(paste0("=> Found ",
|
||||
font_bold(paste0(n_found,
|
||||
ifelse(method == "isolate-based", "", paste0(" '", method, "'")),
|
||||
" first isolates")),
|
||||
" (",
|
||||
ifelse(p_found_total != p_found_scope,
|
||||
paste0(p_found_scope, " within scope and "),
|
||||
""),
|
||||
p_found_total, " of total where a microbial ID was available)"),
|
||||
add_fn = font_black, as_note = FALSE)
|
||||
}
|
||||
|
||||
x$newvar_first_isolate
|
||||
@@ -626,7 +622,7 @@ filter_first_isolate <- function(x = NULL,
|
||||
meet_criteria(col_mo, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
|
||||
meet_criteria(episode_days, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = FALSE)
|
||||
method <- coerce_method(method)
|
||||
meet_criteria(method, allow_class = "character", has_length = 1, is_in = c("phenotype-based", "episode-based", "patient-based", "isolate-based", "p", "e", "i"))
|
||||
meet_criteria(method, allow_class = "character", has_length = 1, is_in = c("phenotype-based", "episode-based", "patient-based", "isolate-based"))
|
||||
|
||||
subset(x, first_isolate(x = x,
|
||||
col_date = col_date,
|
||||
@@ -644,7 +640,7 @@ coerce_method <- function(method) {
|
||||
method <- tolower(as.character(method[1L]))
|
||||
method[method %like% "^(p$|pheno)"] <- "phenotype-based"
|
||||
method[method %like% "^(e$|episode)"] <- "episode-based"
|
||||
method[method %like% "^patient"] <- "patient-based"
|
||||
method[method %like% "^pat"] <- "patient-based"
|
||||
method[method %like% "^(i$|iso)"] <- "isolate-based"
|
||||
method
|
||||
}
|
||||
|
||||
+15
-10
@@ -123,8 +123,7 @@
|
||||
#' mo == as.mo("E. coli")) %>%
|
||||
#' # age_groups() is also a function in this AMR package:
|
||||
#' group_by(age_group = age_groups(age)) %>%
|
||||
#' select(age_group,
|
||||
#' CIP) %>%
|
||||
#' select(age_group, CIP) %>%
|
||||
#' ggplot_rsi(x = "age_group")
|
||||
#'
|
||||
#' # a shorter version which also adjusts data label colours:
|
||||
@@ -135,6 +134,8 @@
|
||||
#'
|
||||
#' # it also supports groups (don't forget to use the group var on `x` or `facet`):
|
||||
#' example_isolates %>%
|
||||
#' filter(mo_is_gram_negative()) %>%
|
||||
#' # select only UTI-specific drugs
|
||||
#' select(hospital_id, AMX, NIT, FOS, TMP, CIP) %>%
|
||||
#' group_by(hospital_id) %>%
|
||||
#' ggplot_rsi(x = "hospital_id",
|
||||
@@ -370,7 +371,6 @@ scale_rsi_colours <- function(...,
|
||||
aesthetics = "fill") {
|
||||
stop_ifnot_installed("ggplot2")
|
||||
meet_criteria(aesthetics, allow_class = "character", is_in = c("alpha", "colour", "color", "fill", "linetype", "shape", "size"))
|
||||
|
||||
# behaviour until AMR pkg v1.5.0 and also when coming from ggplot_rsi()
|
||||
if ("colours" %in% names(list(...))) {
|
||||
original_cols <- c(S = "#3CAEA3",
|
||||
@@ -379,22 +379,25 @@ scale_rsi_colours <- function(...,
|
||||
IR = "#ED553B",
|
||||
R = "#ED553B")
|
||||
colours <- replace(original_cols, names(list(...)$colours), list(...)$colours)
|
||||
return(ggplot2::scale_fill_manual(values = colours))
|
||||
# limits = force is needed in ggplot2 3.3.4 and 3.3.5, see here;
|
||||
# https://github.com/tidyverse/ggplot2/issues/4511#issuecomment-866185530
|
||||
return(ggplot2::scale_fill_manual(values = colours, limits = force))
|
||||
}
|
||||
if (identical(unlist(list(...)), FALSE)) {
|
||||
return(invisible())
|
||||
}
|
||||
|
||||
names_susceptible <- c("S", "SI", "IS", "S+I", "I+S", "susceptible", "Susceptible",
|
||||
unique(translations_file[which(translations_file$pattern == "Susceptible"),
|
||||
unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Susceptible"),
|
||||
"replacement", drop = TRUE]))
|
||||
names_incr_exposure <- c("I", "intermediate", "increased exposure", "incr. exposure", "Increased exposure", "Incr. exposure",
|
||||
unique(translations_file[which(translations_file$pattern == "Intermediate"),
|
||||
names_incr_exposure <- c("I", "intermediate", "increased exposure", "incr. exposure",
|
||||
"Increased exposure", "Incr. exposure", "Susceptible, incr. exp.",
|
||||
unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Intermediate"),
|
||||
"replacement", drop = TRUE]),
|
||||
unique(translations_file[which(translations_file$pattern == "Incr. exposure"),
|
||||
unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Susceptible, incr. exp."),
|
||||
"replacement", drop = TRUE]))
|
||||
names_resistant <- c("R", "IR", "RI", "R+I", "I+R", "resistant", "Resistant",
|
||||
unique(translations_file[which(translations_file$pattern == "Resistant"),
|
||||
unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Resistant"),
|
||||
"replacement", drop = TRUE]))
|
||||
|
||||
susceptible <- rep("#3CAEA3", length(names_susceptible))
|
||||
@@ -411,7 +414,9 @@ scale_rsi_colours <- function(...,
|
||||
dots[dots == "I"] <- "#F6D55C"
|
||||
dots[dots == "R"] <- "#ED553B"
|
||||
cols <- replace(original_cols, names(dots), dots)
|
||||
ggplot2::scale_discrete_manual(aesthetics = aesthetics, values = cols)
|
||||
# limits = force is needed in ggplot2 3.3.4 and 3.3.5, see here;
|
||||
# https://github.com/tidyverse/ggplot2/issues/4511#issuecomment-866185530
|
||||
ggplot2::scale_discrete_manual(aesthetics = aesthetics, values = cols, limits = force)
|
||||
}
|
||||
|
||||
#' @rdname ggplot_rsi
|
||||
|
||||
+6
-2
@@ -40,6 +40,10 @@ EUCAST_VERSION_EXPERT_RULES <- list("3.1" = list(version_txt = "v3.1",
|
||||
"3.2" = list(version_txt = "v3.2",
|
||||
year = 2020,
|
||||
title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
|
||||
url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"),
|
||||
"3.3" = list(version_txt = "v3.3",
|
||||
year = 2021,
|
||||
title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
|
||||
url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"))
|
||||
|
||||
SNOMED_VERSION <- list(title = "Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)",
|
||||
@@ -52,9 +56,9 @@ SNOMED_VERSION <- list(title = "Public Health Information Network Vocabulary Acc
|
||||
CATALOGUE_OF_LIFE <- list(
|
||||
year = 2019,
|
||||
version = "Catalogue of Life: {year} Annual Checklist",
|
||||
url_CoL = "http://www.catalogueoflife.org/col/",
|
||||
url_CoL = "http://www.catalogueoflife.org",
|
||||
url_LPSN = "https://lpsn.dsmz.de",
|
||||
yearmonth_LPSN = "March 2021"
|
||||
yearmonth_LPSN = "5 October 2021"
|
||||
)
|
||||
|
||||
globalVariables(c(".rowid",
|
||||
|
||||
+93
-31
@@ -97,16 +97,39 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE, only_r
|
||||
}
|
||||
|
||||
get_column_abx <- function(x,
|
||||
...,
|
||||
soft_dependencies = NULL,
|
||||
hard_dependencies = NULL,
|
||||
verbose = FALSE,
|
||||
info = TRUE,
|
||||
only_rsi_columns = FALSE,
|
||||
sort = TRUE,
|
||||
...) {
|
||||
reuse_previous_result = TRUE) {
|
||||
|
||||
# check if retrieved before, then get it from package environment
|
||||
if (identical(unique_call_id(entire_session = FALSE), pkg_env$get_column_abx.call)) {
|
||||
if (isTRUE(reuse_previous_result) && identical(unique_call_id(entire_session = FALSE), pkg_env$get_column_abx.call)) {
|
||||
# so within the same call, within the same environment, we got here again.
|
||||
# but we could've come from another function within the same call, so now only check the columns that changed
|
||||
|
||||
# first remove the columns that are not existing anymore
|
||||
previous <- pkg_env$get_column_abx.out
|
||||
current <- previous[previous %in% colnames(x)]
|
||||
|
||||
# then compare columns in current call with columns in original call
|
||||
new_cols <- colnames(x)[!colnames(x) %in% pkg_env$get_column_abx.checked_cols]
|
||||
if (length(new_cols) > 0) {
|
||||
# these columns did not exist in the last call, so add them
|
||||
new_cols_rsi <- get_column_abx(x[, new_cols, drop = FALSE], reuse_previous_result = FALSE, info = FALSE, sort = FALSE)
|
||||
current <- c(current, new_cols_rsi)
|
||||
# order according to columns in current call
|
||||
current <- current[match(colnames(x)[colnames(x) %in% current], current)]
|
||||
}
|
||||
|
||||
# update pkg environment to improve speed on next run
|
||||
pkg_env$get_column_abx.out <- current
|
||||
pkg_env$get_column_abx.checked_cols <- colnames(x)
|
||||
|
||||
# and return right values
|
||||
return(pkg_env$get_column_abx.out)
|
||||
}
|
||||
|
||||
@@ -123,6 +146,7 @@ get_column_abx <- function(x,
|
||||
}
|
||||
|
||||
x <- as.data.frame(x, stringsAsFactors = FALSE)
|
||||
x.bak <- x
|
||||
if (only_rsi_columns == TRUE) {
|
||||
x <- x[, which(is.rsi(x)), drop = FALSE]
|
||||
}
|
||||
@@ -155,7 +179,7 @@ get_column_abx <- function(x,
|
||||
} else {
|
||||
return(NA_character_)
|
||||
}
|
||||
})
|
||||
}, USE.NAMES = FALSE)
|
||||
|
||||
x_columns <- x_columns[!is.na(x_columns)]
|
||||
x <- x[, x_columns, drop = FALSE] # without drop = FALSE, x will become a vector when x_columns is length 1
|
||||
@@ -163,62 +187,77 @@ get_column_abx <- function(x,
|
||||
abcode = suppressWarnings(as.ab(colnames(x), info = FALSE)),
|
||||
stringsAsFactors = FALSE)
|
||||
df_trans <- df_trans[!is.na(df_trans$abcode), , drop = FALSE]
|
||||
x <- as.character(df_trans$colnames)
|
||||
names(x) <- df_trans$abcode
|
||||
out <- as.character(df_trans$colnames)
|
||||
names(out) <- df_trans$abcode
|
||||
|
||||
# add from self-defined dots (...):
|
||||
# such as get_column_abx(example_isolates %>% rename(thisone = AMX), amox = "thisone")
|
||||
all_okay <- TRUE
|
||||
dots <- list(...)
|
||||
if (length(dots) > 0) {
|
||||
newnames <- suppressWarnings(as.ab(names(dots), info = FALSE))
|
||||
if (any(is.na(newnames))) {
|
||||
warning_("Invalid antibiotic reference(s): ", toString(names(dots)[is.na(newnames)]),
|
||||
if (info == TRUE) {
|
||||
message_(" WARNING", add_fn = list(font_yellow, font_bold), as_note = FALSE)
|
||||
}
|
||||
warning_("Invalid antibiotic reference(s): ", vector_and(names(dots)[is.na(newnames)], quotes = FALSE),
|
||||
call = FALSE,
|
||||
immediate = TRUE)
|
||||
all_okay <- FALSE
|
||||
}
|
||||
unexisting_cols <- which(!vapply(FUN.VALUE = logical(1), dots, function(col) all(col %in% x_columns)))
|
||||
if (length(unexisting_cols) > 0) {
|
||||
if (info == TRUE) {
|
||||
message_(" ERROR", add_fn = list(font_red, font_bold), as_note = FALSE)
|
||||
}
|
||||
stop_("Column(s) not found: ", vector_and(unlist(dots[[unexisting_cols]]), quotes = FALSE),
|
||||
call = FALSE)
|
||||
all_okay <- FALSE
|
||||
}
|
||||
# turn all NULLs to NAs
|
||||
dots <- unlist(lapply(dots, function(x) if (is.null(x)) NA else x))
|
||||
dots <- unlist(lapply(dots, function(dot) if (is.null(dot)) NA else dot))
|
||||
names(dots) <- newnames
|
||||
dots <- dots[!is.na(names(dots))]
|
||||
# merge, but overwrite automatically determined ones by 'dots'
|
||||
x <- c(x[!x %in% dots & !names(x) %in% names(dots)], dots)
|
||||
out <- c(out[!out %in% dots & !names(out) %in% names(dots)], dots)
|
||||
# delete NAs, this will make e.g. eucast_rules(... TMP = NULL) work to prevent TMP from being used
|
||||
x <- x[!is.na(x)]
|
||||
out <- out[!is.na(out)]
|
||||
}
|
||||
|
||||
if (length(x) == 0) {
|
||||
if (info == TRUE) {
|
||||
if (length(out) == 0) {
|
||||
if (info == TRUE & all_okay == TRUE) {
|
||||
message_("No columns found.")
|
||||
}
|
||||
pkg_env$get_column_abx.call <- unique_call_id(entire_session = FALSE)
|
||||
pkg_env$get_column_abx.out <- x
|
||||
return(x)
|
||||
pkg_env$get_column_abx.checked_cols <- colnames(x.bak)
|
||||
pkg_env$get_column_abx.out <- out
|
||||
return(out)
|
||||
}
|
||||
|
||||
# sort on name
|
||||
if (sort == TRUE) {
|
||||
x <- x[order(names(x), x)]
|
||||
out <- out[order(names(out), out)]
|
||||
}
|
||||
duplicates <- c(x[duplicated(x)], x[duplicated(names(x))])
|
||||
duplicates <- c(out[duplicated(out)], out[duplicated(names(out))])
|
||||
duplicates <- duplicates[unique(names(duplicates))]
|
||||
x <- c(x[!names(x) %in% names(duplicates)], duplicates)
|
||||
out <- c(out[!names(out) %in% names(duplicates)], duplicates)
|
||||
if (sort == TRUE) {
|
||||
x <- x[order(names(x), x)]
|
||||
out <- out[order(names(out), out)]
|
||||
}
|
||||
|
||||
# succeeded with auto-guessing
|
||||
if (info == TRUE) {
|
||||
if (info == TRUE & all_okay == TRUE) {
|
||||
message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
|
||||
}
|
||||
|
||||
for (i in seq_len(length(x))) {
|
||||
if (info == TRUE & verbose == TRUE & !names(x[i]) %in% names(duplicates)) {
|
||||
message_("Using column '", font_bold(x[i]), "' as input for ", names(x)[i],
|
||||
" (", ab_name(names(x)[i], tolower = TRUE, language = NULL), ").")
|
||||
for (i in seq_len(length(out))) {
|
||||
if (info == TRUE & verbose == TRUE & !names(out[i]) %in% names(duplicates)) {
|
||||
message_("Using column '", font_bold(out[i]), "' as input for ", names(out)[i],
|
||||
" (", ab_name(names(out)[i], tolower = TRUE, language = NULL), ").")
|
||||
}
|
||||
if (info == TRUE & names(x[i]) %in% names(duplicates)) {
|
||||
warning_(paste0("Using column '", font_bold(x[i]), "' as input for ", names(x)[i],
|
||||
" (", ab_name(names(x)[i], tolower = TRUE, language = NULL),
|
||||
if (info == TRUE & names(out[i]) %in% names(duplicates)) {
|
||||
warning_(paste0("Using column '", font_bold(out[i]), "' as input for ", names(out)[i],
|
||||
" (", ab_name(names(out)[i], tolower = TRUE, language = NULL),
|
||||
"), although it was matched for multiple antibiotics or columns."),
|
||||
add_fn = font_red,
|
||||
call = FALSE,
|
||||
@@ -228,18 +267,18 @@ get_column_abx <- function(x,
|
||||
|
||||
if (!is.null(hard_dependencies)) {
|
||||
hard_dependencies <- unique(hard_dependencies)
|
||||
if (!all(hard_dependencies %in% names(x))) {
|
||||
if (!all(hard_dependencies %in% names(out))) {
|
||||
# missing a hard dependency will return NA and consequently the data will not be analysed
|
||||
missing <- hard_dependencies[!hard_dependencies %in% names(x)]
|
||||
missing <- hard_dependencies[!hard_dependencies %in% names(out)]
|
||||
generate_warning_abs_missing(missing, any = FALSE)
|
||||
return(NA)
|
||||
}
|
||||
}
|
||||
if (!is.null(soft_dependencies)) {
|
||||
soft_dependencies <- unique(soft_dependencies)
|
||||
if (info == TRUE & !all(soft_dependencies %in% names(x))) {
|
||||
if (info == TRUE & !all(soft_dependencies %in% names(out))) {
|
||||
# missing a soft dependency may lower the reliability
|
||||
missing <- soft_dependencies[!soft_dependencies %in% names(x)]
|
||||
missing <- soft_dependencies[!soft_dependencies %in% names(out)]
|
||||
missing_msg <- vector_and(paste0(ab_name(missing, tolower = TRUE, language = NULL),
|
||||
" (", font_bold(missing, collapse = NULL), ")"),
|
||||
quotes = FALSE)
|
||||
@@ -249,8 +288,31 @@ get_column_abx <- function(x,
|
||||
}
|
||||
|
||||
pkg_env$get_column_abx.call <- unique_call_id(entire_session = FALSE)
|
||||
pkg_env$get_column_abx.out <- x
|
||||
x
|
||||
pkg_env$get_column_abx.checked_cols <- colnames(x.bak)
|
||||
pkg_env$get_column_abx.out <- out
|
||||
out
|
||||
}
|
||||
|
||||
get_ab_from_namespace <- function(x, cols_ab) {
|
||||
# cols_ab comes from get_column_abx()
|
||||
|
||||
x <- trimws(unique(toupper(unlist(strsplit(x, ",")))))
|
||||
x_new <- character()
|
||||
for (val in x) {
|
||||
if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) {
|
||||
# antibiotic group names, as defined in data-raw/_internals.R, such as `AB_CARBAPENEMS`
|
||||
val <- eval(parse(text = paste0("AB_", val)), envir = asNamespace("AMR"))
|
||||
} else if (val %in% AB_lookup$ab) {
|
||||
# separate drugs, such as `AMX`
|
||||
val <- as.ab(val)
|
||||
} else {
|
||||
stop_("unknown antimicrobial agent (group): ", val, call = FALSE)
|
||||
}
|
||||
x_new <- c(x_new, val)
|
||||
}
|
||||
x_new <- unique(x_new)
|
||||
out <- cols_ab[match(x_new, names(cols_ab))]
|
||||
out[!is.na(out)]
|
||||
}
|
||||
|
||||
generate_warning_abs_missing <- function(missing, any = FALSE) {
|
||||
|
||||
@@ -26,7 +26,7 @@
|
||||
#' Italicise Taxonomic Families, Genera, Species, Subspecies
|
||||
#'
|
||||
#' According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italic. This function finds taxonomic names within strings and makes them italic.
|
||||
#' @inheritSection lifecycle Maturing Lifecycle
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param string a [character] (vector)
|
||||
#' @param type type of conversion of the taxonomic names, either "markdown" or "ansi", see *Details*
|
||||
#' @details
|
||||
@@ -44,11 +44,11 @@
|
||||
#' cat(italicise_taxonomy("An overview of S. aureus isolates", type = "ansi"))
|
||||
#'
|
||||
#' # since ggplot2 supports no markdown (yet), use
|
||||
#' # italicise_taxonomy() and the `ggtext` pkg for titles:
|
||||
#' # italicise_taxonomy() and the `ggtext` package for titles:
|
||||
#' \donttest{
|
||||
#' if (require("ggplot2") && require("ggtext")) {
|
||||
#' ggplot(example_isolates$AMC,
|
||||
#' title = italicise_taxonomy("Amoxi/clav in E. coli")) +
|
||||
#' autoplot(example_isolates$AMC,
|
||||
#' title = italicise_taxonomy("Amoxi/clav in E. coli")) +
|
||||
#' theme(plot.title = ggtext::element_markdown())
|
||||
#' }
|
||||
#' }
|
||||
|
||||
@@ -36,7 +36,7 @@
|
||||
#' @param ... ignored, only in place to allow future extensions
|
||||
#' @details **Note:** As opposed to the `join()` functions of `dplyr`, [character] vectors are supported and at default existing columns will get a suffix `"2"` and the newly joined columns will not get a suffix.
|
||||
#'
|
||||
#' If the `dplyr` package is installed, their join functions will be used. Otherwise, the much slower [merge()] and [interaction()] functions from base R will be used.
|
||||
#' If the `dplyr` package is installed, their join functions will be used. Otherwise, the much slower [merge()] and [interaction()] functions from base \R will be used.
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
#' @return a [data.frame]
|
||||
#' @export
|
||||
|
||||
+17
-8
@@ -177,7 +177,6 @@ key_antimicrobials <- function(x = NULL,
|
||||
paste0("Only using ", values_new_length, " out of ", values_old_length, " defined columns ")),
|
||||
"as key antimicrobials for ", name, "s. See ?key_antimicrobials.",
|
||||
call = FALSE)
|
||||
remember_thrown_message(paste0("key_antimicrobials.", name))
|
||||
}
|
||||
|
||||
generate_antimcrobials_string(x[which(filter), c(universal, values), drop = FALSE])
|
||||
@@ -251,16 +250,16 @@ generate_antimcrobials_string <- function(df) {
|
||||
if (NROW(df) == 0) {
|
||||
return(character(0))
|
||||
}
|
||||
out <- tryCatch(
|
||||
tryCatch({
|
||||
do.call(paste0,
|
||||
lapply(as.list(df),
|
||||
function(x) {
|
||||
x <- toupper(as.character(x))
|
||||
x[!x %in% c("R", "S", "I")] <- "."
|
||||
paste(x)
|
||||
})),
|
||||
error = function(e) rep(strrep(".", NCOL(df)), NROW(df)))
|
||||
out
|
||||
}))
|
||||
},
|
||||
error = function(e) rep(strrep(".", NCOL(df)), NROW(df)))
|
||||
}
|
||||
|
||||
#' @rdname key_antimicrobials
|
||||
@@ -280,10 +279,20 @@ antimicrobials_equal <- function(y,
|
||||
stop_ifnot(length(y) == length(z), "length of `y` and `z` must be equal")
|
||||
|
||||
key2rsi <- function(val) {
|
||||
as.double(as.rsi(gsub(".", NA_character_, unlist(strsplit(val, "")), fixed = TRUE)))
|
||||
val <- strsplit(val, "")[[1L]]
|
||||
val.int <- rep(NA_real_, length(val))
|
||||
val.int[val == "S"] <- 1
|
||||
val.int[val == "I"] <- 2
|
||||
val.int[val == "R"] <- 3
|
||||
val.int
|
||||
}
|
||||
y <- lapply(y, key2rsi)
|
||||
z <- lapply(z, key2rsi)
|
||||
# only run on uniques
|
||||
uniq <- unique(c(y, z))
|
||||
uniq_list <- lapply(uniq, key2rsi)
|
||||
names(uniq_list) <- uniq
|
||||
|
||||
y <- uniq_list[match(y, names(uniq_list))]
|
||||
z <- uniq_list[match(z, names(uniq_list))]
|
||||
|
||||
determine_equality <- function(a, b, type, points_threshold, ignore_I) {
|
||||
if (length(a) != length(b)) {
|
||||
|
||||
+1
-1
@@ -44,7 +44,7 @@
|
||||
#' \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
#' The [lifecycle][AMR::lifecycle] of this function is **stable**. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
#'
|
||||
#' If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
#' If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
#' @section Retired Lifecycle:
|
||||
#' \if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:5px} \cr}
|
||||
#' The [lifecycle][AMR::lifecycle] of this function is **retired**. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.
|
||||
|
||||
@@ -187,13 +187,9 @@ mdro <- function(x = NULL,
|
||||
check_dataset_integrity()
|
||||
|
||||
info.bak <- info
|
||||
if (message_not_thrown_before("mdro")) {
|
||||
remember_thrown_message("mdro")
|
||||
} else {
|
||||
# don't thrown info's more than once per call
|
||||
info <- FALSE
|
||||
}
|
||||
|
||||
# don't thrown info's more than once per call
|
||||
info <- message_not_thrown_before("mdro")
|
||||
|
||||
if (interactive() & verbose == TRUE & info == TRUE) {
|
||||
txt <- paste0("WARNING: In Verbose mode, the mdro() function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.",
|
||||
"\n\nThis may overwrite your existing data if you use e.g.:",
|
||||
@@ -252,7 +248,7 @@ mdro <- function(x = NULL,
|
||||
if (info == TRUE) {
|
||||
txt <- paste0("Determining MDROs based on custom rules",
|
||||
ifelse(isTRUE(attributes(guideline)$as_factor),
|
||||
paste0(", resulting in [factor] levels: ", paste0(attributes(guideline)$values, collapse = " < ")),
|
||||
paste0(", resulting in factor levels: ", paste0(attributes(guideline)$values, collapse = " < ")),
|
||||
""),
|
||||
".")
|
||||
txt <- word_wrap(txt)
|
||||
@@ -540,6 +536,13 @@ mdro <- function(x = NULL,
|
||||
only_rsi_columns = only_rsi_columns,
|
||||
...)
|
||||
}
|
||||
if (!"AMP" %in% names(cols_ab) & "AMX" %in% names(cols_ab)) {
|
||||
# ampicillin column is missing, but amoxicillin is available
|
||||
if (info == TRUE) {
|
||||
message_("Using column '", cols_ab[names(cols_ab) == "AMX"], "' as input for ampicillin since many EUCAST rules depend on it.")
|
||||
}
|
||||
cols_ab <- c(cols_ab, c(AMP = unname(cols_ab[names(cols_ab) == "AMX"])))
|
||||
}
|
||||
|
||||
# nolint start
|
||||
AMC <- cols_ab["AMC"]
|
||||
@@ -742,7 +745,8 @@ mdro <- function(x = NULL,
|
||||
x[rows, "columns_nonsusceptible"] <<- vapply(FUN.VALUE = character(1),
|
||||
rows,
|
||||
function(row, group_vct = cols) {
|
||||
cols_nonsus <- vapply(FUN.VALUE = logical(1), x[row, group_vct, drop = FALSE],
|
||||
cols_nonsus <- vapply(FUN.VALUE = logical(1),
|
||||
x[row, group_vct, drop = FALSE],
|
||||
function(y) y %in% search_result)
|
||||
paste(sort(c(unlist(strsplit(x[row, "columns_nonsusceptible", drop = TRUE], ", ")),
|
||||
names(cols_nonsus)[cols_nonsus])),
|
||||
@@ -756,17 +760,20 @@ mdro <- function(x = NULL,
|
||||
}
|
||||
x_transposed <- as.list(as.data.frame(t(x[, cols, drop = FALSE]),
|
||||
stringsAsFactors = FALSE))
|
||||
row_filter <- vapply(FUN.VALUE = logical(1), x_transposed, function(y) search_function(y %in% search_result, na.rm = TRUE))
|
||||
row_filter <- x[which(row_filter), "row_number", drop = TRUE]
|
||||
rows <- rows[rows %in% row_filter]
|
||||
x[rows, "MDRO"] <<- to
|
||||
x[rows, "reason"] <<- paste0(any_all,
|
||||
" of the required antibiotics ",
|
||||
ifelse(any_all == "any", "is", "are"),
|
||||
" R",
|
||||
ifelse(!isTRUE(combine_SI), " or I", ""))
|
||||
rows_affected <- vapply(FUN.VALUE = logical(1),
|
||||
x_transposed,
|
||||
function(y) search_function(y %in% search_result, na.rm = TRUE))
|
||||
rows_affected <- x[which(rows_affected), "row_number", drop = TRUE]
|
||||
rows_to_change <- rows[rows %in% rows_affected]
|
||||
x[rows_to_change, "MDRO"] <<- to
|
||||
x[rows_to_change, "reason"] <<- paste0(any_all,
|
||||
" of the required antibiotics ",
|
||||
ifelse(any_all == "any", "is", "are"),
|
||||
" R",
|
||||
ifelse(!isTRUE(combine_SI), " or I", ""))
|
||||
}
|
||||
}
|
||||
|
||||
trans_tbl2 <- function(txt, rows, lst) {
|
||||
if (info == TRUE) {
|
||||
message_(txt, "...", appendLF = FALSE, as_note = FALSE)
|
||||
@@ -1386,16 +1393,6 @@ mdro <- function(x = NULL,
|
||||
x$reason <- "PDR/MDR/XDR criteria were met"
|
||||
}
|
||||
|
||||
if (info.bak == TRUE) {
|
||||
cat(group_msg)
|
||||
if (sum(!is.na(x$MDRO)) == 0) {
|
||||
cat(font_bold(paste0("=> Found 0 MDROs since no isolates are covered by the guideline")))
|
||||
} else {
|
||||
cat(font_bold(paste0("=> Found ", sum(x$MDRO %in% c(2:5), na.rm = TRUE), " ", guideline$type, " out of ", sum(!is.na(x$MDRO)),
|
||||
" isolates (", trimws(percentage(sum(x$MDRO %in% c(2:5), na.rm = TRUE) / sum(!is.na(x$MDRO)))), ")\n")))
|
||||
}
|
||||
}
|
||||
|
||||
# some more info on negative results
|
||||
if (verbose == TRUE) {
|
||||
if (guideline$code == "cmi2012") {
|
||||
@@ -1410,13 +1407,37 @@ mdro <- function(x = NULL,
|
||||
}
|
||||
}
|
||||
|
||||
if (info.bak == TRUE) {
|
||||
cat(group_msg)
|
||||
if (sum(!is.na(x$MDRO)) == 0) {
|
||||
cat(font_bold(paste0("=> Found 0 MDROs since no isolates are covered by the guideline")))
|
||||
} else {
|
||||
cat(font_bold(paste0("=> Found ", sum(x$MDRO %in% c(2:5), na.rm = TRUE), " ", guideline$type, " out of ", sum(!is.na(x$MDRO)),
|
||||
" isolates (", trimws(percentage(sum(x$MDRO %in% c(2:5), na.rm = TRUE) / sum(!is.na(x$MDRO)))), ")")))
|
||||
}
|
||||
}
|
||||
|
||||
# Fill in blanks ----
|
||||
# for rows that have no results
|
||||
x_transposed <- as.list(as.data.frame(t(x[, cols_ab, drop = FALSE]),
|
||||
stringsAsFactors = FALSE))
|
||||
rows_empty <- which(vapply(FUN.VALUE = logical(1),
|
||||
x_transposed,
|
||||
function(y) all(is.na(y))))
|
||||
if (length(rows_empty) > 0) {
|
||||
cat(font_italic(paste0(" (", length(rows_empty), " isolates had no test results)\n")))
|
||||
x[rows_empty, "MDRO"] <- NA
|
||||
x[rows_empty, "reason"] <- "none of the antibiotics have test results"
|
||||
} else {
|
||||
cat("\n")
|
||||
}
|
||||
|
||||
# Results ----
|
||||
if (guideline$code == "cmi2012") {
|
||||
if (any(x$MDRO == -1, na.rm = TRUE)) {
|
||||
if (message_not_thrown_before("mdro.availability")) {
|
||||
warning_("NA introduced for isolates where the available percentage of antimicrobial classes was below ",
|
||||
percentage(pct_required_classes), " (set with `pct_required_classes`)", call = FALSE)
|
||||
remember_thrown_message("mdro.availability")
|
||||
}
|
||||
# set these -1s to NA
|
||||
x[which(x$MDRO == -1), "MDRO"] <- NA_integer_
|
||||
|
||||
@@ -23,9 +23,26 @@
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
# these are allowed MIC values and will become [factor] levels
|
||||
ops <- c("<", "<=", "", ">=", ">")
|
||||
valid_mic_levels <- c(c(t(vapply(FUN.VALUE = character(9), ops,
|
||||
function(x) paste0(x, "0.00", 1:9)))),
|
||||
unique(c(t(vapply(FUN.VALUE = character(104), ops,
|
||||
function(x) paste0(x, sort(as.double(paste0("0.0",
|
||||
sort(c(1:99, 125, 128, 256, 512, 625)))))))))),
|
||||
unique(c(t(vapply(FUN.VALUE = character(103), ops,
|
||||
function(x) paste0(x, sort(as.double(paste0("0.",
|
||||
c(1:99, 125, 128, 256, 512))))))))),
|
||||
c(t(vapply(FUN.VALUE = character(10), ops,
|
||||
function(x) paste0(x, sort(c(1:9, 1.5)))))),
|
||||
c(t(vapply(FUN.VALUE = character(45), ops,
|
||||
function(x) paste0(x, c(10:98)[9:98 %% 2 == TRUE])))),
|
||||
c(t(vapply(FUN.VALUE = character(15), ops,
|
||||
function(x) paste0(x, sort(c(2 ^ c(7:10), 80 * c(2:12))))))))
|
||||
|
||||
#' Transform Input to Minimum Inhibitory Concentrations (MIC)
|
||||
#'
|
||||
#' This ransforms vectors to a new class [`mic`], which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology.
|
||||
#' This transforms vectors to a new class [`mic`], which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @rdname as.mic
|
||||
#' @param x a [character] or [numeric] vector
|
||||
@@ -117,6 +134,8 @@ as.mic <- function(x, na.rm = FALSE) {
|
||||
# transform Unicode for >= and <=
|
||||
x <- gsub("\u2264", "<=", x, fixed = TRUE)
|
||||
x <- gsub("\u2265", ">=", x, fixed = TRUE)
|
||||
# remove other invalid characters
|
||||
x <- gsub("[^a-zA-Z0-9.><= ]+", "", x, perl = TRUE)
|
||||
# remove space between operator and number ("<= 0.002" -> "<=0.002")
|
||||
x <- gsub("(<|=|>) +", "\\1", x, perl = TRUE)
|
||||
# transform => to >= and =< to <=
|
||||
@@ -141,27 +160,14 @@ as.mic <- function(x, na.rm = FALSE) {
|
||||
x[x %like% "[.]"] <- gsub("0+$", "", x[x %like% "[.]"])
|
||||
# never end with dot
|
||||
x <- gsub("[.]$", "", x, perl = TRUE)
|
||||
# force to be character
|
||||
x <- as.character(x)
|
||||
# trim it
|
||||
x <- trimws(x)
|
||||
|
||||
## previously unempty values now empty - should return a warning later on
|
||||
x[x.bak != "" & x == ""] <- "invalid"
|
||||
|
||||
# these are allowed MIC values and will become [factor] levels
|
||||
ops <- c("<", "<=", "", ">=", ">")
|
||||
lvls <- c(c(t(vapply(FUN.VALUE = character(9), ops, function(x) paste0(x, "0.00", 1:9)))),
|
||||
unique(c(t(vapply(FUN.VALUE = character(104), ops, function(x) paste0(x, sort(as.double(paste0("0.0",
|
||||
sort(c(1:99, 125, 128, 256, 512, 625)))))))))),
|
||||
unique(c(t(vapply(FUN.VALUE = character(103), ops, function(x) paste0(x, sort(as.double(paste0("0.",
|
||||
c(1:99, 125, 128, 256, 512))))))))),
|
||||
c(t(vapply(FUN.VALUE = character(10), ops, function(x) paste0(x, sort(c(1:9, 1.5)))))),
|
||||
c(t(vapply(FUN.VALUE = character(45), ops, function(x) paste0(x, c(10:98)[9:98 %% 2 == TRUE])))),
|
||||
c(t(vapply(FUN.VALUE = character(15), ops, function(x) paste0(x, sort(c(2 ^ c(7:10), 80 * c(2:12))))))))
|
||||
|
||||
na_before <- x[is.na(x) | x == ""] %pm>% length()
|
||||
x[!x %in% lvls] <- NA
|
||||
x[!x %in% valid_mic_levels] <- NA
|
||||
na_after <- x[is.na(x) | x == ""] %pm>% length()
|
||||
|
||||
if (na_before != na_after) {
|
||||
@@ -175,7 +181,7 @@ as.mic <- function(x, na.rm = FALSE) {
|
||||
list_missing, call = FALSE)
|
||||
}
|
||||
|
||||
set_clean_class(factor(x, levels = lvls, ordered = TRUE),
|
||||
set_clean_class(factor(x, levels = valid_mic_levels, ordered = TRUE),
|
||||
new_class = c("mic", "ordered", "factor"))
|
||||
}
|
||||
}
|
||||
@@ -189,6 +195,12 @@ all_valid_mics <- function(x) {
|
||||
!any(is.na(x_mic)) && !all(is.na(x))
|
||||
}
|
||||
|
||||
#' @rdname as.mic
|
||||
#' @details `NA_mic_` is a missing value of the new `<mic>` class.
|
||||
#' @export
|
||||
NA_mic_ <- set_clean_class(factor(NA, levels = valid_mic_levels, ordered = TRUE),
|
||||
new_class = c("mic", "ordered", "factor"))
|
||||
|
||||
#' @rdname as.mic
|
||||
#' @export
|
||||
is.mic <- function(x) {
|
||||
@@ -320,6 +332,15 @@ unique.mic <- function(x, incomparables = FALSE, ...) {
|
||||
y
|
||||
}
|
||||
|
||||
#' @method rep mic
|
||||
#' @export
|
||||
#' @noRd
|
||||
rep.mic <- function(x, ...) {
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(x)
|
||||
y
|
||||
}
|
||||
|
||||
#' @method sort mic
|
||||
#' @export
|
||||
#' @noRd
|
||||
@@ -337,7 +358,7 @@ sort.mic <- function(x, decreasing = FALSE, ...) {
|
||||
#' @export
|
||||
#' @noRd
|
||||
hist.mic <- function(x, ...) {
|
||||
warning_("Use `plot()` or `ggplot()` for optimal plotting of MIC values", call = FALSE)
|
||||
warning_("Use `plot()` or ggplot2's `autoplot()` for optimal plotting of MIC values", call = FALSE)
|
||||
hist(log2(x))
|
||||
}
|
||||
|
||||
|
||||
@@ -201,7 +201,8 @@ as.mo <- function(x,
|
||||
& isFALSE(Becker)
|
||||
& isFALSE(Lancefield), error = function(e) FALSE)) {
|
||||
# to improve speed, special case for taxonomically correct full names (case-insensitive)
|
||||
return(MO_lookup[match(gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE), MO_lookup$fullname_lower), "mo", drop = TRUE])
|
||||
return(set_clean_class(MO_lookup[match(gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE), MO_lookup$fullname_lower), "mo", drop = TRUE],
|
||||
new_class = c("mo", "character")))
|
||||
}
|
||||
|
||||
if (!is.null(reference_df)
|
||||
@@ -233,7 +234,7 @@ as.mo <- function(x,
|
||||
info = info,
|
||||
...)
|
||||
}
|
||||
|
||||
|
||||
set_clean_class(y,
|
||||
new_class = c("mo", "character"))
|
||||
}
|
||||
@@ -372,7 +373,7 @@ exec_as.mo <- function(x,
|
||||
# Laboratory systems: remove (translated) entries like "no growth", etc.
|
||||
x[trimws2(x) %like% translate_AMR("no .*growth", language = language)] <- NA_character_
|
||||
x[trimws2(x) %like% paste0("^(", translate_AMR("no|not", language = language), ") [a-z]+")] <- "UNKNOWN"
|
||||
|
||||
|
||||
if (initial_search == TRUE) {
|
||||
# keep track of time - give some hints to improve speed if it takes a long time
|
||||
start_time <- Sys.time()
|
||||
@@ -469,7 +470,7 @@ exec_as.mo <- function(x,
|
||||
x <- strip_whitespace(x, dyslexia_mode)
|
||||
# translate 'unknown' names back to English
|
||||
if (any(x %like% "unbekannt|onbekend|desconocid|sconosciut|iconnu|desconhecid", na.rm = TRUE)) {
|
||||
trns <- subset(translations_file, pattern %like% "unknown" | affect_mo_name == TRUE)
|
||||
trns <- subset(TRANSLATIONS, pattern %like% "unknown")
|
||||
langs <- LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED != "en"]
|
||||
for (l in langs) {
|
||||
for (i in seq_len(nrow(trns))) {
|
||||
@@ -492,12 +493,16 @@ exec_as.mo <- function(x,
|
||||
x_backup[x %like_case% "^(fungus|fungi)$"] <- "(unknown fungus)" # will otherwise become the kingdom
|
||||
x_backup[x_backup_untouched == "Fungi"] <- "Fungi" # is literally the kingdom
|
||||
|
||||
# Fill in fullnames and MO codes at once
|
||||
# Fill in fullnames and MO codes directly
|
||||
known_names <- tolower(x_backup) %in% MO_lookup$fullname_lower
|
||||
x[known_names] <- MO_lookup[match(tolower(x_backup)[known_names], MO_lookup$fullname_lower), property, drop = TRUE]
|
||||
known_codes <- toupper(x_backup) %in% MO_lookup$mo
|
||||
x[known_codes] <- MO_lookup[match(toupper(x_backup)[known_codes], MO_lookup$mo), property, drop = TRUE]
|
||||
already_known <- known_names | known_codes
|
||||
known_codes_mo <- toupper(x_backup) %in% MO_lookup$mo
|
||||
x[known_codes_mo] <- MO_lookup[match(toupper(x_backup)[known_codes_mo], MO_lookup$mo), property, drop = TRUE]
|
||||
known_codes_lis <- toupper(x_backup) %in% microorganisms.codes$code
|
||||
x[known_codes_lis] <- MO_lookup[match(microorganisms.codes[match(toupper(x_backup)[known_codes_lis],
|
||||
microorganisms.codes$code), "mo", drop = TRUE],
|
||||
MO_lookup$mo), property, drop = TRUE]
|
||||
already_known <- known_names | known_codes_mo | known_codes_lis
|
||||
|
||||
# now only continue where the right taxonomic output is not already known
|
||||
if (any(!already_known)) {
|
||||
@@ -799,7 +804,7 @@ exec_as.mo <- function(x,
|
||||
perl = TRUE)), uncertainty = -1)
|
||||
next
|
||||
}
|
||||
if (x_backup_without_spp[i] %like_case% "haemoly.*strep") {
|
||||
if (x_backup_without_spp[i] %like_case% "ha?emoly.*strep") {
|
||||
# Haemolytic streptococci in different languages
|
||||
x[i] <- lookup(mo == "B_STRPT_HAEM", uncertainty = -1)
|
||||
next
|
||||
@@ -1495,20 +1500,23 @@ exec_as.mo <- function(x,
|
||||
# - Becker et al. 2014, PMID 25278577
|
||||
# - Becker et al. 2019, PMID 30872103
|
||||
# - Becker et al. 2020, PMID 32056452
|
||||
post_Becker <- character(0) # 2020-10-20 currently all are mentioned in above papers (otherwise uncomment the section below)
|
||||
post_Becker <- c("caledonicus", "canis", "durrellii", "lloydii", "roterodami")
|
||||
|
||||
# nolint start
|
||||
# if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) {
|
||||
# warning_("Becker ", font_italic("et al."), " (2014, 2019) does not contain these species named after their publication: ",
|
||||
# font_italic(paste("S.",
|
||||
# sort(mo_species(unique(x[x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property]]))),
|
||||
# collapse = ", ")),
|
||||
# ".",
|
||||
# call = FALSE,
|
||||
# immediate = TRUE)
|
||||
# }
|
||||
# comment below code if all staphylococcal species are categorised as CoNS/CoPS
|
||||
if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) {
|
||||
if (message_not_thrown_before("as.mo_becker")) {
|
||||
warning_("Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
|
||||
font_italic(paste("S.",
|
||||
sort(mo_species(unique(x[x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property]]))),
|
||||
collapse = ", ")),
|
||||
". Categorisation to CoNS/CoPS was taken from the original scientific publication(s).",
|
||||
call = FALSE,
|
||||
immediate = TRUE)
|
||||
}
|
||||
}
|
||||
# nolint end
|
||||
|
||||
|
||||
# 'MO_CONS' and 'MO_COPS' are <mo> vectors created in R/zzz.R
|
||||
CoNS <- MO_lookup[which(MO_lookup$mo %in% MO_CONS), property, drop = TRUE]
|
||||
x[x %in% CoNS] <- lookup(mo == "B_STPHY_CONS", uncertainty = -1)
|
||||
@@ -1551,16 +1559,7 @@ exec_as.mo <- function(x,
|
||||
& !identical(x_input, "")
|
||||
& !identical(x_input, "xxx")])
|
||||
|
||||
# left join the found results to the original input values (x_input)
|
||||
df_found <- data.frame(input = as.character(x_input_unique_nonempty),
|
||||
found = as.character(x),
|
||||
stringsAsFactors = FALSE)
|
||||
df_input <- data.frame(input = as.character(x_input),
|
||||
stringsAsFactors = FALSE)
|
||||
|
||||
# super fast using match() which is a lot faster than merge()
|
||||
x <- df_found$found[match(df_input$input, df_found$input)]
|
||||
|
||||
x <- x[match(x_input, x_input_unique_nonempty)]
|
||||
if (property == "mo") {
|
||||
x <- set_clean_class(x, new_class = c("mo", "character"))
|
||||
}
|
||||
@@ -1664,16 +1663,23 @@ pillar_shaft.mo <- function(x, ...) {
|
||||
out[is.na(x)] <- font_na(" NA")
|
||||
out[x == "UNKNOWN"] <- font_na(" UNKNOWN")
|
||||
|
||||
if (!all(x[!is.na(x)] %in% MO_lookup$mo)) {
|
||||
df <- tryCatch(get_current_data(arg_name = "x", call = 0),
|
||||
error = function(e) NULL)
|
||||
if (!is.null(df)) {
|
||||
mo_cols <- vapply(FUN.VALUE = logical(1), df, is.mo)
|
||||
} else {
|
||||
mo_cols <- NULL
|
||||
}
|
||||
|
||||
if (!all(x[!is.na(x)] %in% MO_lookup$mo) |
|
||||
(!is.null(df) && !all(unlist(df[, which(mo_cols), drop = FALSE]) %in% MO_lookup$mo))) {
|
||||
# markup old mo codes
|
||||
out[!x %in% MO_lookup$mo] <- font_italic(font_na(x[!x %in% MO_lookup$mo],
|
||||
collapse = NULL),
|
||||
collapse = NULL)
|
||||
# throw a warning with the affected column name
|
||||
mo <- tryCatch(search_type_in_df(get_current_data(arg_name = "x", call = 0), type = "mo", info = FALSE),
|
||||
error = function(e) NULL)
|
||||
if (!is.null(mo)) {
|
||||
col <- paste0("Column '", mo, "'")
|
||||
# throw a warning with the affected column name(s)
|
||||
if (!is.null(mo_cols)) {
|
||||
col <- paste0("Column ", vector_or(colnames(df)[mo_cols], quotes = TRUE, sort = FALSE))
|
||||
} else {
|
||||
col <- "The data"
|
||||
}
|
||||
@@ -1681,7 +1687,7 @@ pillar_shaft.mo <- function(x, ...) {
|
||||
"Please update your MO codes with `as.mo()`.",
|
||||
call = FALSE)
|
||||
}
|
||||
|
||||
|
||||
# make it always fit exactly
|
||||
max_char <- max(nchar(x))
|
||||
if (is.na(max_char)) {
|
||||
@@ -1880,36 +1886,30 @@ print.mo_uncertainties <- function(x, ...) {
|
||||
if (NROW(x) == 0) {
|
||||
return(NULL)
|
||||
}
|
||||
message_("Matching scores are based on human pathogenic prevalence and the resemblance between the input and the full taxonomic name. See `?mo_matching_score`.", as_note = FALSE)
|
||||
|
||||
msg <- ""
|
||||
cat(word_wrap("Matching scores", ifelse(has_colour(), " (in blue)", ""), " are based on human pathogenic prevalence and the resemblance between the input and the full taxonomic name. See `?mo_matching_score`.\n\n", add_fn = font_blue))
|
||||
|
||||
txt <- ""
|
||||
for (i in seq_len(nrow(x))) {
|
||||
if (x[i, ]$candidates != "") {
|
||||
candidates <- unlist(strsplit(x[i, ]$candidates, ", ", fixed = TRUE))
|
||||
scores <- mo_matching_score(x = x[i, ]$input, n = candidates)
|
||||
# sort on descending scores
|
||||
candidates <- candidates[order(1 - scores)]
|
||||
scores_formatted <- trimws(formatC(round(scores, 3), format = "f", digits = 3))
|
||||
n_candidates <- length(candidates)
|
||||
candidates <- vector_and(paste0(candidates, " (", scores_formatted[order(1 - scores)], ")"),
|
||||
quotes = FALSE,
|
||||
sort = FALSE)
|
||||
# align with input after arrow
|
||||
candidates <- paste0("\n",
|
||||
strwrap(paste0("Also matched",
|
||||
ifelse(n_candidates >= 25, " (max 25)", ""), ": ",
|
||||
candidates), # this is already max 25 due to format_uncertainty_as_df()
|
||||
indent = nchar(x[i, ]$input) + 6,
|
||||
exdent = nchar(x[i, ]$input) + 6,
|
||||
width = 0.98 * getOption("width")),
|
||||
collapse = "")
|
||||
# after strwrap, make taxonomic names italic
|
||||
candidates <- gsub("([A-Za-z]+)", font_italic("\\1"), candidates, perl = TRUE)
|
||||
candidates <- gsub(font_italic("and"), "and", candidates, fixed = TRUE)
|
||||
candidates <- gsub(paste(font_italic(c("Also", "matched"), collapse = NULL), collapse = " "),
|
||||
"Also matched",
|
||||
candidates, fixed = TRUE)
|
||||
candidates <- gsub(font_italic("max"), "max", candidates, fixed = TRUE)
|
||||
|
||||
candidates_formatted <- font_italic(candidates, collapse = NULL)
|
||||
scores_formatted <- trimws(formatC(round(scores, 3), format = "f", digits = 3))
|
||||
|
||||
# sort on descending scores
|
||||
candidates_formatted <- candidates_formatted[order(1 - scores)]
|
||||
scores_formatted <- scores_formatted[order(1 - scores)]
|
||||
|
||||
candidates <- word_wrap(paste0("Also matched: ",
|
||||
vector_and(paste0(candidates_formatted,
|
||||
font_blue(paste0(" (", scores_formatted, ")"), collapse = NULL)),
|
||||
quotes = FALSE, sort = FALSE),
|
||||
ifelse(n_candidates > 25,
|
||||
paste0(" [showing first 25 of ", n_candidates, "]"),
|
||||
"")),
|
||||
extra_indent = nchar("Also matched: "))
|
||||
} else {
|
||||
candidates <- ""
|
||||
}
|
||||
@@ -1917,23 +1917,24 @@ print.mo_uncertainties <- function(x, ...) {
|
||||
n = x[i, ]$fullname),
|
||||
3),
|
||||
format = "f", digits = 3))
|
||||
msg <- paste(msg,
|
||||
txt <- paste(txt,
|
||||
paste0(
|
||||
strwrap(
|
||||
paste0('"', x[i, ]$input, '" -> ',
|
||||
paste0('"', x[i, ]$input, '"',
|
||||
" -> ",
|
||||
paste0(font_bold(font_italic(x[i, ]$fullname)),
|
||||
ifelse(!is.na(x[i, ]$renamed_to), paste(", renamed to", font_italic(x[i, ]$renamed_to)), ""),
|
||||
" (", x[i, ]$mo,
|
||||
", matching score = ", score,
|
||||
", ", font_blue(score),
|
||||
") ")),
|
||||
width = 0.98 * getOption("width"),
|
||||
exdent = nchar(x[i, ]$input) + 6),
|
||||
collapse = "\n"),
|
||||
candidates,
|
||||
sep = "\n")
|
||||
msg <- paste0(gsub("\n\n", "\n", msg), "\n\n")
|
||||
txt <- paste0(gsub("\n\n", "\n", txt), "\n\n")
|
||||
}
|
||||
cat(msg)
|
||||
cat(txt)
|
||||
}
|
||||
|
||||
#' @rdname as.mo
|
||||
@@ -2039,17 +2040,19 @@ parse_and_convert <- function(x) {
|
||||
x <- as.data.frame(x, stringsAsFactors = FALSE)[[1]]
|
||||
}
|
||||
}
|
||||
x[is.null(x)] <- NA
|
||||
parsed <- iconv(x, to = "UTF-8")
|
||||
parsed <- iconv(as.character(x), to = "UTF-8")
|
||||
parsed[is.na(parsed) & !is.na(x)] <- iconv(x[is.na(parsed) & !is.na(x)], from = "Latin1", to = "ASCII//TRANSLIT")
|
||||
parsed <- gsub('"', "", parsed, fixed = TRUE)
|
||||
parsed <- gsub(" +", " ", parsed, perl = TRUE)
|
||||
parsed <- trimws(parsed)
|
||||
parsed
|
||||
}, error = function(e) stop(e$message, call. = FALSE)) # this will also be thrown when running `as.mo(no_existing_object)`
|
||||
parsed
|
||||
}
|
||||
|
||||
replace_old_mo_codes <- function(x, property) {
|
||||
# this function transform old MO codes to current codes, such as:
|
||||
# B_ESCH_COL (AMR v0.5.0) -> B_ESCHR_COLI
|
||||
ind <- x %like_case% "^[A-Z]_[A-Z_]+$" & !x %in% MO_lookup$mo
|
||||
if (any(ind)) {
|
||||
# get the ones that match
|
||||
@@ -2069,6 +2072,12 @@ replace_old_mo_codes <- function(x, property) {
|
||||
MO_lookup$fullname_lower %like_case% name]
|
||||
if (length(results) > 1) {
|
||||
all_direct_matches <<- FALSE
|
||||
} else if (length(results) == 0) {
|
||||
# not found, so now search in old taxonomic names
|
||||
results <- MO.old_lookup$fullname_new[MO.old_lookup$fullname_lower %like% name]
|
||||
if (length(results) > 0) {
|
||||
results <- MO_lookup$mo[match(results, MO_lookup$fullname)]
|
||||
}
|
||||
}
|
||||
results[1L]
|
||||
}), use.names = FALSE)
|
||||
@@ -2076,6 +2085,8 @@ replace_old_mo_codes <- function(x, property) {
|
||||
# assign on places where a match was found
|
||||
x[ind] <- solved
|
||||
n_matched <- length(affected[!is.na(affected)])
|
||||
n_solved <- length(affected[!is.na(solved)])
|
||||
n_unsolved <- length(affected[is.na(solved)])
|
||||
n_unique <- length(affected_unique[!is.na(affected_unique)])
|
||||
if (n_unique < n_matched) {
|
||||
n_unique <- paste0(n_unique, " unique, ")
|
||||
@@ -2089,12 +2100,17 @@ replace_old_mo_codes <- function(x, property) {
|
||||
"Please update your MO codes with `as.mo()` to increase speed."),
|
||||
call = FALSE)
|
||||
} else {
|
||||
warning_(paste0(n_matched, " old MO code", ifelse(n_matched == 1, "", "s"),
|
||||
" (", n_unique, "from a previous AMR package version) ",
|
||||
ifelse(n_matched == 1, "was", "were"),
|
||||
warning_(paste0("The input contained ", n_matched,
|
||||
" old MO code", ifelse(n_matched == 1, "", "s"),
|
||||
" (", n_unique, "from a previous AMR package version). ",
|
||||
n_solved, " old MO code", ifelse(n_solved == 1, "", "s"),
|
||||
ifelse(n_solved == 1, " was", " were"),
|
||||
ifelse(all_direct_matches, " updated ", font_bold(" guessed ")),
|
||||
"to ", ifelse(n_matched == 1, "a ", ""),
|
||||
"currently used MO code", ifelse(n_matched == 1, "", "s"), "."),
|
||||
"to ", ifelse(n_solved == 1, "a ", ""),
|
||||
"currently used MO code", ifelse(n_solved == 1, "", "s"),
|
||||
ifelse(n_unsolved > 0,
|
||||
paste0(" and ", n_unsolved, " old MO code", ifelse(n_unsolved == 1, "", "s"), " could not be updated."),
|
||||
".")),
|
||||
call = FALSE)
|
||||
}
|
||||
}
|
||||
|
||||
@@ -46,6 +46,8 @@
|
||||
#'
|
||||
#' The grouping into human pathogenic prevalence (\eqn{p}) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. **Group 1** (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is *Enterococcus*, *Staphylococcus* or *Streptococcus*. This group consequently contains all common Gram-negative bacteria, such as *Pseudomonas* and *Legionella* and all species within the order Enterobacterales. **Group 2** consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is *Absidia*, *Acremonium*, *Actinotignum*, *Alternaria*, *Anaerosalibacter*, *Apophysomyces*, *Arachnia*, *Aspergillus*, *Aureobacterium*, *Aureobasidium*, *Bacteroides*, *Basidiobolus*, *Beauveria*, *Blastocystis*, *Branhamella*, *Calymmatobacterium*, *Candida*, *Capnocytophaga*, *Catabacter*, *Chaetomium*, *Chryseobacterium*, *Chryseomonas*, *Chrysonilia*, *Cladophialophora*, *Cladosporium*, *Conidiobolus*, *Cryptococcus*, *Curvularia*, *Exophiala*, *Exserohilum*, *Flavobacterium*, *Fonsecaea*, *Fusarium*, *Fusobacterium*, *Hendersonula*, *Hypomyces*, *Koserella*, *Lelliottia*, *Leptosphaeria*, *Leptotrichia*, *Malassezia*, *Malbranchea*, *Mortierella*, *Mucor*, *Mycocentrospora*, *Mycoplasma*, *Nectria*, *Ochroconis*, *Oidiodendron*, *Phoma*, *Piedraia*, *Pithomyces*, *Pityrosporum*, *Prevotella*, *Pseudallescheria*, *Rhizomucor*, *Rhizopus*, *Rhodotorula*, *Scolecobasidium*, *Scopulariopsis*, *Scytalidium*, *Sporobolomyces*, *Stachybotrys*, *Stomatococcus*, *Treponema*, *Trichoderma*, *Trichophyton*, *Trichosporon*, *Tritirachium* or *Ureaplasma*. **Group 3** consists of all other microorganisms.
|
||||
#'
|
||||
#' All characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
|
||||
#'
|
||||
#' All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., `"E. coli"` will return the microbial ID of *Escherichia coli* (\eqn{m = `r round(mo_matching_score("E. coli", "Escherichia coli"), 3)`}, a highly prevalent microorganism found in humans) and not *Entamoeba coli* (\eqn{m = `r round(mo_matching_score("E. coli", "Entamoeba coli"), 3)`}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
|
||||
#' @export
|
||||
#' @inheritSection AMR Reference Data Publicly Available
|
||||
|
||||
+53
-67
@@ -42,7 +42,7 @@
|
||||
#'
|
||||
#' Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions [mo_kingdom()] and [mo_domain()] return the exact same results.
|
||||
#'
|
||||
#' The Gram stain - [mo_gramstain()] - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, [PMID 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318)), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`. Functions [mo_is_gram_negative()] and [mo_is_gram_positive()] always return `TRUE` or `FALSE` (except when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.
|
||||
#' The Gram stain - [mo_gramstain()] - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, [PMID 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318)), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive, except for members of the class Negativicutes which are Gram-negative. Members of other bacterial phyla are all considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`. Functions [mo_is_gram_negative()] and [mo_is_gram_positive()] always return `TRUE` or `FALSE` (except when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.
|
||||
#'
|
||||
#' Determination of yeasts - [mo_is_yeast()] - will be based on the taxonomic kingdom and class. *Budding yeasts* are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). *True yeasts* are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return `TRUE`. It returns `FALSE` otherwise (except when the input is `NA` or the MO code is `UNKNOWN`).
|
||||
#'
|
||||
@@ -52,7 +52,7 @@
|
||||
#'
|
||||
#' The function [mo_url()] will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
|
||||
#'
|
||||
#' SNOMED codes - [mo_snomed()] - are from the `r SNOMED_VERSION$current_source`. See the [microorganisms] data set for more info.
|
||||
#' SNOMED codes - [mo_snomed()] - are from the `r SNOMED_VERSION$current_source`. See *Source* and the [microorganisms] data set for more info.
|
||||
#' @inheritSection mo_matching_score Matching Score for Microorganisms
|
||||
#' @inheritSection catalogue_of_life Catalogue of Life
|
||||
#' @inheritSection as.mo Source
|
||||
@@ -65,7 +65,7 @@
|
||||
#' - A [numeric] in case of [mo_snomed()]
|
||||
#' - A [character] in all other cases
|
||||
#' @export
|
||||
#' @seealso [microorganisms]
|
||||
#' @seealso Data set [microorganisms]
|
||||
#' @inheritSection AMR Reference Data Publicly Available
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
#' @examples
|
||||
@@ -216,15 +216,17 @@ mo_shortname <- function(x, language = get_locale(), ...) {
|
||||
shortnames[shortnames == "S. coagulase-negative"] <- "CoNS"
|
||||
shortnames[shortnames == "S. coagulase-positive"] <- "CoPS"
|
||||
# exceptions for streptococci: Group A Streptococcus -> GAS
|
||||
shortnames[shortnames %like% "S. group [ABCDFGHK]"] <- paste0("G", gsub("S. group ([ABCDFGHK])", "\\1", shortnames[shortnames %like% "S. group [ABCDFGHK]"]), "S")
|
||||
shortnames[shortnames %like% "S. group [ABCDFGHK]"] <- paste0("G", gsub("S. group ([ABCDFGHK])", "\\1", shortnames[shortnames %like% "S. group [ABCDFGHK]"], perl = TRUE), "S")
|
||||
# unknown species etc.
|
||||
shortnames[shortnames %like% "unknown"] <- paste0("(", trimws(gsub("[^a-zA-Z -]", "", shortnames[shortnames %like% "unknown"])), ")")
|
||||
shortnames[shortnames %like% "unknown"] <- paste0("(", trimws(gsub("[^a-zA-Z -]", "", shortnames[shortnames %like% "unknown"], perl = TRUE)), ")")
|
||||
|
||||
shortnames[is.na(x.mo)] <- NA_character_
|
||||
load_mo_failures_uncertainties_renamed(metadata)
|
||||
translate_AMR(shortnames, language = language, only_unknown = FALSE, only_affect_mo_names = TRUE)
|
||||
}
|
||||
|
||||
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_subspecies <- function(x, language = get_locale(), ...) {
|
||||
@@ -362,25 +364,18 @@ mo_gramstain <- function(x, language = get_locale(), ...) {
|
||||
x.mo <- as.mo(x, language = language, ...)
|
||||
metadata <- get_mo_failures_uncertainties_renamed()
|
||||
|
||||
x.phylum <- mo_phylum(x.mo)
|
||||
# DETERMINE GRAM STAIN FOR BACTERIA
|
||||
# Source: https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=956097
|
||||
# It says this:
|
||||
# Kingdom Bacteria (Cavalier-Smith, 2002)
|
||||
# Subkingdom Posibacteria (Cavalier-Smith, 2002)
|
||||
# Direct Children:
|
||||
# Phylum Actinobacteria (Cavalier-Smith, 2002)
|
||||
# Phylum Chloroflexi (Garrity and Holt, 2002)
|
||||
# Phylum Firmicutes (corrig. Gibbons and Murray, 1978)
|
||||
# Phylum Tenericutes (Murray, 1984)
|
||||
x <- NA_character_
|
||||
x <- rep(NA_character_, length(x))
|
||||
# make all bacteria Gram negative
|
||||
x[mo_kingdom(x.mo) == "Bacteria"] <- "Gram-negative"
|
||||
# overwrite these phyla with Gram positive
|
||||
x[x.phylum %in% c("Actinobacteria",
|
||||
"Chloroflexi",
|
||||
"Firmicutes",
|
||||
"Tenericutes")
|
||||
# overwrite these 4 phyla with Gram-positives
|
||||
# Source: https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=956097 (Cavalier-Smith, 2002)
|
||||
x[(mo_phylum(x.mo) %in% c("Actinobacteria",
|
||||
"Chloroflexi",
|
||||
"Firmicutes",
|
||||
"Tenericutes") &
|
||||
# but class Negativicutes (of phylum Firmicutes) are Gram-negative!
|
||||
mo_class(x.mo) != "Negativicutes")
|
||||
# and of course our own ID for Gram-positives
|
||||
| x.mo == "B_GRAMP"] <- "Gram-positive"
|
||||
|
||||
load_mo_failures_uncertainties_renamed(metadata)
|
||||
@@ -475,11 +470,10 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_locale(), ...) {
|
||||
}
|
||||
|
||||
# show used version number once per session (pkg_env will reload every session)
|
||||
if (message_not_thrown_before("intrinsic_resistant_version", entire_session = TRUE)) {
|
||||
if (message_not_thrown_before("intrinsic_resistant_version.mo", entire_session = TRUE)) {
|
||||
message_("Determining intrinsic resistance based on ",
|
||||
format_eucast_version_nr(3.2, markdown = FALSE), ". ",
|
||||
font_red("This note will be shown once per session."))
|
||||
remember_thrown_message("intrinsic_resistant_version", entire_session = TRUE)
|
||||
}
|
||||
|
||||
# runs against internal vector: INTRINSIC_R (see zzz.R)
|
||||
@@ -524,7 +518,7 @@ mo_authors <- function(x, language = get_locale(), ...) {
|
||||
|
||||
x <- mo_validate(x = x, property = "ref", language = language, ...)
|
||||
# remove last 4 digits and presumably the comma and space that preceed them
|
||||
x[!is.na(x)] <- gsub(",? ?[0-9]{4}", "", x[!is.na(x)])
|
||||
x[!is.na(x)] <- gsub(",? ?[0-9]{4}", "", x[!is.na(x)], perl = TRUE)
|
||||
suppressWarnings(x)
|
||||
}
|
||||
|
||||
@@ -540,7 +534,7 @@ mo_year <- function(x, language = get_locale(), ...) {
|
||||
|
||||
x <- mo_validate(x = x, property = "ref", language = language, ...)
|
||||
# get last 4 digits
|
||||
x[!is.na(x)] <- gsub(".*([0-9]{4})$", "\\1", x[!is.na(x)])
|
||||
x[!is.na(x)] <- gsub(".*([0-9]{4})$", "\\1", x[!is.na(x)], perl = TRUE)
|
||||
suppressWarnings(as.integer(x))
|
||||
}
|
||||
|
||||
@@ -570,17 +564,17 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
|
||||
x <- as.mo(x, language = language, ...)
|
||||
metadata <- get_mo_failures_uncertainties_renamed()
|
||||
|
||||
result <- list(kingdom = mo_kingdom(x, language = language),
|
||||
phylum = mo_phylum(x, language = language),
|
||||
class = mo_class(x, language = language),
|
||||
order = mo_order(x, language = language),
|
||||
family = mo_family(x, language = language),
|
||||
genus = mo_genus(x, language = language),
|
||||
species = mo_species(x, language = language),
|
||||
subspecies = mo_subspecies(x, language = language))
|
||||
out <- list(kingdom = mo_kingdom(x, language = language),
|
||||
phylum = mo_phylum(x, language = language),
|
||||
class = mo_class(x, language = language),
|
||||
order = mo_order(x, language = language),
|
||||
family = mo_family(x, language = language),
|
||||
genus = mo_genus(x, language = language),
|
||||
species = mo_species(x, language = language),
|
||||
subspecies = mo_subspecies(x, language = language))
|
||||
|
||||
load_mo_failures_uncertainties_renamed(metadata)
|
||||
result
|
||||
out
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
@@ -658,31 +652,23 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
|
||||
meet_criteria(open, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
mo <- as.mo(x = x, language = language, ... = ...)
|
||||
mo_names <- mo_name(mo)
|
||||
x.mo <- as.mo(x = x, language = language, ... = ...)
|
||||
metadata <- get_mo_failures_uncertainties_renamed()
|
||||
|
||||
df <- data.frame(mo, stringsAsFactors = FALSE) %pm>%
|
||||
pm_left_join(pm_select(microorganisms, mo, source, species_id), by = "mo")
|
||||
df$url <- ifelse(df$source == "CoL",
|
||||
paste0(CATALOGUE_OF_LIFE$url_CoL, "details/species/id/", df$species_id, "/"),
|
||||
NA_character_)
|
||||
df <- microorganisms[match(x.mo, microorganisms$mo), c("mo", "fullname", "source", "kingdom", "rank")]
|
||||
df$url <- ifelse(df$source == "LPSN",
|
||||
paste0(CATALOGUE_OF_LIFE$url_LPSN, "/species/", gsub(" ", "-", tolower(df$fullname), fixed = TRUE)),
|
||||
paste0(CATALOGUE_OF_LIFE$url_CoL, "/data/search?type=EXACT&q=", gsub(" ", "%20", df$fullname, fixed = TRUE)))
|
||||
|
||||
genera <- which(df$kingdom == "Bacteria" & df$rank == "genus")
|
||||
df$url[genera] <- gsub("/species/", "/genus/", df$url[genera], fixed = TRUE)
|
||||
subsp <- which(df$kingdom == "Bacteria" & df$rank %in% c("subsp.", "infraspecies"))
|
||||
df$url[subsp] <- gsub("/species/", "/subspecies/", df$url[subsp], fixed = TRUE)
|
||||
|
||||
u <- df$url
|
||||
u[mo_kingdom(mo) == "Bacteria"] <- paste0(CATALOGUE_OF_LIFE$url_LPSN, "/species/", gsub(" ", "-", tolower(mo_names), fixed = TRUE))
|
||||
u[mo_kingdom(mo) == "Bacteria" & mo_rank(mo) == "genus"] <- gsub("/species/",
|
||||
"/genus/",
|
||||
u[mo_kingdom(mo) == "Bacteria" & mo_rank(mo) == "genus"],
|
||||
fixed = TRUE)
|
||||
u[mo_kingdom(mo) == "Bacteria" &
|
||||
mo_rank(mo) %in% c("subsp.", "infraspecies")] <- gsub("/species/",
|
||||
"/subspecies/",
|
||||
u[mo_kingdom(mo) == "Bacteria" &
|
||||
mo_rank(mo) %in% c("subsp.", "infraspecies")],
|
||||
fixed = TRUE)
|
||||
names(u) <- df$fullname
|
||||
|
||||
names(u) <- mo_names
|
||||
|
||||
if (open == TRUE) {
|
||||
if (isTRUE(open)) {
|
||||
if (length(u) > 1) {
|
||||
warning_("Only the first URL will be opened, as `browseURL()` only suports one string.")
|
||||
}
|
||||
@@ -723,16 +709,17 @@ mo_validate <- function(x, property, language, ...) {
|
||||
|
||||
if (tryCatch(all(x[!is.na(x)] %in% MO_lookup$mo) & !has_Becker_or_Lancefield, error = function(e) FALSE)) {
|
||||
# special case for mo_* functions where class is already <mo>
|
||||
return(MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE])
|
||||
}
|
||||
|
||||
# try to catch an error when inputting an invalid argument
|
||||
# so the 'call.' can be set to FALSE
|
||||
tryCatch(x[1L] %in% MO_lookup[1, property, drop = TRUE],
|
||||
error = function(e) stop(e$message, call. = FALSE))
|
||||
x <- MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE]
|
||||
|
||||
if (!all(x[!is.na(x)] %in% MO_lookup[, property, drop = TRUE]) | has_Becker_or_Lancefield) {
|
||||
x <- exec_as.mo(x, property = property, language = language, ...)
|
||||
} else {
|
||||
# try to catch an error when inputting an invalid argument
|
||||
# so the 'call.' can be set to FALSE
|
||||
tryCatch(x[1L] %in% MO_lookup[1, property, drop = TRUE],
|
||||
error = function(e) stop(e$message, call. = FALSE))
|
||||
|
||||
if (!all(x[!is.na(x)] %in% MO_lookup[, property, drop = TRUE]) | has_Becker_or_Lancefield) {
|
||||
x <- exec_as.mo(x, property = property, language = language, ...)
|
||||
}
|
||||
}
|
||||
|
||||
if (property == "mo") {
|
||||
@@ -754,8 +741,7 @@ find_mo_col <- function(fn) {
|
||||
}, silent = TRUE)
|
||||
if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
|
||||
if (message_not_thrown_before(fn = fn)) {
|
||||
message_("Using column '", font_bold(mo), "' as input for ", fn, "()")
|
||||
remember_thrown_message(fn = fn)
|
||||
message_("Using column '", font_bold(mo), "' as input for `", fn, "()`")
|
||||
}
|
||||
return(df[, mo, drop = TRUE])
|
||||
} else {
|
||||
|
||||
@@ -90,7 +90,7 @@ pca <- function(x,
|
||||
# this is to support quoted variables: df %pm>% pca("mycol1", "mycol2")
|
||||
new_list[[i]] <- x[, new_list[[i]]]
|
||||
} else {
|
||||
# remove item - it's a argument like `center`
|
||||
# remove item - it's an argument like `center`
|
||||
new_list[[i]] <- NULL
|
||||
}
|
||||
}
|
||||
|
||||
@@ -25,16 +25,15 @@
|
||||
|
||||
#' Plotting for Classes `rsi`, `mic` and `disk`
|
||||
#'
|
||||
#' Functions to plot classes `rsi`, `mic` and `disk`, with support for base R and `ggplot2`.
|
||||
#' Functions to plot classes `rsi`, `mic` and `disk`, with support for base \R and `ggplot2`.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
#' @param x,data MIC values created with [as.mic()] or disk diffusion values created with [as.disk()]
|
||||
#' @param mapping aesthetic mappings to use for [`ggplot()`][ggplot2::ggplot()]
|
||||
#' @param main,title title of the plot
|
||||
#' @param xlab,ylab axis title
|
||||
#' @param x,object values created with [as.mic()], [as.disk()] or [as.rsi()] (or their `random_*` variants, such as [random_mic()])
|
||||
#' @param mo any (vector of) text that can be coerced to a valid microorganism code with [as.mo()]
|
||||
#' @param ab any (vector of) text that can be coerced to a valid antimicrobial code with [as.ab()]
|
||||
#' @param guideline interpretation guideline to use, defaults to the latest included EUCAST guideline, see *Details*
|
||||
#' @param main,title title of the plot
|
||||
#' @param xlab,ylab axis title
|
||||
#' @param colours_RSI colours to use for filling in the bars, must be a vector of three values (in the order R, S and I). The default colours are colour-blind friendly.
|
||||
#' @param language language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant', defaults to system language (see [get_locale()]) and can be overwritten by setting the option `AMR_locale`, e.g. `options(AMR_locale = "de")`, see [translate]. Use `language = NULL` or `language = ""` to prevent translation.
|
||||
#' @param expand a [logical] to indicate whether the range on the x axis should be expanded between the lowest and highest value. For MIC values, intermediate values will be factors of 2 starting from the highest MIC value. For disk diameters, the whole diameter range will be filled.
|
||||
@@ -46,8 +45,10 @@
|
||||
#' Simply using `"CLSI"` or `"EUCAST"` as input will automatically select the latest version of that guideline.
|
||||
#' @name plot
|
||||
#' @rdname plot
|
||||
#' @return The `ggplot` functions return a [`ggplot`][ggplot2::ggplot()] model that is extendible with any `ggplot2` function.
|
||||
#' @param ... arguments passed on to [as.rsi()]
|
||||
#' @return The `autoplot()` functions return a [`ggplot`][ggplot2::ggplot()] model that is extendible with any `ggplot2` function.
|
||||
#'
|
||||
#' The `fortify()` functions return a [data.frame] as an extension for usage in the [ggplot2::ggplot()] function.
|
||||
#' @param ... arguments passed on to methods
|
||||
#' @examples
|
||||
#' some_mic_values <- random_mic(size = 100)
|
||||
#' some_disk_values <- random_disk(size = 100, mo = "Escherichia coli", ab = "cipro")
|
||||
@@ -63,9 +64,9 @@
|
||||
#'
|
||||
#' \donttest{
|
||||
#' if (require("ggplot2")) {
|
||||
#' ggplot(some_mic_values)
|
||||
#' ggplot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
|
||||
#' ggplot(some_rsi_values)
|
||||
#' autoplot(some_mic_values)
|
||||
#' autoplot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
|
||||
#' autoplot(some_rsi_values)
|
||||
#' }
|
||||
#' }
|
||||
NULL
|
||||
@@ -75,22 +76,22 @@ NULL
|
||||
#' @export
|
||||
#' @rdname plot
|
||||
plot.mic <- function(x,
|
||||
main = paste("MIC values of", deparse(substitute(x))),
|
||||
ylab = "Frequency",
|
||||
xlab = "Minimum Inhibitory Concentration (mg/L)",
|
||||
mo = NULL,
|
||||
ab = NULL,
|
||||
guideline = "EUCAST",
|
||||
main = paste("MIC values of", deparse(substitute(x))),
|
||||
ylab = "Frequency",
|
||||
xlab = "Minimum Inhibitory Concentration (mg/L)",
|
||||
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
|
||||
language = get_locale(),
|
||||
expand = TRUE,
|
||||
...) {
|
||||
meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
|
||||
meet_criteria(ylab, allow_class = "character", has_length = 1)
|
||||
meet_criteria(xlab, allow_class = "character", has_length = 1)
|
||||
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
|
||||
meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
|
||||
meet_criteria(guideline, allow_class = "character", has_length = 1)
|
||||
meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
|
||||
meet_criteria(ylab, allow_class = "character", has_length = 1)
|
||||
meet_criteria(xlab, allow_class = "character", has_length = 1)
|
||||
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(expand, allow_class = "logical", has_length = 1)
|
||||
@@ -161,12 +162,12 @@ plot.mic <- function(x,
|
||||
#' @export
|
||||
#' @noRd
|
||||
barplot.mic <- function(height,
|
||||
main = paste("MIC values of", deparse(substitute(height))),
|
||||
ylab = "Frequency",
|
||||
xlab = "Minimum Inhibitory Concentration (mg/L)",
|
||||
mo = NULL,
|
||||
ab = NULL,
|
||||
guideline = "EUCAST",
|
||||
main = paste("MIC values of", deparse(substitute(height))),
|
||||
ylab = "Frequency",
|
||||
xlab = "Minimum Inhibitory Concentration (mg/L)",
|
||||
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
|
||||
language = get_locale(),
|
||||
expand = TRUE,
|
||||
@@ -202,28 +203,27 @@ barplot.mic <- function(height,
|
||||
...)
|
||||
}
|
||||
|
||||
#' @method ggplot mic
|
||||
#' @method autoplot mic
|
||||
#' @rdname plot
|
||||
# will be exported using s3_register() in R/zzz.R
|
||||
ggplot.mic <- function(data,
|
||||
mapping = NULL,
|
||||
title = paste("MIC values of", deparse(substitute(data))),
|
||||
ylab = "Frequency",
|
||||
xlab = "Minimum Inhibitory Concentration (mg/L)",
|
||||
mo = NULL,
|
||||
ab = NULL,
|
||||
guideline = "EUCAST",
|
||||
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
|
||||
language = get_locale(),
|
||||
expand = TRUE,
|
||||
...) {
|
||||
autoplot.mic <- function(object,
|
||||
mo = NULL,
|
||||
ab = NULL,
|
||||
guideline = "EUCAST",
|
||||
title = paste("MIC values of", deparse(substitute(object))),
|
||||
ylab = "Frequency",
|
||||
xlab = "Minimum Inhibitory Concentration (mg/L)",
|
||||
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
|
||||
language = get_locale(),
|
||||
expand = TRUE,
|
||||
...) {
|
||||
stop_ifnot_installed("ggplot2")
|
||||
meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
|
||||
meet_criteria(ylab, allow_class = "character", has_length = 1)
|
||||
meet_criteria(xlab, allow_class = "character", has_length = 1)
|
||||
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
|
||||
meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
|
||||
meet_criteria(guideline, allow_class = "character", has_length = 1)
|
||||
meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
|
||||
meet_criteria(ylab, allow_class = "character", has_length = 1)
|
||||
meet_criteria(xlab, allow_class = "character", has_length = 1)
|
||||
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(expand, allow_class = "logical", has_length = 1)
|
||||
@@ -243,7 +243,7 @@ ggplot.mic <- function(data,
|
||||
title <- gsub(" +", " ", paste0(title, collapse = " "))
|
||||
}
|
||||
|
||||
x <- plot_prepare_table(data, expand = expand)
|
||||
x <- plot_prepare_table(object, expand = expand)
|
||||
cols_sub <- plot_colours_subtitle_guideline(x = x,
|
||||
mo = mo,
|
||||
ab = ab,
|
||||
@@ -262,22 +262,20 @@ ggplot.mic <- function(data,
|
||||
levels = translate_AMR(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"),
|
||||
language = language),
|
||||
ordered = TRUE)
|
||||
if (!is.null(mapping)) {
|
||||
p <- ggplot2::ggplot(df, mapping = mapping)
|
||||
} else {
|
||||
p <- ggplot2::ggplot(df)
|
||||
}
|
||||
p <- ggplot2::ggplot(df)
|
||||
|
||||
if (any(colours_RSI %in% cols_sub$cols)) {
|
||||
vals <- c("Resistant" = colours_RSI[1],
|
||||
"Susceptible" = colours_RSI[2],
|
||||
"Incr. exposure" = colours_RSI[3],
|
||||
"Susceptible, incr. exp." = colours_RSI[3],
|
||||
"Intermediate" = colours_RSI[3])
|
||||
names(vals) <- translate_AMR(names(vals), language = language)
|
||||
p <- p +
|
||||
ggplot2::geom_col(ggplot2::aes(x = mic, y = count, fill = cols)) +
|
||||
# limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
|
||||
ggplot2::scale_fill_manual(values = vals,
|
||||
name = NULL)
|
||||
name = NULL,
|
||||
limits = force)
|
||||
} else {
|
||||
p <- p +
|
||||
ggplot2::geom_col(ggplot2::aes(x = mic, y = count))
|
||||
@@ -287,6 +285,14 @@ ggplot.mic <- function(data,
|
||||
ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
|
||||
}
|
||||
|
||||
#' @method fortify mic
|
||||
#' @rdname plot
|
||||
# will be exported using s3_register() in R/zzz.R
|
||||
fortify.mic <- function(object, ...) {
|
||||
stats::setNames(as.data.frame(plot_prepare_table(object, expand = FALSE)),
|
||||
c("x", "y"))
|
||||
}
|
||||
|
||||
#' @method plot disk
|
||||
#' @export
|
||||
#' @importFrom graphics barplot axis mtext legend
|
||||
@@ -420,21 +426,20 @@ barplot.disk <- function(height,
|
||||
...)
|
||||
}
|
||||
|
||||
#' @method ggplot disk
|
||||
#' @method autoplot disk
|
||||
#' @rdname plot
|
||||
# will be exported using s3_register() in R/zzz.R
|
||||
ggplot.disk <- function(data,
|
||||
mapping = NULL,
|
||||
title = paste("Disk zones of", deparse(substitute(data))),
|
||||
ylab = "Frequency",
|
||||
xlab = "Disk diffusion diameter (mm)",
|
||||
mo = NULL,
|
||||
ab = NULL,
|
||||
guideline = "EUCAST",
|
||||
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
|
||||
language = get_locale(),
|
||||
expand = TRUE,
|
||||
...) {
|
||||
autoplot.disk <- function(object,
|
||||
mo = NULL,
|
||||
ab = NULL,
|
||||
title = paste("Disk zones of", deparse(substitute(object))),
|
||||
ylab = "Frequency",
|
||||
xlab = "Disk diffusion diameter (mm)",
|
||||
guideline = "EUCAST",
|
||||
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
|
||||
language = get_locale(),
|
||||
expand = TRUE,
|
||||
...) {
|
||||
stop_ifnot_installed("ggplot2")
|
||||
meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
|
||||
meet_criteria(ylab, allow_class = "character", has_length = 1)
|
||||
@@ -461,7 +466,7 @@ ggplot.disk <- function(data,
|
||||
title <- gsub(" +", " ", paste0(title, collapse = " "))
|
||||
}
|
||||
|
||||
x <- plot_prepare_table(data, expand = expand)
|
||||
x <- plot_prepare_table(object, expand = expand)
|
||||
cols_sub <- plot_colours_subtitle_guideline(x = x,
|
||||
mo = mo,
|
||||
ab = ab,
|
||||
@@ -481,22 +486,20 @@ ggplot.disk <- function(data,
|
||||
levels = translate_AMR(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"),
|
||||
language = language),
|
||||
ordered = TRUE)
|
||||
if (!is.null(mapping)) {
|
||||
p <- ggplot2::ggplot(df, mapping = mapping)
|
||||
} else {
|
||||
p <- ggplot2::ggplot(df)
|
||||
}
|
||||
p <- ggplot2::ggplot(df)
|
||||
|
||||
if (any(colours_RSI %in% cols_sub$cols)) {
|
||||
vals <- c("Resistant" = colours_RSI[1],
|
||||
"Susceptible" = colours_RSI[2],
|
||||
"Incr. exposure" = colours_RSI[3],
|
||||
"Susceptible, incr. exp." = colours_RSI[3],
|
||||
"Intermediate" = colours_RSI[3])
|
||||
names(vals) <- translate_AMR(names(vals), language = language)
|
||||
p <- p +
|
||||
ggplot2::geom_col(ggplot2::aes(x = disk, y = count, fill = cols)) +
|
||||
# limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
|
||||
ggplot2::scale_fill_manual(values = vals,
|
||||
name = NULL)
|
||||
name = NULL,
|
||||
limits = force)
|
||||
} else {
|
||||
p <- p +
|
||||
ggplot2::geom_col(ggplot2::aes(x = disk, y = count))
|
||||
@@ -506,6 +509,14 @@ ggplot.disk <- function(data,
|
||||
ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
|
||||
}
|
||||
|
||||
#' @method fortify disk
|
||||
#' @rdname plot
|
||||
# will be exported using s3_register() in R/zzz.R
|
||||
fortify.disk <- function(object, ...) {
|
||||
stats::setNames(as.data.frame(plot_prepare_table(object, expand = FALSE)),
|
||||
c("x", "y"))
|
||||
}
|
||||
|
||||
#' @method plot rsi
|
||||
#' @export
|
||||
#' @importFrom graphics plot text axis
|
||||
@@ -604,17 +615,16 @@ barplot.rsi <- function(height,
|
||||
axis(2, seq(0, max(x)))
|
||||
}
|
||||
|
||||
#' @method ggplot rsi
|
||||
#' @method autoplot rsi
|
||||
#' @rdname plot
|
||||
# will be exported using s3_register() in R/zzz.R
|
||||
ggplot.rsi <- function(data,
|
||||
mapping = NULL,
|
||||
title = paste("Resistance Overview of", deparse(substitute(data))),
|
||||
xlab = "Antimicrobial Interpretation",
|
||||
ylab = "Frequency",
|
||||
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
|
||||
language = get_locale(),
|
||||
...) {
|
||||
autoplot.rsi <- function(object,
|
||||
title = paste("Resistance Overview of", deparse(substitute(object))),
|
||||
xlab = "Antimicrobial Interpretation",
|
||||
ylab = "Frequency",
|
||||
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
|
||||
language = get_locale(),
|
||||
...) {
|
||||
stop_ifnot_installed("ggplot2")
|
||||
meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
|
||||
meet_criteria(ylab, allow_class = "character", has_length = 1)
|
||||
@@ -640,29 +650,34 @@ ggplot.rsi <- function(data,
|
||||
colours_RSI <- rep(colours_RSI, 3)
|
||||
}
|
||||
|
||||
df <- as.data.frame(table(data), stringsAsFactors = TRUE)
|
||||
df <- as.data.frame(table(object), stringsAsFactors = TRUE)
|
||||
colnames(df) <- c("rsi", "count")
|
||||
if (!is.null(mapping)) {
|
||||
p <- ggplot2::ggplot(df, mapping = mapping)
|
||||
} else {
|
||||
p <- ggplot2::ggplot(df)
|
||||
}
|
||||
|
||||
p +
|
||||
ggplot2::ggplot(df) +
|
||||
ggplot2::geom_col(ggplot2::aes(x = rsi, y = count, fill = rsi)) +
|
||||
# limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
|
||||
ggplot2::scale_fill_manual(values = c("R" = colours_RSI[1],
|
||||
"S" = colours_RSI[2],
|
||||
"I" = colours_RSI[3])) +
|
||||
"I" = colours_RSI[3]),
|
||||
limits = force) +
|
||||
ggplot2::labs(title = title, x = xlab, y = ylab) +
|
||||
ggplot2::theme(legend.position = "none")
|
||||
}
|
||||
|
||||
#' @method fortify rsi
|
||||
#' @rdname plot
|
||||
# will be exported using s3_register() in R/zzz.R
|
||||
fortify.rsi <- function(object, ...) {
|
||||
stats::setNames(as.data.frame(table(object)),
|
||||
c("x", "y"))
|
||||
}
|
||||
|
||||
plot_prepare_table <- function(x, expand) {
|
||||
x <- x[!is.na(x)]
|
||||
stop_if(length(x) == 0, "no observations to plot", call = FALSE)
|
||||
if (is.mic(x)) {
|
||||
if (expand == TRUE) {
|
||||
# expand range for MIC by adding factors of 2 from lowest to highest so all MICs in between also print
|
||||
valid_lvls <- levels(x)
|
||||
extra_range <- max(x) / 2
|
||||
while (min(extra_range) / 2 > min(x)) {
|
||||
extra_range <- c(min(extra_range) / 2, extra_range)
|
||||
@@ -671,7 +686,7 @@ plot_prepare_table <- function(x, expand) {
|
||||
extra_range <- rep(0, length(extra_range))
|
||||
names(extra_range) <- nms
|
||||
x <- table(droplevels(x, as.mic = FALSE))
|
||||
extra_range <- extra_range[!names(extra_range) %in% names(x)]
|
||||
extra_range <- extra_range[!names(extra_range) %in% names(x) & names(extra_range) %in% valid_lvls]
|
||||
x <- as.table(c(x, extra_range))
|
||||
} else {
|
||||
x <- table(droplevels(x, as.mic = FALSE))
|
||||
@@ -696,7 +711,7 @@ plot_prepare_table <- function(x, expand) {
|
||||
plot_name_of_I <- function(guideline) {
|
||||
if (guideline %unlike% "CLSI" && as.double(gsub("[^0-9]+", "", guideline)) >= 2019) {
|
||||
# interpretation since 2019
|
||||
"Incr. exposure"
|
||||
"Susceptible, incr. exp."
|
||||
} else {
|
||||
# interpretation until 2019
|
||||
"Intermediate"
|
||||
|
||||
+67
-51
@@ -167,12 +167,14 @@ resistance <- function(...,
|
||||
minimum = 30,
|
||||
as_percent = FALSE,
|
||||
only_all_tested = FALSE) {
|
||||
rsi_calc(...,
|
||||
ab_result = "R",
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = FALSE)
|
||||
tryCatch(
|
||||
rsi_calc(...,
|
||||
ab_result = "R",
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = FALSE),
|
||||
error = function(e) stop_(e$message, call = -5))
|
||||
}
|
||||
|
||||
#' @rdname proportion
|
||||
@@ -181,12 +183,14 @@ susceptibility <- function(...,
|
||||
minimum = 30,
|
||||
as_percent = FALSE,
|
||||
only_all_tested = FALSE) {
|
||||
rsi_calc(...,
|
||||
ab_result = c("S", "I"),
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = FALSE)
|
||||
tryCatch(
|
||||
rsi_calc(...,
|
||||
ab_result = c("S", "I"),
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = FALSE),
|
||||
error = function(e) stop_(e$message, call = -5))
|
||||
}
|
||||
|
||||
#' @rdname proportion
|
||||
@@ -195,12 +199,14 @@ proportion_R <- function(...,
|
||||
minimum = 30,
|
||||
as_percent = FALSE,
|
||||
only_all_tested = FALSE) {
|
||||
rsi_calc(...,
|
||||
ab_result = "R",
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = FALSE)
|
||||
tryCatch(
|
||||
rsi_calc(...,
|
||||
ab_result = "R",
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = FALSE),
|
||||
error = function(e) stop_(e$message, call = -5))
|
||||
}
|
||||
|
||||
#' @rdname proportion
|
||||
@@ -209,12 +215,14 @@ proportion_IR <- function(...,
|
||||
minimum = 30,
|
||||
as_percent = FALSE,
|
||||
only_all_tested = FALSE) {
|
||||
rsi_calc(...,
|
||||
ab_result = c("I", "R"),
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = FALSE)
|
||||
tryCatch(
|
||||
rsi_calc(...,
|
||||
ab_result = c("I", "R"),
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = FALSE),
|
||||
error = function(e) stop_(e$message, call = -5))
|
||||
}
|
||||
|
||||
#' @rdname proportion
|
||||
@@ -223,12 +231,14 @@ proportion_I <- function(...,
|
||||
minimum = 30,
|
||||
as_percent = FALSE,
|
||||
only_all_tested = FALSE) {
|
||||
rsi_calc(...,
|
||||
ab_result = "I",
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = FALSE)
|
||||
tryCatch(
|
||||
rsi_calc(...,
|
||||
ab_result = "I",
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = FALSE),
|
||||
error = function(e) stop_(e$message, call = -5))
|
||||
}
|
||||
|
||||
#' @rdname proportion
|
||||
@@ -237,12 +247,14 @@ proportion_SI <- function(...,
|
||||
minimum = 30,
|
||||
as_percent = FALSE,
|
||||
only_all_tested = FALSE) {
|
||||
rsi_calc(...,
|
||||
ab_result = c("S", "I"),
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = FALSE)
|
||||
tryCatch(
|
||||
rsi_calc(...,
|
||||
ab_result = c("S", "I"),
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = FALSE),
|
||||
error = function(e) stop_(e$message, call = -5))
|
||||
}
|
||||
|
||||
#' @rdname proportion
|
||||
@@ -251,12 +263,14 @@ proportion_S <- function(...,
|
||||
minimum = 30,
|
||||
as_percent = FALSE,
|
||||
only_all_tested = FALSE) {
|
||||
rsi_calc(...,
|
||||
ab_result = "S",
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = FALSE)
|
||||
tryCatch(
|
||||
rsi_calc(...,
|
||||
ab_result = "S",
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = FALSE),
|
||||
error = function(e) stop_(e$message, call = -5))
|
||||
}
|
||||
|
||||
#' @rdname proportion
|
||||
@@ -268,13 +282,15 @@ proportion_df <- function(data,
|
||||
as_percent = FALSE,
|
||||
combine_SI = TRUE,
|
||||
combine_IR = FALSE) {
|
||||
rsi_calc_df(type = "proportion",
|
||||
data = data,
|
||||
translate_ab = translate_ab,
|
||||
language = language,
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
combine_SI = combine_SI,
|
||||
combine_IR = combine_IR,
|
||||
combine_SI_missing = missing(combine_SI))
|
||||
tryCatch(
|
||||
rsi_calc_df(type = "proportion",
|
||||
data = data,
|
||||
translate_ab = translate_ab,
|
||||
language = language,
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
combine_SI = combine_SI,
|
||||
combine_IR = combine_IR,
|
||||
combine_SI_missing = missing(combine_SI)),
|
||||
error = function(e) stop_(e$message, call = -5))
|
||||
}
|
||||
|
||||
+37
-21
@@ -27,12 +27,12 @@
|
||||
#'
|
||||
#' These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial agent, the generated results will reflect reality as much as possible.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param size desired size of the returned vector
|
||||
#' @param size desired size of the returned vector. If used in a [data.frame] call or `dplyr` verb, will get the current (group) size if left blank.
|
||||
#' @param mo any [character] that can be coerced to a valid microorganism code with [as.mo()]
|
||||
#' @param ab any [character] that can be coerced to a valid antimicrobial agent code with [as.ab()]
|
||||
#' @param prob_RSI a vector of length 3: the probabilities for R (1st value), S (2nd value) and I (3rd value)
|
||||
#' @param prob_RSI a vector of length 3: the probabilities for "R" (1st value), "S" (2nd value) and "I" (3rd value)
|
||||
#' @param ... ignored, only in place to allow future extensions
|
||||
#' @details The base R function [sample()] is used for generating values.
|
||||
#' @details The base \R function [sample()] is used for generating values.
|
||||
#'
|
||||
#' Generated values are based on the latest EUCAST guideline implemented in the [rsi_translation] data set. To create specific generated values per bug or drug, set the `mo` and/or `ab` argument.
|
||||
#' @return class `<mic>` for [random_mic()] (see [as.mic()]) and class `<disk>` for [random_disk()] (see [as.disk()])
|
||||
@@ -55,19 +55,36 @@
|
||||
#' random_disk(100, "Klebsiella pneumoniae", "ampicillin") # range 11-17
|
||||
#' random_disk(100, "Streptococcus pneumoniae", "ampicillin") # range 12-27
|
||||
#' }
|
||||
random_mic <- function(size, mo = NULL, ab = NULL, ...) {
|
||||
random_mic <- function(size = NULL, mo = NULL, ab = NULL, ...) {
|
||||
meet_criteria(size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE, allow_NULL = TRUE)
|
||||
meet_criteria(mo, allow_class = "character", has_length = 1, allow_NULL = TRUE)
|
||||
meet_criteria(ab, allow_class = "character", has_length = 1, allow_NULL = TRUE)
|
||||
if (is.null(size)) {
|
||||
size <- NROW(get_current_data(arg_name = "size", call = -3))
|
||||
}
|
||||
random_exec("MIC", size = size, mo = mo, ab = ab)
|
||||
}
|
||||
|
||||
#' @rdname random
|
||||
#' @export
|
||||
random_disk <- function(size, mo = NULL, ab = NULL, ...) {
|
||||
random_disk <- function(size = NULL, mo = NULL, ab = NULL, ...) {
|
||||
meet_criteria(size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE, allow_NULL = TRUE)
|
||||
meet_criteria(mo, allow_class = "character", has_length = 1, allow_NULL = TRUE)
|
||||
meet_criteria(ab, allow_class = "character", has_length = 1, allow_NULL = TRUE)
|
||||
if (is.null(size)) {
|
||||
size <- NROW(get_current_data(arg_name = "size", call = -3))
|
||||
}
|
||||
random_exec("DISK", size = size, mo = mo, ab = ab)
|
||||
}
|
||||
|
||||
#' @rdname random
|
||||
#' @export
|
||||
random_rsi <- function(size, prob_RSI = c(0.33, 0.33, 0.33), ...) {
|
||||
random_rsi <- function(size = NULL, prob_RSI = c(0.33, 0.33, 0.33), ...) {
|
||||
meet_criteria(size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE, allow_NULL = TRUE)
|
||||
meet_criteria(prob_RSI, allow_class = c("numeric", "integer"), has_length = 3)
|
||||
if (is.null(size)) {
|
||||
size <- NROW(get_current_data(arg_name = "size", call = -3))
|
||||
}
|
||||
sample(as.rsi(c("R", "S", "I")), size = size, replace = TRUE, prob = prob_RSI)
|
||||
}
|
||||
|
||||
@@ -103,23 +120,22 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
|
||||
warning_("No rows found that match ab '", ab, "', ignoring argument `ab`", call = FALSE)
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
if (type == "MIC") {
|
||||
# all valid MIC levels
|
||||
valid_range <- as.mic(levels(as.mic(1)))
|
||||
set_range_max <- max(df$breakpoint_R)
|
||||
if (log(set_range_max, 2) %% 1 == 0) {
|
||||
# return powers of 2
|
||||
valid_range <- unique(as.double(valid_range))
|
||||
# add 1-3 higher MIC levels to set_range_max
|
||||
set_range_max <- 2 ^ (log(set_range_max, 2) + sample(c(1:3), 1))
|
||||
set_range <- as.mic(valid_range[log(valid_range, 2) %% 1 == 0 & valid_range <= set_range_max])
|
||||
} else {
|
||||
# no power of 2, return factors of 2 to left and right side
|
||||
valid_mics <- suppressWarnings(as.mic(set_range_max / (2 ^ c(-3:3))))
|
||||
set_range <- valid_mics[!is.na(valid_mics)]
|
||||
# set range
|
||||
mic_range <- c(0.001, 0.002, 0.005, 0.010, 0.025, 0.0625, 0.125, 0.250, 0.5, 1, 2, 4, 8, 16, 32, 64, 128, 256)
|
||||
|
||||
# get highest/lowest +/- random 1 to 3 higher factors of two
|
||||
max_range <- mic_range[min(length(mic_range),
|
||||
which(mic_range == max(df$breakpoint_R)) + sample(c(1:3), 1))]
|
||||
min_range <- mic_range[max(1,
|
||||
which(mic_range == min(df$breakpoint_S)) - sample(c(1:3), 1))]
|
||||
|
||||
mic_range_new <- mic_range[mic_range <= max_range & mic_range >= min_range]
|
||||
if (length(mic_range_new) == 0) {
|
||||
mic_range_new <- mic_range
|
||||
}
|
||||
out <- as.mic(sample(set_range, size = size, replace = TRUE))
|
||||
out <- as.mic(sample(mic_range_new, size = size, replace = TRUE))
|
||||
# 50% chance that lowest will get <= and highest will get >=
|
||||
if (stats::runif(1) > 0.5) {
|
||||
out[out == min(out)] <- paste0("<=", out[out == min(out)])
|
||||
|
||||
+26
-19
@@ -23,10 +23,11 @@
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Predict antimicrobial resistance
|
||||
#' Predict Antimicrobial Resistance
|
||||
#'
|
||||
#' Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns `se_min` and `se_max`. See *Examples* for a real live example.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param object model data to be plotted
|
||||
#' @param col_ab column name of `x` containing antimicrobial interpretations (`"R"`, `"I"` and `"S"`)
|
||||
#' @param col_date column name of the date, will be used to calculate years if this column doesn't consist of years already, defaults to the first column of with a date class
|
||||
#' @param year_min lowest year to use in the prediction model, dafaults to the lowest year in `col_date`
|
||||
@@ -99,9 +100,9 @@
|
||||
#' info = FALSE,
|
||||
#' minimum = 15)
|
||||
#'
|
||||
#' ggplot(data)
|
||||
#' autoplot(data)
|
||||
#'
|
||||
#' ggplot(as.data.frame(data),
|
||||
#' ggplot(data,
|
||||
#' aes(x = year)) +
|
||||
#' geom_col(aes(y = value),
|
||||
#' fill = "grey75") +
|
||||
@@ -143,7 +144,7 @@ resistance_predict <- function(x,
|
||||
meet_criteria(info, allow_class = "logical", has_length = 1)
|
||||
|
||||
stop_if(is.null(model), 'choose a regression model with the `model` argument, e.g. resistance_predict(..., model = "binomial")')
|
||||
|
||||
|
||||
dots <- unlist(list(...))
|
||||
if (length(dots) != 0) {
|
||||
# backwards compatibility with old arguments
|
||||
@@ -321,7 +322,7 @@ plot.resistance_predict <- function(x, main = paste("Resistance Prediction of",
|
||||
} else {
|
||||
ylab <- "%IR"
|
||||
}
|
||||
|
||||
|
||||
plot(x = x$year,
|
||||
y = x$value,
|
||||
ylim = c(0, 1),
|
||||
@@ -351,20 +352,6 @@ plot.resistance_predict <- function(x, main = paste("Resistance Prediction of",
|
||||
col = "grey40")
|
||||
}
|
||||
|
||||
|
||||
#' @method ggplot resistance_predict
|
||||
#' @rdname resistance_predict
|
||||
# will be exported using s3_register() in R/zzz.R
|
||||
ggplot.resistance_predict <- function(x,
|
||||
main = paste("Resistance Prediction of", x_name),
|
||||
ribbon = TRUE,
|
||||
...) {
|
||||
x_name <- paste0(ab_name(attributes(x)$ab), " (", attributes(x)$ab, ")")
|
||||
meet_criteria(main, allow_class = "character", has_length = 1)
|
||||
meet_criteria(ribbon, allow_class = "logical", has_length = 1)
|
||||
ggplot_rsi_predict(x = x, main = main, ribbon = ribbon, ...)
|
||||
}
|
||||
|
||||
#' @rdname resistance_predict
|
||||
#' @export
|
||||
ggplot_rsi_predict <- function(x,
|
||||
@@ -407,3 +394,23 @@ ggplot_rsi_predict <- function(x,
|
||||
colour = "grey40")
|
||||
p
|
||||
}
|
||||
|
||||
#' @method autoplot resistance_predict
|
||||
#' @rdname resistance_predict
|
||||
# will be exported using s3_register() in R/zzz.R
|
||||
autoplot.resistance_predict <- function(object,
|
||||
main = paste("Resistance Prediction of", x_name),
|
||||
ribbon = TRUE,
|
||||
...) {
|
||||
x_name <- paste0(ab_name(attributes(object)$ab), " (", attributes(object)$ab, ")")
|
||||
meet_criteria(main, allow_class = "character", has_length = 1)
|
||||
meet_criteria(ribbon, allow_class = "logical", has_length = 1)
|
||||
ggplot_rsi_predict(x = object, main = main, ribbon = ribbon, ...)
|
||||
}
|
||||
|
||||
#' @method fortify resistance_predict
|
||||
#' @noRd
|
||||
# will be exported using s3_register() in R/zzz.R
|
||||
fortify.resistance_predict <- function(model, data, ...) {
|
||||
as.data.frame(model)
|
||||
}
|
||||
|
||||
@@ -75,7 +75,7 @@
|
||||
#'
|
||||
#' ## Machine-Readable Interpretation Guidelines
|
||||
#'
|
||||
#' The repository of this package [contains a machine-readable version](https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt) of all guidelines. This is a CSV file consisting of `r format(nrow(AMR::rsi_translation), big.mark = ",")` rows and `r ncol(AMR::rsi_translation)` columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. **This allows for easy implementation of these rules in laboratory information systems (LIS)**. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
|
||||
#' The repository of this package [contains a machine-readable version](https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt) of all guidelines. This is a CSV file consisting of `r format(nrow(AMR::rsi_translation), big.mark = ",")` rows and `r ncol(AMR::rsi_translation)` columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. **This allows for easy implementation of these rules in laboratory information systems (LIS)**. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
|
||||
#'
|
||||
#' ## Other
|
||||
#'
|
||||
@@ -89,7 +89,7 @@
|
||||
#' A microorganism is categorised as *Resistant* when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
|
||||
#' - **S = Susceptible**\cr
|
||||
#' A microorganism is categorised as *Susceptible, standard dosing regimen*, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
|
||||
#' - **I = Increased exposure, but still susceptible**\cr
|
||||
#' - **I = Susceptible, Increased exposure**\cr
|
||||
#' A microorganism is categorised as *Susceptible, Increased exposure* when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
|
||||
#'
|
||||
#' This AMR package honours this (new) insight. Use [susceptibility()] (equal to [proportion_SI()]) to determine antimicrobial susceptibility and [count_susceptible()] (equal to [count_SI()]) to count susceptible isolates.
|
||||
@@ -188,6 +188,12 @@ as.rsi <- function(x, ...) {
|
||||
UseMethod("as.rsi")
|
||||
}
|
||||
|
||||
#' @rdname as.rsi
|
||||
#' @details `NA_rsi_` is a missing value of the new `<rsi>` class.
|
||||
#' @export
|
||||
NA_rsi_ <- set_clean_class(factor(NA, levels = c("S", "I", "R"), ordered = TRUE),
|
||||
new_class = c("rsi", "ordered", "factor"))
|
||||
|
||||
#' @rdname as.rsi
|
||||
#' @export
|
||||
is.rsi <- function(x) {
|
||||
@@ -257,12 +263,12 @@ as.rsi.default <- function(x, ...) {
|
||||
return(x)
|
||||
}
|
||||
|
||||
if (inherits(x, c("integer", "numeric", "double")) && all(x %in% c(1:3, NA))) {
|
||||
x.bak <- x
|
||||
x <- as.character(x) # this is needed to prevent the vctrs pkg from throwing an error
|
||||
|
||||
x.bak <- x
|
||||
x <- as.character(x) # this is needed to prevent the vctrs pkg from throwing an error
|
||||
|
||||
if (inherits(x.bak, c("integer", "numeric", "double")) && all(x %in% c(1:3, NA))) {
|
||||
# support haven package for importing e.g., from SPSS - it adds the 'labels' attribute
|
||||
lbls <- attributes(x)$labels
|
||||
lbls <- attributes(x.bak)$labels
|
||||
if (!is.null(lbls) && all(c("R", "S", "I") %in% names(lbls)) && all(c(1:3) %in% lbls)) {
|
||||
x[x.bak == 1] <- names(lbls[lbls == 1])
|
||||
x[x.bak == 2] <- names(lbls[lbls == 2])
|
||||
@@ -278,34 +284,42 @@ as.rsi.default <- function(x, ...) {
|
||||
if (all(x %unlike% "(R|S|I)", na.rm = TRUE)) {
|
||||
# check if they are actually MICs or disks
|
||||
if (all_valid_mics(x)) {
|
||||
warning_("The input seems to be MIC values. Transform them with `as.mic()` before running `as.rsi()` to interpret them.")
|
||||
warning_("The input seems to contain MIC values. You can transform them with `as.mic()` before running `as.rsi()` to interpret them.", call = FALSE)
|
||||
} else if (all_valid_disks(x)) {
|
||||
warning_("The input seems to be disk diffusion values. Transform them with `as.disk()` before running `as.rsi()` to interpret them.")
|
||||
warning_("The input seems to contain disk diffusion values. You can transform them with `as.disk()` before running `as.rsi()` to interpret them.", call = FALSE)
|
||||
}
|
||||
}
|
||||
|
||||
x <- as.character(unlist(x))
|
||||
# trim leading and trailing spaces, new lines, etc.
|
||||
x <- trimws2(as.character(unlist(x)))
|
||||
x.bak <- x
|
||||
|
||||
na_before <- length(x[is.na(x) | x == ""])
|
||||
# remove all spaces
|
||||
x <- gsub(" +", "", x)
|
||||
# remove all MIC-like values: numbers, operators and periods
|
||||
x <- gsub("[0-9.,;:<=>]+", "", x)
|
||||
# remove everything between brackets, and 'high' and 'low'
|
||||
x <- gsub("([(].*[)])", "", x)
|
||||
x <- gsub("(high|low)", "", x, ignore.case = TRUE)
|
||||
# disallow more than 3 characters
|
||||
x[nchar(x) > 3] <- NA
|
||||
|
||||
# correct for translations
|
||||
trans_R <- unlist(TRANSLATIONS[which(TRANSLATIONS$pattern == "Resistant"),
|
||||
LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED %in% colnames(TRANSLATIONS)]])
|
||||
trans_S <- unlist(TRANSLATIONS[which(TRANSLATIONS$pattern == "Susceptible"),
|
||||
LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED %in% colnames(TRANSLATIONS)]])
|
||||
trans_I <- unlist(TRANSLATIONS[which(TRANSLATIONS$pattern %in% c("Incr. exposure", "Susceptible, incr. exp.", "Intermediate")),
|
||||
LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED %in% colnames(TRANSLATIONS)]])
|
||||
x <- gsub(paste0(unique(trans_R[!is.na(trans_R)]), collapse = "|"), "R", x, ignore.case = TRUE)
|
||||
x <- gsub(paste0(unique(trans_S[!is.na(trans_S)]), collapse = "|"), "S", x, ignore.case = TRUE)
|
||||
x <- gsub(paste0(unique(trans_I[!is.na(trans_I)]), collapse = "|"), "I", x, ignore.case = TRUE)
|
||||
# replace all English textual input
|
||||
x[x %like% "([^a-z]|^)res(is(tant)?)?"] <- "R"
|
||||
x[x %like% "([^a-z]|^)sus(cep(tible)?)?"] <- "S"
|
||||
x[x %like% "([^a-z]|^)int(er(mediate)?)?|incr.*exp"] <- "I"
|
||||
# remove other invalid characters
|
||||
x <- gsub("[^rsiRSIHi]+", "", x, perl = TRUE)
|
||||
# some labs now report "H" instead of "I" to not interfere with EUCAST prior to 2019
|
||||
x <- gsub("H", "I", x, ignore.case = TRUE)
|
||||
# set to capitals
|
||||
x <- toupper(x)
|
||||
# remove all invalid characters
|
||||
x <- gsub("[^RSI]+", "", x)
|
||||
# in cases of "S;S" keep S, but in case of "S;I" make it NA
|
||||
x <- gsub("^S+$", "S", x)
|
||||
x <- gsub("^I+$", "I", x)
|
||||
x <- gsub("^R+$", "R", x)
|
||||
x[!x %in% c("S", "I", "R")] <- NA
|
||||
x[!x %in% c("S", "I", "R")] <- NA_character_
|
||||
na_after <- length(x[is.na(x) | x == ""])
|
||||
|
||||
if (!isFALSE(list(...)$warn)) { # so as.rsi(..., warn = FALSE) will never throw a warning
|
||||
@@ -349,7 +363,7 @@ as.rsi.mic <- function(x,
|
||||
|
||||
# for dplyr's across()
|
||||
cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
|
||||
if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", 0)), error = function(e) FALSE)) {
|
||||
if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", call = 0)), error = function(e) FALSE)) {
|
||||
# try to get current column, which will only be available when in across()
|
||||
ab <- tryCatch(cur_column_dplyr(),
|
||||
error = function(e) ab)
|
||||
@@ -395,13 +409,18 @@ as.rsi.mic <- function(x,
|
||||
uti <- rep(uti, length(x))
|
||||
}
|
||||
|
||||
message_("=> Interpreting MIC values of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""), "'", font_bold(ab), "' (",
|
||||
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
|
||||
ab_name(ab_coerced, tolower = TRUE), ")", mo_var_found,
|
||||
agent_formatted <- paste0("'", font_bold(ab), "'")
|
||||
agent_name <- ab_name(ab_coerced, tolower = TRUE, language = NULL)
|
||||
if (generalise_antibiotic_name(ab) != generalise_antibiotic_name(agent_name)) {
|
||||
agent_formatted <- paste0(agent_formatted, " (", ab_coerced, ", ", agent_name, ")")
|
||||
}
|
||||
message_("=> Interpreting MIC values of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
|
||||
agent_formatted,
|
||||
mo_var_found,
|
||||
" according to ", ifelse(identical(reference_data, AMR::rsi_translation),
|
||||
font_bold(guideline_coerced),
|
||||
"manually defined 'reference_data'"),
|
||||
" ... ",
|
||||
"... ",
|
||||
appendLF = FALSE,
|
||||
as_note = FALSE)
|
||||
|
||||
@@ -438,7 +457,7 @@ as.rsi.disk <- function(x,
|
||||
|
||||
# for dplyr's across()
|
||||
cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
|
||||
if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", 0)), error = function(e) FALSE)) {
|
||||
if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", call = 0)), error = function(e) FALSE)) {
|
||||
# try to get current column, which will only be available when in across()
|
||||
ab <- tryCatch(cur_column_dplyr(),
|
||||
error = function(e) ab)
|
||||
@@ -484,13 +503,18 @@ as.rsi.disk <- function(x,
|
||||
uti <- rep(uti, length(x))
|
||||
}
|
||||
|
||||
message_("=> Interpreting disk zones of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""), "'", font_bold(ab), "' (",
|
||||
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
|
||||
ab_name(ab_coerced, tolower = TRUE), ")", mo_var_found,
|
||||
agent_formatted <- paste0("'", font_bold(ab), "'")
|
||||
agent_name <- ab_name(ab_coerced, tolower = TRUE, language = NULL)
|
||||
if (generalise_antibiotic_name(ab) != generalise_antibiotic_name(agent_name)) {
|
||||
agent_formatted <- paste0(agent_formatted, " (", ab_coerced, ", ", agent_name, ")")
|
||||
}
|
||||
message_("=> Interpreting disk zones of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
|
||||
agent_formatted,
|
||||
mo_var_found,
|
||||
" according to ", ifelse(identical(reference_data, AMR::rsi_translation),
|
||||
font_bold(guideline_coerced),
|
||||
"manually defined 'reference_data'"),
|
||||
" ... ",
|
||||
"... ",
|
||||
appendLF = FALSE,
|
||||
as_note = FALSE)
|
||||
|
||||
@@ -580,7 +604,11 @@ as.rsi.data.frame <- function(x,
|
||||
}
|
||||
|
||||
i <- 0
|
||||
sel <- colnames(pm_select(x, ...))
|
||||
if (tryCatch(length(list(...)) > 0, error = function(e) TRUE)) {
|
||||
sel <- colnames(pm_select(x, ...))
|
||||
} else {
|
||||
sel <- colnames(x)
|
||||
}
|
||||
if (!is.null(col_mo)) {
|
||||
sel <- sel[sel != col_mo]
|
||||
}
|
||||
@@ -624,10 +652,9 @@ as.rsi.data.frame <- function(x,
|
||||
if (is.null(col_mo.bak)) {
|
||||
col_mo <- search_type_in_df(x = x, type = "mo")
|
||||
}
|
||||
x_mo <- as.mo(x[, col_mo, drop = TRUE])
|
||||
}
|
||||
|
||||
x_mo <- as.mo(x %pm>% pm_pull(col_mo))
|
||||
|
||||
for (i in seq_len(length(ab_cols))) {
|
||||
if (types[i] == "mic") {
|
||||
x[, ab_cols[i]] <- as.rsi(x = x %pm>%
|
||||
@@ -658,11 +685,11 @@ as.rsi.data.frame <- function(x,
|
||||
show_message <- FALSE
|
||||
ab <- ab_cols[i]
|
||||
ab_coerced <- suppressWarnings(as.ab(ab))
|
||||
if (!all(x[, ab_cols[i], drop = TRUE] %in% c("R", "S", "I"), na.rm = TRUE)) {
|
||||
if (!all(x[, ab_cols[i], drop = TRUE] %in% c("R", "S", "I", NA), na.rm = TRUE)) {
|
||||
show_message <- TRUE
|
||||
# only print message if values are not already clean
|
||||
message_("=> Cleaning values in column '", font_bold(ab), "' (",
|
||||
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
|
||||
ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
|
||||
ab_name(ab_coerced, tolower = TRUE), ")... ",
|
||||
appendLF = FALSE,
|
||||
as_note = FALSE)
|
||||
@@ -670,7 +697,7 @@ as.rsi.data.frame <- function(x,
|
||||
show_message <- TRUE
|
||||
# only print message if class not already set
|
||||
message_("=> Assigning class <rsi> to already clean column '", font_bold(ab), "' (",
|
||||
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
|
||||
ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
|
||||
ab_name(ab_coerced, tolower = TRUE), ")... ",
|
||||
appendLF = FALSE,
|
||||
as_note = FALSE)
|
||||
@@ -750,7 +777,6 @@ exec_as.rsi <- function(method,
|
||||
if (guideline_coerced != guideline) {
|
||||
if (message_not_thrown_before("as.rsi")) {
|
||||
message_("Using guideline ", font_bold(guideline_coerced), " as input for `guideline`.")
|
||||
remember_thrown_message("as.rsi")
|
||||
}
|
||||
}
|
||||
|
||||
@@ -789,7 +815,6 @@ exec_as.rsi <- function(method,
|
||||
if (guideline_coerced %unlike% "EUCAST") {
|
||||
if (message_not_thrown_before("as.rsi2")) {
|
||||
warning_("Using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.", call = FALSE)
|
||||
remember_thrown_message("as.rsi2")
|
||||
}
|
||||
} else {
|
||||
new_rsi[i] <- "R"
|
||||
@@ -854,7 +879,6 @@ exec_as.rsi <- function(method,
|
||||
message_("WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
|
||||
if (message_not_thrown_before("as.rsi3")) {
|
||||
warning_("Found intrinsic resistance in some bug/drug combinations, although it was not applied.\nUse `as.rsi(..., add_intrinsic_resistance = TRUE)` to apply it.", call = FALSE)
|
||||
remember_thrown_message("as.rsi3")
|
||||
}
|
||||
warned <- TRUE
|
||||
}
|
||||
@@ -915,7 +939,7 @@ freq.rsi <- function(x, ...) {
|
||||
if (!is.na(ab)) {
|
||||
cleaner::freq.default(x = x, ...,
|
||||
.add_header = list(
|
||||
Drug = paste0(ab_name(ab, language = NULL), " (", ab, ", ", ab_atc(ab), ")"),
|
||||
Drug = paste0(ab_name(ab, language = NULL), " (", ab, ", ", paste(ab_atc(ab), collapse = "/"), ")"),
|
||||
`Drug group` = ab_group(ab, language = NULL),
|
||||
`%SI` = percentage(susceptibility(x, minimum = 0, as_percent = FALSE),
|
||||
digits = digits)))
|
||||
@@ -1038,6 +1062,15 @@ unique.rsi <- function(x, incomparables = FALSE, ...) {
|
||||
y
|
||||
}
|
||||
|
||||
#' @method rep rsi
|
||||
#' @export
|
||||
#' @noRd
|
||||
rep.rsi <- function(x, ...) {
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(x)
|
||||
y
|
||||
}
|
||||
|
||||
check_reference_data <- function(reference_data) {
|
||||
if (!identical(reference_data, AMR::rsi_translation)) {
|
||||
class_rsi <- vapply(FUN.VALUE = character(1), rsi_translation, function(x) paste0("<", class(x), ">", collapse = " and "))
|
||||
|
||||
+26
-4
@@ -27,7 +27,7 @@ dots2vars <- function(...) {
|
||||
# this function is to give more informative output about
|
||||
# variable names in count_* and proportion_* functions
|
||||
dots <- substitute(list(...))
|
||||
vector_and(as.character(dots)[2:length(dots)], quotes = FALSE)
|
||||
as.character(dots)[2:length(dots)]
|
||||
}
|
||||
|
||||
rsi_calc <- function(...,
|
||||
@@ -152,7 +152,6 @@ rsi_calc <- function(...,
|
||||
" your_data %>% mutate_if(is.rsi.eligible, as.rsi)\n",
|
||||
" your_data %>% mutate(across(where(is.rsi.eligible), as.rsi))",
|
||||
call = FALSE)
|
||||
remember_thrown_message("rsi_calc")
|
||||
}
|
||||
}
|
||||
|
||||
@@ -163,8 +162,30 @@ rsi_calc <- function(...,
|
||||
if (denominator < minimum) {
|
||||
if (data_vars != "") {
|
||||
data_vars <- paste(" for", data_vars)
|
||||
# also add group name if used in dplyr::group_by()
|
||||
cur_group <- import_fn("cur_group", "dplyr", error_on_fail = FALSE)
|
||||
if (!is.null(cur_group)) {
|
||||
group_df <- tryCatch(cur_group(), error = function(e) data.frame())
|
||||
if (NCOL(group_df) > 0) {
|
||||
# transform factors to characters
|
||||
group <- vapply(FUN.VALUE = character(1), group_df, function(x) {
|
||||
if (is.numeric(x)) {
|
||||
format(x)
|
||||
} else if (is.logical(x)) {
|
||||
as.character(x)
|
||||
} else {
|
||||
paste0('"', x, '"')
|
||||
}
|
||||
})
|
||||
data_vars <- paste0(data_vars, " in group: ", paste0(names(group), " = ", group, collapse = ", "))
|
||||
}
|
||||
}
|
||||
}
|
||||
warning_("Introducing NA: only ", denominator, " results available", data_vars, " (`minimum` = ", minimum, ").", call = FALSE)
|
||||
warning_("Introducing NA: ",
|
||||
ifelse(denominator == 0, "no", paste("only", denominator)),
|
||||
" results available",
|
||||
data_vars,
|
||||
" (`minimum` = ", minimum, ").", call = FALSE)
|
||||
fraction <- NA_real_
|
||||
} else {
|
||||
fraction <- numerator / denominator
|
||||
@@ -206,7 +227,7 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
|
||||
translate_ab <- get_translate_ab(translate_ab)
|
||||
|
||||
# select only groups and antibiotics
|
||||
if (inherits(data, "grouped_df")) {
|
||||
if (is_null_or_grouped_tbl(data)) {
|
||||
data_has_groups <- TRUE
|
||||
groups <- setdiff(names(attributes(data)$groups), ".rows")
|
||||
data <- data[, c(groups, colnames(data)[vapply(FUN.VALUE = logical(1), data, is.rsi)]), drop = FALSE]
|
||||
@@ -323,6 +344,7 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
|
||||
}
|
||||
|
||||
rownames(out) <- NULL
|
||||
class(out) <- c("rsi_df", class(out))
|
||||
out
|
||||
}
|
||||
|
||||
|
||||
Binary file not shown.
+16
-10
@@ -27,9 +27,9 @@
|
||||
#'
|
||||
#' For language-dependent output of AMR functions, like [mo_name()], [mo_gramstain()], [mo_type()] and [ab_name()].
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @details Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv>. This file will be read by all functions where a translated output can be desired, like all [`mo_*`][mo_property()] functions (such as [mo_name()], [mo_gramstain()], [mo_type()], etc.) and [`ab_*`][ab_property()] functions (such as [ab_name()], [ab_group()], etc.).
|
||||
#' @details Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <https://github.com/msberends/AMR/blob/main/data-raw/translations.tsv>. This file will be read by all functions where a translated output can be desired, like all [`mo_*`][mo_property()] functions (such as [mo_name()], [mo_gramstain()], [mo_type()], etc.) and [`ab_*`][ab_property()] functions (such as [ab_name()], [ab_group()], etc.).
|
||||
#'
|
||||
#' Currently supported languages are: `r vector_and(gsub(";.*", "", ISOcodes::ISO_639_2[which(ISOcodes::ISO_639_2$Alpha_2 %in% LANGUAGES_SUPPORTED), "Name"]), quotes = FALSE)`. Please note that currently not all these languages have translations available for all antimicrobial agents and colloquial microorganism names.
|
||||
#' Currently supported languages are: `r vector_and(gsub(";.*", "", ISOcodes::ISO_639_2[which(ISOcodes::ISO_639_2$Alpha_2 %in% LANGUAGES_SUPPORTED), "Name"]), quotes = FALSE)`. All these languages have translations available for all antimicrobial agents and colloquial microorganism names.
|
||||
#'
|
||||
#' Please suggest your own translations [by creating a new issue on our repository](https://github.com/msberends/AMR/issues/new?title=Translations).
|
||||
#'
|
||||
@@ -53,17 +53,17 @@
|
||||
#' mo_name("CoNS", language = "en")
|
||||
#' #> "Coagulase-negative Staphylococcus (CoNS)"
|
||||
#'
|
||||
#' # German
|
||||
#' mo_name("CoNS", language = "de")
|
||||
#' #> "Koagulase-negative Staphylococcus (KNS)"
|
||||
#'
|
||||
#' # Danish
|
||||
#' mo_name("CoNS", language = "nl")
|
||||
#' #> "Koagulase-negative stafylokokker (CoNS)"
|
||||
#'
|
||||
#' # Dutch
|
||||
#' mo_name("CoNS", language = "nl")
|
||||
#' #> "Coagulase-negatieve Staphylococcus (CNS)"
|
||||
#'
|
||||
#' # Spanish
|
||||
#' mo_name("CoNS", language = "es")
|
||||
#' #> "Staphylococcus coagulasa negativo (SCN)"
|
||||
#' # German
|
||||
#' mo_name("CoNS", language = "de")
|
||||
#' #> "Koagulase-negative Staphylococcus (KNS)"
|
||||
#'
|
||||
#' # Italian
|
||||
#' mo_name("CoNS", language = "it")
|
||||
@@ -72,6 +72,10 @@
|
||||
#' # Portuguese
|
||||
#' mo_name("CoNS", language = "pt")
|
||||
#' #> "Staphylococcus coagulase negativo (CoNS)"
|
||||
#'
|
||||
#' # Spanish
|
||||
#' mo_name("CoNS", language = "es")
|
||||
#' #> "Staphylococcus coagulasa negativo (SCN)"
|
||||
get_locale <- function() {
|
||||
# AMR versions 1.3.0 and prior used the environmental variable:
|
||||
if (!identical("", Sys.getenv("AMR_locale"))) {
|
||||
@@ -108,6 +112,8 @@ coerce_language_setting <- function(lang) {
|
||||
"de"
|
||||
} else if (grepl("^(Dutch|Nederlands|nl_|NL_)", lang, ignore.case = FALSE, perl = TRUE)) {
|
||||
"nl"
|
||||
} else if (grepl("^(Danish|Dansk|da_|DA_)", lang, ignore.case = FALSE, perl = TRUE)) {
|
||||
"da"
|
||||
} else if (grepl("^(Spanish|Espa.+ol|es_|ES_)", lang, ignore.case = FALSE, perl = TRUE)) {
|
||||
"es"
|
||||
} else if (grepl("^(Italian|Italiano|it_|IT_)", lang, ignore.case = FALSE, perl = TRUE)) {
|
||||
@@ -136,7 +142,7 @@ translate_AMR <- function(from,
|
||||
return(from)
|
||||
}
|
||||
|
||||
df_trans <- translations_file # internal data file
|
||||
df_trans <- TRANSLATIONS # internal data file
|
||||
from.bak <- from
|
||||
from_unique <- unique(from)
|
||||
from_unique_translated <- from_unique
|
||||
|
||||
@@ -0,0 +1,74 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# #
|
||||
# This R package is free software; you can freely use and distribute #
|
||||
# it for both personal and commercial purposes under the terms of the #
|
||||
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
||||
# the Free Software Foundation. #
|
||||
# We created this package for both routine data analysis and academic #
|
||||
# research and it was publicly released in the hope that it will be #
|
||||
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||
# #
|
||||
# Visit our website for the full manual and a complete tutorial about #
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
# These are all S3 implementations for the vctrs package,
|
||||
# that is used internally by tidyverse packages such as dplyr.
|
||||
# They are to convert AMR-specific classes to bare characters and integers.
|
||||
# All of them will be exported using s3_register() in R/zzz.R when loading the package.
|
||||
|
||||
# S3: ab
|
||||
vec_ptype2.character.ab <- function(x, y, ...) {
|
||||
x
|
||||
}
|
||||
vec_ptype2.ab.character <- function(x, y, ...) {
|
||||
y
|
||||
}
|
||||
vec_cast.character.ab <- function(x, to, ...) {
|
||||
unclass(x)
|
||||
}
|
||||
|
||||
# S3: mo
|
||||
vec_ptype2.character.mo <- function(x, y, ...) {
|
||||
x
|
||||
}
|
||||
vec_ptype2.mo.character <- function(x, y, ...) {
|
||||
y
|
||||
}
|
||||
vec_cast.character.mo <- function(x, to, ...) {
|
||||
unclass(x)
|
||||
}
|
||||
|
||||
# S3: disk
|
||||
vec_ptype2.integer.disk <- function(x, y, ...) {
|
||||
x
|
||||
}
|
||||
vec_ptype2.disk.integer <- function(x, y, ...) {
|
||||
y
|
||||
}
|
||||
vec_cast.integer.disk <- function(x, to, ...) {
|
||||
unclass(x)
|
||||
}
|
||||
|
||||
# S3: ab_selector
|
||||
# see https://github.com/tidyverse/dplyr/issues/5955 why this is required
|
||||
vec_ptype2.character.ab_selector <- function(x, y, ...) {
|
||||
x
|
||||
}
|
||||
vec_ptype2.ab_selector.character <- function(x, y, ...) {
|
||||
y
|
||||
}
|
||||
vec_cast.character.ab_selector <- function(x, to, ...) {
|
||||
unclass(x)
|
||||
}
|
||||
@@ -38,7 +38,7 @@ if (utf8_supported && !is_latex) {
|
||||
pkg_env$info_icon <- "i"
|
||||
}
|
||||
|
||||
.onLoad <- function(libname, pkgname) {
|
||||
.onLoad <- function(...) {
|
||||
# Support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
|
||||
# without the need to depend on other packages. This was suggested by the
|
||||
# developers of the vctrs package:
|
||||
@@ -56,15 +56,33 @@ if (utf8_supported && !is_latex) {
|
||||
# Support for frequency tables from the cleaner package
|
||||
s3_register("cleaner::freq", "mo")
|
||||
s3_register("cleaner::freq", "rsi")
|
||||
# Support from skim() from the skimr package
|
||||
# Support for skim() from the skimr package
|
||||
s3_register("skimr::get_skimmers", "mo")
|
||||
s3_register("skimr::get_skimmers", "rsi")
|
||||
s3_register("skimr::get_skimmers", "mic")
|
||||
s3_register("skimr::get_skimmers", "disk")
|
||||
s3_register("ggplot2::ggplot", "rsi")
|
||||
s3_register("ggplot2::ggplot", "mic")
|
||||
s3_register("ggplot2::ggplot", "disk")
|
||||
s3_register("ggplot2::ggplot", "resistance_predict")
|
||||
# Support for autoplot() from the ggplot2 package
|
||||
s3_register("ggplot2::autoplot", "rsi")
|
||||
s3_register("ggplot2::autoplot", "mic")
|
||||
s3_register("ggplot2::autoplot", "disk")
|
||||
s3_register("ggplot2::autoplot", "resistance_predict")
|
||||
# Support for fortify from the ggplot2 package
|
||||
s3_register("ggplot2::fortify", "rsi")
|
||||
s3_register("ggplot2::fortify", "mic")
|
||||
s3_register("ggplot2::fortify", "disk")
|
||||
# Support vctrs package for use in e.g. dplyr verbs
|
||||
s3_register("vctrs::vec_ptype2", "ab.character")
|
||||
s3_register("vctrs::vec_ptype2", "character.ab")
|
||||
s3_register("vctrs::vec_cast", "character.ab")
|
||||
s3_register("vctrs::vec_ptype2", "mo.character")
|
||||
s3_register("vctrs::vec_ptype2", "character.mo")
|
||||
s3_register("vctrs::vec_cast", "character.mo")
|
||||
s3_register("vctrs::vec_ptype2", "ab_selector.character")
|
||||
s3_register("vctrs::vec_ptype2", "character.ab_selector")
|
||||
s3_register("vctrs::vec_cast", "character.ab_selector")
|
||||
s3_register("vctrs::vec_ptype2", "disk.integer")
|
||||
s3_register("vctrs::vec_ptype2", "integer.disk")
|
||||
s3_register("vctrs::vec_cast", "integer.disk")
|
||||
|
||||
# if mo source exists, fire it up (see mo_source())
|
||||
try({
|
||||
@@ -75,14 +93,19 @@ if (utf8_supported && !is_latex) {
|
||||
|
||||
|
||||
# reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed
|
||||
# they cannott be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
|
||||
assign(x = "AB_lookup", value = create_AB_lookup(), envir = asNamespace("AMR"))
|
||||
assign(x = "MO_lookup", value = create_MO_lookup(), envir = asNamespace("AMR"))
|
||||
assign(x = "MO.old_lookup", value = create_MO.old_lookup(), envir = asNamespace("AMR"))
|
||||
# for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
|
||||
assign(x = "INTRINSIC_R", value = create_intr_resistance(), envir = asNamespace("AMR"))
|
||||
|
||||
# for building the website, only print first 5 rows of a data set
|
||||
# if (Sys.getenv("IN_PKGDOWN") != "" && !interactive()) {
|
||||
# ...
|
||||
# }
|
||||
}
|
||||
|
||||
|
||||
# Helper functions --------------------------------------------------------
|
||||
|
||||
create_AB_lookup <- function() {
|
||||
|
||||
@@ -2,17 +2,17 @@
|
||||
|
||||
# `AMR` (for R)
|
||||
|
||||
|
||||
|
||||
[](https://www.codefactor.io/repository/github/msberends/amr)
|
||||
[](https://codecov.io/gh/msberends/AMR?branch=master)
|
||||
[](https://codecov.io/gh/msberends/AMR?branch=main)
|
||||
|
||||
<img src="https://msberends.github.io/AMR/works_great_on.png" align="center" height="150px" />
|
||||
|
||||
The latest built **source package** (`AMR_latest.tar.gz`) can be found in folder [/data-raw/](https://github.com/msberends/AMR/tree/master/data-raw).
|
||||
The latest built **source package** (`AMR_latest.tar.gz`) can be found in folder [/data-raw/](https://github.com/msberends/AMR/tree/main/data-raw).
|
||||
|
||||
`AMR` is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. It is currently being used in over 150 countries.
|
||||
|
||||
After installing this package, R knows ~70,000 distinct microbial species and all ~550 antibiotic, antimycotic, and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
|
||||
After installing this package, R knows ~71,000 distinct microbial species and all ~560 antibiotic, antimycotic, and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. Antimicrobial names and group names are available in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish.
|
||||
|
||||
This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen. This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.
|
||||
|
||||
@@ -33,7 +33,7 @@ It will be downloaded and installed automatically. For RStudio, click on the men
|
||||
|
||||
### Copyright
|
||||
|
||||
This R package is licensed under the [GNU General Public License (GPL) v2.0](https://github.com/msberends/AMR/blob/master/LICENSE). In a nutshell, this means that this package:
|
||||
This R package is licensed under the [GNU General Public License (GPL) v2.0](https://github.com/msberends/AMR/blob/main/LICENSE). In a nutshell, this means that this package:
|
||||
|
||||
- May be used for commercial purposes
|
||||
|
||||
|
||||
+31
-40
@@ -32,6 +32,7 @@ development:
|
||||
|
||||
news:
|
||||
one_page: true
|
||||
cran_dates: true
|
||||
|
||||
navbar:
|
||||
title: "AMR (for R)"
|
||||
@@ -88,32 +89,11 @@ navbar:
|
||||
- text: "Source Code"
|
||||
icon: "fab fa-github"
|
||||
href: "https://github.com/msberends/AMR"
|
||||
- text: "Survey"
|
||||
icon: "fa-clipboard-list"
|
||||
href: "survey.html"
|
||||
# - text: "Survey"
|
||||
# icon: "fa-clipboard-list"
|
||||
# href: "survey.html"
|
||||
|
||||
reference:
|
||||
- title: "Background information on included data"
|
||||
desc: >
|
||||
Some pages about our package and its external sources. Be sure to read our [How To's](./../articles/index.html)
|
||||
for more information about how to work with functions in this package.
|
||||
contents:
|
||||
- "`AMR`"
|
||||
- "`example_isolates`"
|
||||
- "`microorganisms`"
|
||||
- "`microorganisms.codes`"
|
||||
- "`microorganisms.old`"
|
||||
- "`antibiotics`"
|
||||
- "`intrinsic_resistant`"
|
||||
- "`dosage`"
|
||||
- "`catalogue_of_life`"
|
||||
- "`catalogue_of_life_version`"
|
||||
- "`WHOCC`"
|
||||
- "`lifecycle`"
|
||||
- "`example_isolates_unclean`"
|
||||
- "`rsi_translation`"
|
||||
- "`WHONET`"
|
||||
|
||||
- title: "Preparing data: microorganisms"
|
||||
desc: >
|
||||
These functions are meant to get taxonomically valid properties of microorganisms from any input.
|
||||
@@ -164,6 +144,27 @@ reference:
|
||||
- "`antibiotic_class_selectors`"
|
||||
- "`resistance_predict`"
|
||||
- "`guess_ab_col`"
|
||||
|
||||
- title: "Background information on included data"
|
||||
desc: >
|
||||
Some pages about our package and its external sources. Be sure to read our [How To's](./../articles/index.html)
|
||||
for more information about how to work with functions in this package.
|
||||
contents:
|
||||
- "`AMR`"
|
||||
- "`example_isolates`"
|
||||
- "`microorganisms`"
|
||||
- "`microorganisms.codes`"
|
||||
- "`microorganisms.old`"
|
||||
- "`antibiotics`"
|
||||
- "`intrinsic_resistant`"
|
||||
- "`dosage`"
|
||||
- "`catalogue_of_life`"
|
||||
- "`catalogue_of_life_version`"
|
||||
- "`WHOCC`"
|
||||
- "`lifecycle`"
|
||||
- "`example_isolates_unclean`"
|
||||
- "`rsi_translation`"
|
||||
- "`WHONET`"
|
||||
|
||||
- title: "Other: miscellaneous functions"
|
||||
desc: >
|
||||
@@ -199,23 +200,13 @@ reference:
|
||||
contents:
|
||||
- "`AMR-deprecated`"
|
||||
|
||||
authors:
|
||||
Matthijs S. Berends:
|
||||
href: https://www.rug.nl/staff/m.s.berends/
|
||||
Christian F. Luz:
|
||||
href: https://www.rug.nl/staff/c.f.luz/
|
||||
Alexander W. Friedrich:
|
||||
href: https://www.rug.nl/staff/a.w.friedrich/
|
||||
Bhanu N. M. Sinha:
|
||||
href: https://www.rug.nl/staff/b.sinha/
|
||||
Casper J. Albers:
|
||||
href: https://www.rug.nl/staff/c.j.albers/
|
||||
Corinna Glasner:
|
||||
href: https://www.rug.nl/staff/c.glasner/
|
||||
|
||||
template:
|
||||
# this requires the 'preferably' package, https://github.com/amirmasoudabdol/preferably/
|
||||
# package: preferably
|
||||
bootstrap: 3
|
||||
opengraph:
|
||||
twitter:
|
||||
creator: "@msberends"
|
||||
site: "@univgroningen"
|
||||
card: summary_large_image
|
||||
assets: "pkgdown/logos" # use logos in this folder
|
||||
params:
|
||||
noindex: false
|
||||
|
||||
+1
-1
@@ -25,7 +25,7 @@
|
||||
|
||||
codecov:
|
||||
require_ci_to_pass: no # allow fail
|
||||
branch: master
|
||||
branch: main
|
||||
|
||||
comment: no
|
||||
|
||||
|
||||
Binary file not shown.
Binary file not shown.
@@ -24,12 +24,22 @@
|
||||
# ==================================================================== #
|
||||
|
||||
# some old R instances have trouble installing tinytest, so we ship it too
|
||||
install.packages("data-raw/tinytest_1.2.4.10.tar.gz")
|
||||
install.packages("data-raw/tinytest_1.3.1.tar.gz", dependencies = c("Depends", "Imports", "LinkingTo"))
|
||||
install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
|
||||
install.packages("covr", repos = "https://cran.rstudio.com/")
|
||||
|
||||
pkg_suggests <- gsub("[^a-zA-Z0-9]+", "", unlist(strsplit(packageDescription("AMR", fields = "Suggests"), ", ?")))
|
||||
cat("Packages listed in Suggests:", paste(pkg_suggests, collapse = ", "), "\n")
|
||||
pkg_suggests <- gsub("[^a-zA-Z0-9]+", "",
|
||||
unlist(strsplit(unlist(packageDescription("AMR",
|
||||
fields = c("Suggests", "Enhances", "LinkingTo"))),
|
||||
split = ", ?")))
|
||||
pkg_suggests <- unname(pkg_suggests[!is.na(pkg_suggests)])
|
||||
cat("################################################\n")
|
||||
cat("Packages listed in Suggests/Enhances:", paste(pkg_suggests, collapse = ", "), "\n")
|
||||
cat("################################################\n")
|
||||
|
||||
if (.Platform$OS.type != "unix") {
|
||||
# no compiling on Windows here
|
||||
options(install.packages.compile.from.source = FALSE)
|
||||
}
|
||||
|
||||
to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())]
|
||||
if (length(to_install) == 0) {
|
||||
@@ -37,10 +47,24 @@ if (length(to_install) == 0) {
|
||||
}
|
||||
for (i in seq_len(length(to_install))) {
|
||||
cat("Installing package", to_install[i], "\n")
|
||||
tryCatch(install.packages(to_install[i], repos = "https://cran.rstudio.com/", dependencies = TRUE, quiet = TRUE),
|
||||
tryCatch(install.packages(to_install[i],
|
||||
type = "source",
|
||||
repos = "https://cran.rstudio.com/",
|
||||
dependencies = c("Depends", "Imports", "LinkingTo"),
|
||||
quiet = FALSE),
|
||||
# message = function(m) invisible(),
|
||||
warning = function(w) message(w$message),
|
||||
error = function(e) message(e$message))
|
||||
if (.Platform$OS.type != "unix" && !to_install[i] %in% rownames(utils::installed.packages())) {
|
||||
tryCatch(install.packages(to_install[i],
|
||||
type = "binary",
|
||||
repos = "https://cran.rstudio.com/",
|
||||
dependencies = c("Depends", "Imports", "LinkingTo"),
|
||||
quiet = FALSE),
|
||||
# message = function(m) invisible(),
|
||||
warning = function(w) message(w$message),
|
||||
error = function(e) message(e$message))
|
||||
}
|
||||
}
|
||||
|
||||
to_update <- as.data.frame(utils::old.packages(repos = "https://cran.rstudio.com/"), stringsAsFactors = FALSE)
|
||||
@@ -49,9 +73,10 @@ if (length(to_update) == 0) {
|
||||
message("\nNothing to update\n")
|
||||
}
|
||||
for (i in seq_len(length(to_update))) {
|
||||
cat("Updating package", to_update[i], "\n")
|
||||
cat("Updating package '", to_update[i], "' v", as.character(packageVersion(to_update[i])), "\n", sep = "")
|
||||
tryCatch(update.packages(to_update[i], repos = "https://cran.rstudio.com/", ask = FALSE),
|
||||
# message = function(m) invisible(),
|
||||
warning = function(w) message(w$message),
|
||||
error = function(e) message(e$message))
|
||||
cat("Updated to '", to_update[i], "' v", as.character(packageVersion(to_update[i])), "\n", sep = "")
|
||||
}
|
||||
|
||||
+70
-52
@@ -34,7 +34,7 @@ old_globalenv <- ls(envir = globalenv())
|
||||
# Save internal data to R/sysdata.rda -------------------------------------
|
||||
|
||||
# See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
|
||||
eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
|
||||
EUCAST_RULES_DF <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
|
||||
skip = 10,
|
||||
sep = "\t",
|
||||
stringsAsFactors = FALSE,
|
||||
@@ -54,7 +54,7 @@ eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
|
||||
select(-sorting_rule)
|
||||
|
||||
# Translations
|
||||
translations_file <- utils::read.delim(file = "data-raw/translations.tsv",
|
||||
TRANSLATIONS <- utils::read.delim(file = "data-raw/translations.tsv",
|
||||
sep = "\t",
|
||||
stringsAsFactors = FALSE,
|
||||
header = TRUE,
|
||||
@@ -68,7 +68,9 @@ translations_file <- utils::read.delim(file = "data-raw/translations.tsv",
|
||||
quote = "")
|
||||
|
||||
# for checking input in `language` argument in e.g. mo_*() and ab_*() functions
|
||||
LANGUAGES_SUPPORTED <- sort(c("en", colnames(translations_file)[nchar(colnames(translations_file)) == 2]))
|
||||
LANGUAGES_SUPPORTED <- sort(c("en", colnames(TRANSLATIONS)[nchar(colnames(TRANSLATIONS)) == 2]))
|
||||
|
||||
# EXAMPLE_ISOLATES <- readRDS("data-raw/example_isolates.rds")
|
||||
|
||||
# vectors of CoNS and CoPS, improves speed in as.mo()
|
||||
create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
|
||||
@@ -93,7 +95,9 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
|
||||
"pulvereri", "rostri", "saccharolyticus", "saprophyticus",
|
||||
"sciuri", "simulans", "stepanovicii", "succinus",
|
||||
"ureilyticus",
|
||||
"vitulinus", "vitulus", "warneri", "xylosus")
|
||||
"vitulinus", "vitulus", "warneri", "xylosus",
|
||||
"caledonicus", "canis",
|
||||
"durrellii", "lloydii")
|
||||
| (MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))),
|
||||
"mo", drop = TRUE]
|
||||
} else if (type == "CoPS") {
|
||||
@@ -103,7 +107,8 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
|
||||
"delphini", "lutrae",
|
||||
"hyicus", "intermedius",
|
||||
"pseudintermedius", "pseudointermedius",
|
||||
"schweitzeri", "simiae")
|
||||
"schweitzeri", "simiae",
|
||||
"roterodami")
|
||||
| (MO_staph$species == "schleiferi" & MO_staph$subspecies == "coagulans")),
|
||||
"mo", drop = TRUE]
|
||||
}
|
||||
@@ -114,60 +119,73 @@ MO_COPS <- create_species_cons_cops("CoPS")
|
||||
# antibiotic groups
|
||||
# (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv)
|
||||
globalenv_before_ab <- c(ls(envir = globalenv()), "globalenv_before_ab")
|
||||
AMINOGLYCOSIDES <- antibiotics %>% filter(group %like% "aminoglycoside") %>% pull(ab)
|
||||
AMINOPENICILLINS <- as.ab(c("AMP", "AMX"))
|
||||
CARBAPENEMS <- antibiotics %>% filter(group %like% "carbapenem") %>% pull(ab)
|
||||
CEPHALOSPORINS <- antibiotics %>% filter(group %like% "cephalosporin") %>% pull(ab)
|
||||
CEPHALOSPORINS_1ST <- antibiotics %>% filter(group %like% "cephalosporin.*1") %>% pull(ab)
|
||||
CEPHALOSPORINS_2ND <- antibiotics %>% filter(group %like% "cephalosporin.*2") %>% pull(ab)
|
||||
CEPHALOSPORINS_3RD <- antibiotics %>% filter(group %like% "cephalosporin.*3") %>% pull(ab)
|
||||
CEPHALOSPORINS_EXCEPT_CAZ <- CEPHALOSPORINS[CEPHALOSPORINS != "CAZ"]
|
||||
FLUOROQUINOLONES <- antibiotics %>% filter(atc_group2 %like% "fluoroquinolone") %>% pull(ab)
|
||||
LIPOGLYCOPEPTIDES <- as.ab(c("DAL", "ORI", "TLV")) # dalba/orita/tela
|
||||
GLYCOPEPTIDES <- antibiotics %>% filter(group %like% "glycopeptide") %>% pull(ab)
|
||||
GLYCOPEPTIDES_EXCEPT_LIPO <- GLYCOPEPTIDES[!GLYCOPEPTIDES %in% LIPOGLYCOPEPTIDES]
|
||||
LINCOSAMIDES <- antibiotics %>% filter(atc_group2 %like% "lincosamide") %>% pull(ab) %>% c("PRL")
|
||||
MACROLIDES <- antibiotics %>% filter(atc_group2 %like% "macrolide") %>% pull(ab)
|
||||
OXAZOLIDINONES <- antibiotics %>% filter(group %like% "oxazolidinone") %>% pull(ab)
|
||||
PENICILLINS <- antibiotics %>% filter(group %like% "penicillin") %>% pull(ab)
|
||||
POLYMYXINS <- antibiotics %>% filter(group %like% "polymyxin") %>% pull(ab)
|
||||
STREPTOGRAMINS <- antibiotics %>% filter(atc_group2 %like% "streptogramin") %>% pull(ab)
|
||||
TETRACYCLINES <- antibiotics %>% filter(atc_group2 %like% "tetracycline") %>% pull(ab)
|
||||
TETRACYCLINES_EXCEPT_TGC <- TETRACYCLINES[TETRACYCLINES != "TGC"]
|
||||
UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ"))
|
||||
BETALACTAMS <- c(PENICILLINS, CEPHALOSPORINS, CARBAPENEMS)
|
||||
|
||||
AB_AMINOGLYCOSIDES <- antibiotics %>% filter(group %like% "aminoglycoside") %>% pull(ab)
|
||||
AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX"))
|
||||
AB_ANTIFUNGALS <- AB_lookup %>% filter(group %like% "antifungal") %>% pull(ab)
|
||||
AB_ANTIMYCOBACTERIALS <- AB_lookup %>% filter(group %like% "antimycobacterial") %>% pull(ab)
|
||||
AB_CARBAPENEMS <- antibiotics %>% filter(group %like% "carbapenem") %>% pull(ab)
|
||||
AB_CEPHALOSPORINS <- antibiotics %>% filter(group %like% "cephalosporin") %>% pull(ab)
|
||||
AB_CEPHALOSPORINS_1ST <- antibiotics %>% filter(group %like% "cephalosporin.*1") %>% pull(ab)
|
||||
AB_CEPHALOSPORINS_2ND <- antibiotics %>% filter(group %like% "cephalosporin.*2") %>% pull(ab)
|
||||
AB_CEPHALOSPORINS_3RD <- antibiotics %>% filter(group %like% "cephalosporin.*3") %>% pull(ab)
|
||||
AB_CEPHALOSPORINS_4TH <- antibiotics %>% filter(group %like% "cephalosporin.*4") %>% pull(ab)
|
||||
AB_CEPHALOSPORINS_5TH <- antibiotics %>% filter(group %like% "cephalosporin.*5") %>% pull(ab)
|
||||
AB_CEPHALOSPORINS_EXCEPT_CAZ <- AB_CEPHALOSPORINS[AB_CEPHALOSPORINS != "CAZ"]
|
||||
AB_FLUOROQUINOLONES <- antibiotics %>% filter(atc_group2 %like% "fluoroquinolone" | (group %like% "quinolone" & is.na(atc_group2))) %>% pull(ab)
|
||||
AB_GLYCOPEPTIDES <- antibiotics %>% filter(group %like% "glycopeptide") %>% pull(ab)
|
||||
AB_LIPOGLYCOPEPTIDES <- as.ab(c("DAL", "ORI", "TLV")) # dalba/orita/tela
|
||||
AB_GLYCOPEPTIDES_EXCEPT_LIPO <- AB_GLYCOPEPTIDES[!AB_GLYCOPEPTIDES %in% AB_LIPOGLYCOPEPTIDES]
|
||||
AB_LINCOSAMIDES <- antibiotics %>% filter(atc_group2 %like% "lincosamide" | (group %like% "lincosamide" & is.na(atc_group2))) %>% pull(ab)
|
||||
AB_MACROLIDES <- antibiotics %>% filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2))) %>% pull(ab)
|
||||
AB_OXAZOLIDINONES <- antibiotics %>% filter(group %like% "oxazolidinone") %>% pull(ab)
|
||||
AB_PENICILLINS <- antibiotics %>% filter(group %like% "penicillin") %>% pull(ab)
|
||||
AB_POLYMYXINS <- antibiotics %>% filter(group %like% "polymyxin") %>% pull(ab)
|
||||
AB_QUINOLONES <- antibiotics %>% filter(group %like% "quinolone") %>% pull(ab)
|
||||
AB_STREPTOGRAMINS <- antibiotics %>% filter(atc_group2 %like% "streptogramin") %>% pull(ab)
|
||||
AB_TETRACYCLINES <- antibiotics %>% filter(group %like% "tetracycline") %>% pull(ab)
|
||||
AB_TETRACYCLINES_EXCEPT_TGC <- AB_TETRACYCLINES[AB_TETRACYCLINES != "TGC"]
|
||||
AB_TRIMETHOPRIMS <- antibiotics %>% filter(group %like% "trimethoprim") %>% pull(ab)
|
||||
AB_UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ"))
|
||||
AB_BETALACTAMS <- c(AB_PENICILLINS, AB_CEPHALOSPORINS, AB_CARBAPENEMS)
|
||||
# this will be used for documentation:
|
||||
DEFINED_AB_GROUPS <- ls(envir = globalenv())
|
||||
DEFINED_AB_GROUPS <- DEFINED_AB_GROUPS[!DEFINED_AB_GROUPS %in% globalenv_before_ab]
|
||||
|
||||
# Export to package as internal data ----
|
||||
usethis::use_data(eucast_rules_file,
|
||||
translations_file,
|
||||
usethis::use_data(EUCAST_RULES_DF,
|
||||
TRANSLATIONS,
|
||||
LANGUAGES_SUPPORTED,
|
||||
# EXAMPLE_ISOLATES,
|
||||
MO_CONS,
|
||||
MO_COPS,
|
||||
AMINOGLYCOSIDES,
|
||||
AMINOPENICILLINS,
|
||||
CARBAPENEMS,
|
||||
CEPHALOSPORINS,
|
||||
CEPHALOSPORINS_1ST,
|
||||
CEPHALOSPORINS_2ND,
|
||||
CEPHALOSPORINS_3RD,
|
||||
CEPHALOSPORINS_EXCEPT_CAZ,
|
||||
FLUOROQUINOLONES,
|
||||
LIPOGLYCOPEPTIDES,
|
||||
GLYCOPEPTIDES,
|
||||
GLYCOPEPTIDES_EXCEPT_LIPO,
|
||||
LINCOSAMIDES,
|
||||
MACROLIDES,
|
||||
OXAZOLIDINONES,
|
||||
PENICILLINS,
|
||||
POLYMYXINS,
|
||||
STREPTOGRAMINS,
|
||||
TETRACYCLINES,
|
||||
TETRACYCLINES_EXCEPT_TGC,
|
||||
UREIDOPENICILLINS,
|
||||
BETALACTAMS,
|
||||
AB_AMINOGLYCOSIDES,
|
||||
AB_AMINOPENICILLINS,
|
||||
AB_ANTIFUNGALS,
|
||||
AB_ANTIMYCOBACTERIALS,
|
||||
AB_CARBAPENEMS,
|
||||
AB_CEPHALOSPORINS,
|
||||
AB_CEPHALOSPORINS_1ST,
|
||||
AB_CEPHALOSPORINS_2ND,
|
||||
AB_CEPHALOSPORINS_3RD,
|
||||
AB_CEPHALOSPORINS_4TH,
|
||||
AB_CEPHALOSPORINS_5TH,
|
||||
AB_CEPHALOSPORINS_EXCEPT_CAZ,
|
||||
AB_FLUOROQUINOLONES,
|
||||
AB_LIPOGLYCOPEPTIDES,
|
||||
AB_GLYCOPEPTIDES,
|
||||
AB_GLYCOPEPTIDES_EXCEPT_LIPO,
|
||||
AB_LINCOSAMIDES,
|
||||
AB_MACROLIDES,
|
||||
AB_OXAZOLIDINONES,
|
||||
AB_PENICILLINS,
|
||||
AB_POLYMYXINS,
|
||||
AB_QUINOLONES,
|
||||
AB_STREPTOGRAMINS,
|
||||
AB_TETRACYCLINES,
|
||||
AB_TETRACYCLINES_EXCEPT_TGC,
|
||||
AB_TRIMETHOPRIMS,
|
||||
AB_UREIDOPENICILLINS,
|
||||
AB_BETALACTAMS,
|
||||
DEFINED_AB_GROUPS,
|
||||
internal = TRUE,
|
||||
overwrite = TRUE,
|
||||
|
||||
+1
-1
@@ -1 +1 @@
|
||||
f6b4a2325c4bf3a8d4da337c8cfa07be
|
||||
f7c99b5734e4cdf37f51c55faca6ac2b
|
||||
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
+460
-460
@@ -1,511 +1,511 @@
|
||||
"ab" "atc" "cid" "name" "group" "atc_group1" "atc_group2" "abbreviations" "synonyms" "oral_ddd" "oral_units" "iv_ddd" "iv_units" "loinc"
|
||||
"AMA" "J04AA01" 4649 "4-aminosalicylic acid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" "" "c(\"aminopar\", \"aminosalicylic\", \"aminosalicylic acid\", \"aminosalyl\", \"aminox\", \"apacil\", \"deapasil\", \"entepas\", \"ferrosan\", \"gabbropas\", \"helipidyl\", \"hellipidyl\", \"neopasalate\", \"osacyl\", \"pamacyl\", \"pamisyl\", \"paramycin\", \"parasal\", \"parasalicil\", \"parasalindon\", \"pasalon\", \"pasara\", \"pascorbic\", \"pasdium\", \"paser granules\", \"paskalium\", \"pasmed\", \"pasnodia\", \"pasolac\", \"propasa\", \"rezipas\", \"teebacin\", \"wln: zr cq dvq\")" 12 "g" "character(0)"
|
||||
"FCT" "D01AE21" 3366 "5-fluorocytosine" "Antifungals/antimycotics" "Antifungals for topical use" "Other antifungals for topical use" "c(\"5flc\", \"fcu\", \"fluo\", \"fluy\")" "c(\"alcobon\", \"ancobon\", \"ancotil\", \"ancotyl\", \"flucitosina\", \"flucystine\", \"flucytosin\", \"flucytosine\", \"flucytosinum\", \"flucytosone\", \"fluocytosine\", \"fluorcytosine\")" "c(\"10974-4\", \"23805-5\", \"25142-1\", \"25143-9\", \"3639-2\", \"46218-4\")"
|
||||
"ACM" 6450012 "Acetylmidecamycin" "Macrolides/lincosamides" "" "" ""
|
||||
"ASP" 49787020 "Acetylspiramycin" "Macrolides/lincosamides" "" "c(\"acetylspiramycin\", \"foromacidin b\", \"spiramycin ii\")" "character(0)"
|
||||
"ALS" "J04BA03" 8954 "Aldesulfone sodium" "Other antibacterials" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "" "c(\"adesulfone sodium\", \"aldapsone\", \"aldesulfona sodica\", \"aldesulfone\", \"aldesulfone sodique\", \"aldesulfone sodium\", \"diamidin\", \"diasone\", \"diasone sodium\", \"diazon\", \"novotrone\", \"sodium aldesulphone\", \"sodium sulfoxone\", \"sulfoxone sodium\")" 0.33 "g" "character(0)"
|
||||
"AMK" "J01GB06" 37768 "Amikacin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "c(\"ak\", \"ami\", \"amik\", \"amk\", \"an\")" "c(\"amicacin\", \"amikacillin\", \"amikacin\", \"amikacin base\", \"amikacin dihydrate\", \"amikacin sulfate\", \"amikacina\", \"amikacine\", \"amikacinum\", \"amikavet\", \"amikin\", \"amiklin\", \"amikozit\", \"amukin\", \"arikace\", \"briclin\", \"lukadin\", \"mikavir\", \"pierami\", \"potentox\")" 1 "g" "c(\"13546-7\", \"15098-7\", \"17798-0\", \"31097-9\", \"31098-7\", \"31099-5\", \"3319-1\", \"3320-9\", \"3321-7\", \"35669-1\", \"50802-8\", \"50803-6\", \"56628-1\", \"59378-0\", \"80972-3\")"
|
||||
"AKF" "Amikacin/fosfomycin" "Aminoglycosides" "" "" ""
|
||||
"AMX" "J01CA04" 33613 "Amoxicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"ac\", \"amox\", \"amx\")" "c(\"actimoxi\", \"amoclen\", \"amolin\", \"amopen\", \"amopenixin\", \"amoxibiotic\", \"amoxicaps\", \"amoxicilina\", \"amoxicillin\", \"amoxicilline\", \"amoxicillinum\", \"amoxiden\", \"amoxil\", \"amoxivet\", \"amoxy\", \"amoxycillin\", \"anemolin\", \"aspenil\", \"biomox\", \"bristamox\", \"cemoxin\", \"clamoxyl\", \"delacillin\", \"dispermox\", \"efpenix\", \"flemoxin\", \"hiconcil\", \"histocillin\", \"hydroxyampicillin\", \"ibiamox\", \"imacillin\", \"lamoxy\", \"metafarma capsules\", \"metifarma capsules\", \"moxacin\", \"moxatag\", \"ospamox\", \"pamoxicillin\",
|
||||
"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" "" "c(\"aminopar\", \"aminosalicylic\", \"aminosalicylic acid\", \"aminosalyl\", \"aminox\", \"apacil\", \"deapasil\", \"entepas\", \"ferrosan\", \"gabbropas\", \"helipidyl\", \"hellipidyl\", \"neopasalate\", \"osacyl\", \"pamacyl\", \"pamisyl\", \"paramycin\", \"parasal\", \"parasalicil\", \"parasalindon\", \"pasalon\", \"pasara\", \"pascorbic\", \"pasdium\", \"paser granules\", \"paskalium\", \"pasmed\", \"pasnodia\", \"pasolac\", \"propasa\", \"rezipas\", \"teebacin\", \"wln: zr cq dvq\")" 12 "g" "character(0)"
|
||||
"FCT" 3366 "5-fluorocytosine" "Antifungals/antimycotics" "D01AE21" "Antifungals for topical use" "Other antifungals for topical use" "c(\"5flc\", \"fcu\", \"fluo\", \"fluy\")" "c(\"alcobon\", \"ancobon\", \"ancotil\", \"ancotyl\", \"flucitosina\", \"flucystine\", \"flucytosin\", \"flucytosine\", \"flucytosinum\", \"flucytosone\", \"fluocytosine\", \"fluorcytosine\")" "c(\"10974-4\", \"23805-5\", \"25142-1\", \"25143-9\", \"3639-2\", \"46218-4\")"
|
||||
"ACM" 6450012 "Acetylmidecamycin" "Macrolides/lincosamides" "" "" ""
|
||||
"ASP" 49787020 "Acetylspiramycin" "Macrolides/lincosamides" "" "c(\"acetylspiramycin\", \"foromacidin b\", \"spiramycin ii\")" "character(0)"
|
||||
"ALS" 8954 "Aldesulfone sodium" "Other antibacterials" "J04BA03" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "" "c(\"adesulfone sodium\", \"aldapsone\", \"aldesulfona sodica\", \"aldesulfone\", \"aldesulfone sodique\", \"aldesulfone sodium\", \"diamidin\", \"diasone\", \"diasone sodium\", \"diazon\", \"novotrone\", \"sodium aldesulphone\", \"sodium sulfoxone\", \"sulfoxone sodium\")" 0.33 "g" "character(0)"
|
||||
"AMK" 37768 "Amikacin" "Aminoglycosides" "c(\"D06AX12\", \"J01GB06\", \"S01AA21\")" "Aminoglycoside antibacterials" "Other aminoglycosides" "c(\"ak\", \"ami\", \"amik\", \"amk\", \"an\")" "c(\"amicacin\", \"amikacillin\", \"amikacin\", \"amikacin base\", \"amikacin dihydrate\", \"amikacin sulfate\", \"amikacina\", \"amikacine\", \"amikacinum\", \"amikavet\", \"amikin\", \"amiklin\", \"amikozit\", \"amukin\", \"arikace\", \"briclin\", \"lukadin\", \"mikavir\", \"pierami\", \"potentox\")" 1 "g" "c(\"13546-7\", \"15098-7\", \"17798-0\", \"31097-9\", \"31098-7\", \"31099-5\", \"3319-1\", \"3320-9\", \"3321-7\", \"35669-1\", \"50802-8\", \"50803-6\", \"56628-1\", \"59378-0\", \"80972-3\")"
|
||||
"AKF" "Amikacin/fosfomycin" "Aminoglycosides" "" "" ""
|
||||
"AMX" 33613 "Amoxicillin" "Beta-lactams/penicillins" "J01CA04" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"ac\", \"amox\", \"amx\")" "c(\"actimoxi\", \"amoclen\", \"amolin\", \"amopen\", \"amopenixin\", \"amoxibiotic\", \"amoxicaps\", \"amoxicilina\", \"amoxicillin\", \"amoxicilline\", \"amoxicillinum\", \"amoxiden\", \"amoxil\", \"amoxivet\", \"amoxy\", \"amoxycillin\", \"anemolin\", \"aspenil\", \"biomox\", \"bristamox\", \"cemoxin\", \"clamoxyl\", \"delacillin\", \"dispermox\", \"efpenix\", \"flemoxin\", \"hiconcil\", \"histocillin\", \"hydroxyampicillin\", \"ibiamox\", \"imacillin\", \"lamoxy\", \"metafarma capsules\", \"metifarma capsules\", \"moxacin\", \"moxatag\", \"ospamox\", \"pamoxicillin\",
|
||||
\"piramox\", \"robamox\", \"sawamox pm\", \"tolodina\", \"unicillin\", \"utimox\", \"vetramox\")" 1.5 "g" 3 "g" "c(\"16365-9\", \"25274-2\", \"3344-9\", \"80133-2\")"
|
||||
"AMC" "J01CR02" 23665637 "Amoxicillin/clavulanic acid" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "c(\"a/c\", \"amcl\", \"aml\", \"aug\", \"xl\")" "c(\"amocla\", \"amoclan\", \"amoclav\", \"amoxsiklav\", \"augmentan\", \"augmentin\", \"augmentin xr\", \"augmentine\", \"auspilic\", \"clamentin\", \"clamobit\", \"clavamox\", \"clavinex\", \"clavoxilin plus\", \"clavulin\", \"clavumox\", \"coamoxiclav\", \"eumetinex\", \"kmoxilin\", \"spectramox\", \"spektramox\", \"viaclav\", \"xiclav\")" 1.5 "g" 3 "g" "character(0)"
|
||||
"AXS" 465441 "Amoxicillin/sulbactam" "Beta-lactams/penicillins" "" "" ""
|
||||
"AMB" "J02AA01" 5280965 "Amphotericin B" "Antifungals/antimycotics" "Antimycotics for systemic use" "Antibiotics" "c(\"amf\", \"amfb\", \"amph\")" "c(\"abelcet\", \"abelecet\", \"ambisome\", \"amfotericina b\", \"amphocin\", \"amphomoronal\", \"amphortericin b\", \"amphotec\", \"amphotericin\", \"amphotericin b\", \"amphotericine b\", \"amphotericinum b\", \"amphozone\", \"anfotericine b\", \"fungilin\", \"fungisome\", \"fungisone\", \"fungizone\", \"halizon\")" 35 "mg" "c(\"16370-9\", \"3353-0\", \"3354-8\", \"40707-2\", \"40757-7\", \"49859-2\")"
|
||||
"AMH" "Amphotericin B-high" "Aminoglycosides" "c(\"amfo b high\", \"amhl\", \"ampho b high\", \"amphotericin high\")" "" ""
|
||||
"AMP" "J01CA01" 6249 "Ampicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"am\", \"amp\", \"ampi\")" "c(\"acillin\", \"adobacillin\", \"amblosin\", \"amcill\", \"amfipen\", \"amfipen v\", \"amipenix s\", \"ampichel\", \"ampicil\", \"ampicilina\", \"ampicillin\", \"ampicillin a\", \"ampicillin acid\", \"ampicillin anhydrate\", \"ampicillin anhydrous\", \"ampicillin base\", \"ampicillin sodium\", \"ampicillina\", \"ampicilline\", \"ampicillinum\", \"ampicin\", \"ampifarm\", \"ampikel\", \"ampimed\", \"ampipenin\", \"ampiscel\", \"ampisyn\", \"ampivax\", \"ampivet\", \"amplacilina\", \"amplin\", \"amplipenyl\", \"amplisom\", \"amplital\", \"anhydrous ampicillin\", \"austrapen\",
|
||||
"AMC" 23665637 "Amoxicillin/clavulanic acid" "Beta-lactams/penicillins" "J01CR02" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "c(\"a/c\", \"amcl\", \"aml\", \"aug\", \"xl\")" "c(\"amocla\", \"amoclan\", \"amoclav\", \"amoxsiklav\", \"augmentan\", \"augmentin\", \"augmentin xr\", \"augmentine\", \"auspilic\", \"clamentin\", \"clamobit\", \"clavamox\", \"clavinex\", \"clavoxilin plus\", \"clavulin\", \"clavumox\", \"coamoxiclav\", \"eumetinex\", \"kmoxilin\", \"spectramox\", \"spektramox\", \"viaclav\", \"xiclav\")" 1.5 "g" 3 "g" "character(0)"
|
||||
"AXS" 465441 "Amoxicillin/sulbactam" "Beta-lactams/penicillins" "" "" ""
|
||||
"AMB" 5280965 "Amphotericin B" "Antifungals/antimycotics" "c(\"A01AB04\", \"A07AA07\", \"G01AA03\", \"J02AA01\")" "Antimycotics for systemic use" "Antibiotics" "c(\"amf\", \"amfb\", \"amph\")" "c(\"abelcet\", \"abelecet\", \"ambisome\", \"amfotericina b\", \"amphocin\", \"amphomoronal\", \"amphortericin b\", \"amphotec\", \"amphotericin\", \"amphotericin b\", \"amphotericine b\", \"amphotericinum b\", \"amphozone\", \"anfotericine b\", \"fungilin\", \"fungisome\", \"fungisone\", \"fungizone\", \"halizon\")" 40 "mg" 35 "mg" "c(\"16370-9\", \"3353-0\", \"3354-8\", \"40707-2\", \"40757-7\", \"49859-2\")"
|
||||
"AMH" "Amphotericin B-high" "Aminoglycosides" "c(\"amfo b high\", \"amhl\", \"ampho b high\", \"amphotericin high\")" "" ""
|
||||
"AMP" 6249 "Ampicillin" "Beta-lactams/penicillins" "c(\"J01CA01\", \"S01AA19\")" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"am\", \"amp\", \"ampi\")" "c(\"acillin\", \"adobacillin\", \"amblosin\", \"amcill\", \"amfipen\", \"amfipen v\", \"amipenix s\", \"ampichel\", \"ampicil\", \"ampicilina\", \"ampicillin\", \"ampicillin a\", \"ampicillin acid\", \"ampicillin anhydrate\", \"ampicillin anhydrous\", \"ampicillin base\", \"ampicillin sodium\", \"ampicillina\", \"ampicilline\", \"ampicillinum\", \"ampicin\", \"ampifarm\", \"ampikel\", \"ampimed\", \"ampipenin\", \"ampiscel\", \"ampisyn\", \"ampivax\", \"ampivet\", \"amplacilina\", \"amplin\", \"amplipenyl\", \"amplisom\", \"amplital\", \"anhydrous ampicillin\", \"austrapen\",
|
||||
\"binotal\", \"bonapicillin\", \"britacil\", \"campicillin\", \"copharcilin\", \"delcillin\", \"deripen\", \"divercillin\", \"doktacillin\", \"duphacillin\", \"grampenil\", \"guicitrina\", \"guicitrine\", \"lifeampil\", \"marcillin\", \"morepen\", \"norobrittin\", \"nuvapen\", \"olin kid\", \"omnipen\", \"orbicilina\", \"pen a oral\", \"pen ampil\", \"penbristol\", \"penbritin\", \"penbritin paediatric\", \"penbritin syrup\", \"penbrock\", \"penicline\", \"penimic\", \"pensyn\", \"pentrex\", \"pentrexl\", \"pentrexyl\", \"pentritin\", \"pfizerpen a\", \"polycillin\", \"polyflex\",
|
||||
\"ponecil\", \"princillin\", \"principen\", \"qidamp\", \"racenacillin\", \"rosampline\", \"roscillin\", \"semicillin\", \"semicillin r\", \"servicillin\", \"sumipanto\", \"synpenin\", \"texcillin\", \"tokiocillin\", \"tolomol\", \"totacillin\", \"totalciclina\", \"totapen\", \"trifacilina\", \"ukapen\", \"ultrabion\", \"ultrabron\", \"vampen\", \"viccillin\", \"viccillin s\", \"vidocillin\", \"wypicil\")" 2 "g" 6 "g" "c(\"21066-6\", \"3355-5\", \"33562-0\", \"33919-2\", \"43883-8\", \"43884-6\", \"87604-5\")"
|
||||
"SAM" "J01CR01" 119561 "Ampicillin/sulbactam" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "c(\"a/s\", \"ab\", \"ams\", \"amsu\", \"apsu\", \"sam\")" "" 6 "g" ""
|
||||
"AMR" 73341 "Amprolium" "Other antibacterials" "" "c(\"amprocidum\", \"amprolio\", \"amprolium\", \"amprovine\")" "character(0)"
|
||||
"ANI" "J02AX06" 166548 "Anidulafungin" "Antifungals/antimycotics" "Antimycotics for systemic use" "Other antimycotics for systemic use" "anid" "c(\"anidulafungin\", \"anidulafungina\", \"anidulafungine\", \"anidulafunginum\", \"ecalta\", \"eraxis\")" 0.1 "g" "58420-1"
|
||||
"APL" 6602341 "Apalcillin" "Beta-lactams/penicillins" "" "c(\"apalcilina\", \"apalcillin\", \"apalcilline\", \"apalcillinum\")" "character(0)"
|
||||
"APR" 3081545 "Apramycin" "Aminoglycosides" "" "c(\"ambylan\", \"apralan\", \"apramicina\", \"apramycin\", \"apramycine\", \"apramycinum\", \"nebramycin ii\")" "character(0)"
|
||||
"ARB" 68682 "Arbekacin" "Aminoglycosides" "" "c(\"arbekacin\", \"arbekacina\", \"arbekacine\", \"arbekacini sulfas\", \"arbekacinum\", \"habekacin\", \"haberacin\")" "character(0)"
|
||||
"APX" 71961 "Aspoxicillin" "Beta-lactams/penicillins" "" "c(\"aspoxicilina\", \"aspoxicillan\", \"aspoxicillin\", \"aspoxicilline\", \"aspoxicillinum\")" "character(0)"
|
||||
"AST" 5284517 "Astromicin" "Aminoglycosides" "" "c(\"astromicin\", \"astromicin a\", \"astromicina\", \"astromicine\", \"astromicinum\", \"fortimicin a\")" "character(0)"
|
||||
"AVB" 9835049 "Avibactam" "Beta-lactams/penicillins" "" "c(\"avibactam\", \"avibactam free acid\")" "character(0)"
|
||||
"AVI" 71674 "Avilamycin" "Other antibacterials" "" "c(\"avilamycin\", \"avilamycina\", \"avilamycine\", \"avilamycinum\", \"surmax\")" "character(0)"
|
||||
"AVO" 16131159 "Avoparcin" "Glycopeptides" "" "" ""
|
||||
"AZD" "J01CE04" 15574941 "Azidocillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"azidocilina\", \"azidocillin\", \"azidocillina\", \"azidocilline\", \"azidocillinum\")" 1.5 "g" "character(0)"
|
||||
"AZM" "J01FA10" 447043 "Azithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"az\", \"azi\", \"azit\", \"azm\")" "c(\"aritromicina\", \"azasite\", \"azenil\", \"azifast\", \"azigram\", \"azimakrol\", \"azithramycine\", \"azithromycin\", \"azithromycine\", \"azithromycinum\", \"azitrocin\", \"azitromax\", \"azitromicina\", \"azitromicine\", \"azitromin\", \"aziwok\", \"aztrin\", \"azyter\", \"azythromycin\", \"hemomycin\", \"misultina\", \"mixoterin\", \"setron\", \"sumamed\", \"tromix\", \"trulimax\", \"zentavion\", \"zithrax\", \"zithromac\", \"zithromax\", \"zithromax iv\", \"zithromycin\", \"zitrim\", \"zitromax\", \"zitrotek\", \"zmax sr\")" 0.3 "g" 0.5 "g" "c(\"16420-2\", \"25233-8\")"
|
||||
"AZL" "J01CA09" 6479523 "Azlocillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"az\", \"azl\", \"azlo\")" "" 12 "g" ""
|
||||
"ATM" "J01DF01" 5742832 "Aztreonam" "Beta-lactams/penicillins" "Other beta-lactam antibacterials" "Monobactams" "c(\"at\", \"atm\", \"azm\", \"azt\", \"aztr\")" "c(\"azactam\", \"azetreonam\", \"azthreonam\", \"aztreonam\", \"primbactam\")" 4 "g" "c(\"16423-6\", \"25234-6\", \"3369-6\")"
|
||||
"AZA" "Aztreonam/avibactam" "Beta-lactams/penicillins" "" "" ""
|
||||
"BAM" "J01CA06" 441397 "Bacampicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"bacampicilina\", \"bacampicillin\", \"bacampicilline\", \"bacampicillinum\", \"penglobe\")" 1.2 "g" "character(0)"
|
||||
"BAC" "R02AB04" 78358334 "Bacitracin zinc" "Other antibacterials" "baci" "" ""
|
||||
"BDQ" 5388906 "Bedaquiline" "Other antibacterials" "" "c(\"bedaquiline\", \"sirturo\")" "80637-2"
|
||||
"BEK" 439318 "Bekanamycin" "Aminoglycosides" "" "c(\"aminodeoxykanamycin\", \"becanamicina\", \"bekanamycin\", \"bekanamycine\", \"bekanamycinum\", \"nebramycin v\")" "character(0)"
|
||||
"BNB" "J01CE08" "Benzathine benzylpenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "" 3.6 "g" ""
|
||||
"BNP" "J01CE10" 64725 "Benzathine phenoxymethylpenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"bicillin v\", \"biphecillin\")" 2 "g" "character(0)"
|
||||
"PEN" "J01CE01" 5904 "Benzylpenicillin" "Beta-lactams/penicillins" "Combinations of antibacterials" "Combinations of antibacterials" "c(\"bepe\", \"pen\", \"peni\", \"peni g\", \"penicillin\", \"penicillin g\", \"pg\")" "c(\"abbocillin\", \"ayercillin\", \"bencilpenicilina\", \"benzopenicillin\", \"benzyl penicillin\", \"benzylpenicillin\", \"benzylpenicillin g\", \"benzylpenicilline\", \"benzylpenicillinum\", \"bicillin\", \"cillora\", \"cilloral\", \"cilopen\", \"compocillin g\", \"cosmopen\", \"dropcillin\", \"free penicillin g\", \"free penicillin ii\", \"galofak\", \"gelacillin\", \"liquacillin\", \"megacillin\", \"pencillin g\", \"penicillin\", \"penicilling\", \"pentids\", \"permapen\", \"pfizerpen\", \"pfizerpen g\", \"pharmacillin\", \"pradupen\", \"specilline g\", \"ursopen\"
|
||||
"SAM" 119561 "Ampicillin/sulbactam" "Beta-lactams/penicillins" "J01CR01" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "c(\"a/s\", \"ab\", \"ams\", \"amsu\", \"apsu\", \"sam\")" "" 6 "g" ""
|
||||
"AMR" 73341 "Amprolium" "Other antibacterials" "" "c(\"amprocidum\", \"amprolio\", \"amprolium\", \"amprovine\")" "character(0)"
|
||||
"ANI" 166548 "Anidulafungin" "Antifungals/antimycotics" "J02AX06" "Antimycotics for systemic use" "Other antimycotics for systemic use" "anid" "c(\"anidulafungin\", \"anidulafungina\", \"anidulafungine\", \"anidulafunginum\", \"ecalta\", \"eraxis\")" 0.1 "g" "58420-1"
|
||||
"APL" 6602341 "Apalcillin" "Beta-lactams/penicillins" "" "c(\"apalcilina\", \"apalcillin\", \"apalcilline\", \"apalcillinum\")" "character(0)"
|
||||
"APR" 3081545 "Apramycin" "Aminoglycosides" "" "c(\"ambylan\", \"apralan\", \"apramicina\", \"apramycin\", \"apramycine\", \"apramycinum\", \"nebramycin ii\")" "character(0)"
|
||||
"ARB" 68682 "Arbekacin" "Aminoglycosides" "J01GB12" "" "c(\"arbekacin\", \"arbekacina\", \"arbekacine\", \"arbekacini sulfas\", \"arbekacinum\", \"habekacin\", \"haberacin\")" 0.2 "g" "character(0)"
|
||||
"APX" 71961 "Aspoxicillin" "Beta-lactams/penicillins" "J01CA19" "" "c(\"aspoxicilina\", \"aspoxicillan\", \"aspoxicillin\", \"aspoxicilline\", \"aspoxicillinum\")" 4 "g" "character(0)"
|
||||
"AST" 5284517 "Astromicin" "Aminoglycosides" "" "c(\"astromicin\", \"astromicin a\", \"astromicina\", \"astromicine\", \"astromicinum\", \"fortimicin a\")" "character(0)"
|
||||
"AVB" 9835049 "Avibactam" "Beta-lactams/penicillins" "" "c(\"avibactam\", \"avibactam free acid\")" "character(0)"
|
||||
"AVI" 71674 "Avilamycin" "Other antibacterials" "" "c(\"avilamycin\", \"avilamycina\", \"avilamycine\", \"avilamycinum\", \"surmax\")" "character(0)"
|
||||
"AVO" 16131159 "Avoparcin" "Glycopeptides" "" "" ""
|
||||
"AZD" 15574941 "Azidocillin" "Beta-lactams/penicillins" "J01CE04" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"azidocilina\", \"azidocillin\", \"azidocillina\", \"azidocilline\", \"azidocillinum\")" 1.5 "g" "character(0)"
|
||||
"AZM" 447043 "Azithromycin" "Macrolides/lincosamides" "c(\"J01FA10\", \"S01AA26\")" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"az\", \"azi\", \"azit\", \"azm\")" "c(\"aritromicina\", \"azasite\", \"azenil\", \"azifast\", \"azigram\", \"azimakrol\", \"azithramycine\", \"azithromycin\", \"azithromycine\", \"azithromycinum\", \"azitrocin\", \"azitromax\", \"azitromicina\", \"azitromicine\", \"azitromin\", \"aziwok\", \"aztrin\", \"azyter\", \"azythromycin\", \"hemomycin\", \"misultina\", \"mixoterin\", \"setron\", \"sumamed\", \"tromix\", \"trulimax\", \"zentavion\", \"zithrax\", \"zithromac\", \"zithromax\", \"zithromax iv\", \"zithromycin\", \"zitrim\", \"zitromax\", \"zitrotek\", \"zmax sr\")" 0.3 "g" 0.5 "g" "c(\"16420-2\", \"25233-8\")"
|
||||
"AZL" 6479523 "Azlocillin" "Beta-lactams/penicillins" "J01CA09" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"az\", \"azl\", \"azlo\")" "" 12 "g" ""
|
||||
"ATM" 5742832 "Aztreonam" "Beta-lactams/penicillins" "J01DF01" "Other beta-lactam antibacterials" "Monobactams" "c(\"at\", \"atm\", \"azm\", \"azt\", \"aztr\")" "c(\"azactam\", \"azetreonam\", \"azthreonam\", \"aztreonam\", \"primbactam\")" 4 "g" "c(\"16423-6\", \"25234-6\", \"3369-6\")"
|
||||
"AZA" "Aztreonam/avibactam" "Beta-lactams/penicillins" "" "" ""
|
||||
"BAM" 441397 "Bacampicillin" "Beta-lactams/penicillins" "J01CA06" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"bacampicilina\", \"bacampicillin\", \"bacampicilline\", \"bacampicillinum\", \"penglobe\")" 1.2 "g" "character(0)"
|
||||
"BAC" 78358334 "Bacitracin zinc" "Other antibacterials" "R02AB04" "baci" "" ""
|
||||
"BDQ" 5388906 "Bedaquiline" "Other antibacterials" "J04AK05" "" "c(\"bedaquiline\", \"sirturo\")" 86 "mg" "80637-2"
|
||||
"BEK" 439318 "Bekanamycin" "Aminoglycosides" "J01GB13" "" "c(\"aminodeoxykanamycin\", \"becanamicina\", \"bekanamycin\", \"bekanamycine\", \"bekanamycinum\", \"nebramycin v\")" 0.6 "g" "character(0)"
|
||||
"BNB" "Benzathine benzylpenicillin" "Beta-lactams/penicillins" "J01CE08" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "" 3.6 "g" ""
|
||||
"BNP" 64725 "Benzathine phenoxymethylpenicillin" "Beta-lactams/penicillins" "J01CE10" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"bicillin v\", \"biphecillin\")" 2 "g" "character(0)"
|
||||
"PEN" 5904 "Benzylpenicillin" "Beta-lactams/penicillins" "c(\"J01CE01\", \"S01AA14\")" "Combinations of antibacterials" "Combinations of antibacterials" "c(\"bepe\", \"pen\", \"peni\", \"peni g\", \"penicillin\", \"penicillin g\", \"pg\")" "c(\"abbocillin\", \"ayercillin\", \"bencilpenicilina\", \"benzopenicillin\", \"benzyl penicillin\", \"benzylpenicillin\", \"benzylpenicillin g\", \"benzylpenicilline\", \"benzylpenicillinum\", \"bicillin\", \"cillora\", \"cilloral\", \"cilopen\", \"compocillin g\", \"cosmopen\", \"dropcillin\", \"free penicillin g\", \"free penicillin ii\", \"galofak\", \"gelacillin\", \"liquacillin\", \"megacillin\", \"pencillin g\", \"penicillin\", \"penicilling\", \"pentids\", \"permapen\", \"pfizerpen\", \"pfizerpen g\", \"pharmacillin\", \"pradupen\", \"specilline g\", \"ursopen\"
|
||||
)" 3.6 "g" "3913-1"
|
||||
"BES" 10178705 "Besifloxacin" "Quinolones" "" "besifloxacin" "character(0)"
|
||||
"BIA" 71339 "Biapenem" "Carbapenems" "" "c(\"biapenem\", \"biapenern\", \"bipenem\", \"omegacin\")" "character(0)"
|
||||
"BCZ" 65807 "Bicyclomycin (Bicozamycin)" "Other antibacterials" "" "c(\"aizumycin\", \"bacfeed\", \"bacteron\", \"bicozamicina\", \"bicozamycin\", \"bicozamycine\", \"bicozamycinum\")" "character(0)"
|
||||
"BDP" "J01EA02" 68760 "Brodimoprim" "Trimethoprims" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "" "c(\"brodimoprim\", \"brodimoprima\", \"brodimoprime\", \"brodimoprimum\", \"bromdimoprim\", \"hyprim\", \"unitrim\")" 0.2 "g" "character(0)"
|
||||
"BUT" 47472 "Butoconazole" "Antifungals/antimycotics" "" "c(\"butaconazole\", \"butoconazol\", \"butoconazole\", \"butoconazolum\", \"compositenstarke\", \"dahlin\", \"femstat\", \"gynofort\", \"polyfructosanum\")" "character(0)"
|
||||
"CDZ" "J01DD09" 44242317 "Cadazolid" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "cadazolid" 2 "g" "character(0)"
|
||||
"CLA" "J04AA03" "Calcium aminosalicylate" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" "" "" 15 ""
|
||||
"CAP" "J04AB30" 135565060 "Capreomycin" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Antibiotics" "c(\"\", \"capr\")" "" 1 "g" ""
|
||||
"CRB" "J01CA03" 20824 "Carbenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"bar\", \"carb\", \"cb\")" "c(\"anabactyl\", \"carbenicilina\", \"carbenicillin\", \"carbenicillina\", \"carbenicilline\", \"carbenicillinum\", \"geopen\", \"pyopen\")" 12 "g" "3434-8"
|
||||
"CRN" "J01CA05" 93184 "Carindacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"carindacilina\", \"carindacillin\", \"carindacilline\", \"carindacillinum\")" 4 "g" "character(0)"
|
||||
"CAR" 6540466 "Carumonam" "Other antibacterials" "" "c(\"carumonam\", \"carumonamum\")" "character(0)"
|
||||
"CAS" "J02AX04" 2826718 "Caspofungin" "Antifungals/antimycotics" "Antimycotics for systemic use" "Other antimycotics for systemic use" "casp" "c(\"cancidas\", \"capsofungin\", \"caspofungin\")" 50 "mg" "58419-3"
|
||||
"CAC" "J01DB10" 91562 "Cefacetrile" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"cefacetril\", \"cefacetrile\", \"cefacetrilo\", \"cefacetrilum\", \"celospor\", \"celtol\", \"cephacetrile\", \"cristacef\", \"vetrimast\")" "character(0)"
|
||||
"CEC" "J01DC04" 51039 "Cefaclor" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"ccl\", \"cec\", \"cf\", \"cfac\", \"cfc\", \"cfcl\", \"cfr\", \"fac\")" "c(\"alenfral\", \"alfacet\", \"ceclor\", \"ceclor cd\", \"cefaclor\", \"cefaclor anhydrous\", \"cefaclor monohydrate\", \"cefacloro\", \"cefaclorum\", \"cefeaclor\", \"cephaclor\", \"dystaclor mr\", \"keflor\", \"kefral\", \"raniclor\")" 1 "g" "c(\"16564-7\", \"21149-0\")"
|
||||
"CFR" "J01DB05" 47965 "Cefadroxil" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"cfdx\", \"cfr\", \"fad\")" "c(\"cefadrops\", \"cefadroxil\", \"cefadroxil anhydrous\", \"cefadroxilo\", \"cefadroxilum\", \"cefradroxil\", \"cephadroxil\", \"duricef\", \"sumacef\", \"ultracef\")" 2 "g" "16565-4"
|
||||
"RID" "J01DB02" 5773 "Cefaloridine" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cefa" "c(\"aliporina\", \"ampligram\", \"cefaloridin\", \"cefaloridina\", \"cefaloridine\", \"cefaloridinum\", \"cefalorizin\", \"ceflorin\", \"cepaloridin\", \"cepalorin\", \"cephalomycine\", \"cephaloridin\", \"cephaloridine\", \"cephaloridinum\", \"ceporan\", \"ceporin\", \"ceporine\", \"cilifor\", \"deflorin\", \"faredina\", \"floridin\", \"glaxoridin\", \"intrasporin\", \"keflodin\", \"keflordin\", \"kefloridin\", \"kefspor\", \"lloncefal\", \"loridine\", \"sasperin\", \"sefacin\", \"verolgin\", \"vioviantine\")" 3 "g" "character(0)"
|
||||
"MAN" "J01DC03" 456255 "Cefamandole" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cfam\", \"cfmn\")" "c(\"cefadole\", \"cefamandol\", \"cefamandole\", \"cefamandolum\", \"cephadole\", \"cephamandole\", \"kefamandol\", \"kefdole\", \"mancef\")" 6 "g" "3441-3"
|
||||
"CTZ" "J01DB07" 6410758 "Cefatrizine" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"bricef\", \"cefatrix\", \"cefatrizine\", \"cefatrizino\", \"cefatrizinum\", \"cepticol\", \"cetrazil\", \"latocef\", \"orosporina\", \"trizina\")" 1 "g" "character(0)"
|
||||
"CZD" "J01DB06" 71736 "Cefazedone" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"cefazedon\", \"cefazedona\", \"cefazedone\", \"cefazedone acid\", \"cefazedonum\", \"refosporen\", \"refosporene\", \"refosporin\")" 3 "g" "character(0)"
|
||||
"CZO" "J01DB04" 33255 "Cefazolin" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"cfz\", \"cfzl\", \"cz\", \"czol\", \"faz\", \"kz\")" "c(\"atirin\", \"cefamezin\", \"cefamezine\", \"cefazina\", \"cefazolin\", \"cefazolin acid\", \"cefazolina\", \"cefazoline\", \"cefazolinum\", \"cephamezine\", \"cephazolidin\", \"cephazolin\", \"cephazoline\", \"elzogram\", \"firmacef\", \"kefzol\", \"liviclina\", \"totacef\")" 3 "g" "c(\"16566-2\", \"25235-3\", \"3442-1\", \"3443-9\", \"80962-4\")"
|
||||
"CFB" 127527 "Cefbuperazone" "Other antibacterials" "" "c(\"cefbuperazona\", \"cefbuperazone\", \"cefbuperazonum\", \"cefbuperzaone\", \"cerbuperazone\", \"tomiporan\")" "character(0)"
|
||||
"CCP" 6436055 "Cefcapene" "Cephalosporins (3rd gen.)" "" "c(\"cefcamate\", \"cefcapene\")" "character(0)"
|
||||
"CCX" 5282438 "Cefcapene pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefcamate pivoxil\", \"cefcapene piroxil\")" "character(0)"
|
||||
"CDR" "J01DD15" 6915944 "Cefdinir" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cd\", \"cdn\", \"cdr\", \"cfd\", \"din\")" "c(\"cefdinir\", \"cefdinirum\", \"cefdinyl\", \"cefdirnir\", \"ceftinex\", \"cefzon\", \"omnicef\")" 0.6 "g" "character(0)"
|
||||
"DIT" "J01DD16" 9870843 "Cefditoren" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cdn" "cefditoren" 0.4 "g" "character(0)"
|
||||
"DIX" 6437877 "Cefditoren pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefditoren\", \"cefditoren pi voxil\", \"cefditoren pivoxil\", \"cefditorin\", \"cefditorin pivoxil\", \"meiact\", \"spectracef\")" "character(0)"
|
||||
"FEP" "J01DE01" 5479537 "Cefepime" "Cephalosporins (4th gen.)" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "c(\"cfep\", \"cfpi\", \"cpe\", \"cpm\", \"fep\", \"pm\", \"xpm\")" "c(\"axepim\", \"cefepima\", \"cefepime\", \"cefepimum\", \"cepimax\", \"cepimex\", \"maxcef\", \"maxipime\")" 4 "g" "38363-8"
|
||||
"CPC" 9567559 "Cefepime/clavulanic acid" "Cephalosporins (4th gen.)" "c(\"cicl\", \"xpml\")" "" ""
|
||||
"FPT" 9567558 "Cefepime/tazobactam" "Cephalosporins (4th gen.)" "" "" ""
|
||||
"FPZ" "Cefepime/zidebactam" "Other antibacterials" "" "" ""
|
||||
"CAT" "J01DD10" 5487888 "Cefetamet" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "c(\"cefetamet\", \"cefetametum\", \"cepime o\", \"deacetoxycefotaxime\")" 1 "g" "character(0)"
|
||||
"CPI" 5486182 "Cefetamet pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefetamet pivoxyl\", \"globocef\")" "character(0)"
|
||||
"CCL" 71719688 "Cefetecol (Cefcatacol)" "Cephalosporins (4th gen.)" "" "" ""
|
||||
"CZL" 193956 "Cefetrizole" "Cephalosporins (unclassified gen.)" "" "c(\"cefetrizole\", \"cefetrizolum\")" "character(0)"
|
||||
"FDC" 77843966 "Cefiderocol" "Other antibacterials" "" "cefiderocol" "character(0)"
|
||||
"CFM" "J01DD08" 5362065 "Cefixime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfe\", \"cfix\", \"cfxm\", \"dcfm\", \"fix\", \"ix\")" "c(\"cefixim\", \"cefixima\", \"cefixime\", \"cefixime anhydrous\", \"cefiximum\", \"cefixoral\", \"cefspan\", \"cephoral\", \"denvar\", \"necopen\", \"suprax\", \"tricef\", \"unixime\")" 0.4 "g" "c(\"16567-0\", \"25236-1\")"
|
||||
"CMX" "J01DD05" 9570757 "Cefmenoxime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "c(\"bestron\", \"cefmax\", \"cefmenoxima\", \"cefmenoxime\", \"cefmenoximum\")" 2 "g" "character(0)"
|
||||
"CMZ" "J01DC09" 42008 "Cefmetazole" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "c(\"cefmetazole\", \"cefmetazolo\", \"cefmetazolum\")" 4 "g" "character(0)"
|
||||
"CNX" 71141 "Cefminox" "Other antibacterials" "" "c(\"cefminox\", \"cefminoxum\")" "character(0)"
|
||||
"DIZ" "J01DD09" 5361871 "Cefodizime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "c(\"cefodizima\", \"cefodizime\", \"cefodizime acid\", \"cefodizimum\", \"cefodizme\", \"diezime\", \"modivid\", \"neucef\", \"timecef\")" 2 "g" "character(0)"
|
||||
"CID" "J01DC06" 43594 "Cefonicid" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "c(\"cefonicid\", \"cefonicido\", \"cefonicidum\", \"monocef\")" 1 "g" "c(\"25237-9\", \"3444-7\")"
|
||||
"CFP" "J01DD12" 44187 "Cefoperazone" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfp\", \"cfpz\", \"cp\", \"cpz\", \"fop\", \"per\")" "c(\"bioperazone\", \"cefobid\", \"cefoperazine\", \"cefoperazon\", \"cefoperazone\", \"cefoperazone acid\", \"cefoperazono\", \"cefoperazonum\", \"cefozon\", \"medocef\", \"myticef\", \"pathozone\", \"peracef\")" 4 "g" "3445-4"
|
||||
"CSL" "J01DD62" "Cefoperazone/sulbactam" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "" 4 "g" ""
|
||||
"CND" "J01DC11" 43507 "Ceforanide" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "c(\"ceforanide\", \"ceforanido\", \"ceforanidum\", \"precef\", \"radacef\")" 4 "g" "character(0)"
|
||||
"CSE" 9830519 "Cefoselis" "Cephalosporins (4th gen.)" "" "c(\"cefoselis\", \"cefoselis sulfate\", \"winsef\")" "character(0)"
|
||||
"CTX" "J01DD01" 5742673 "Cefotaxime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfot\", \"cft\", \"cftx\", \"ct\", \"ctx\", \"fot\", \"tax\", \"xct\")" "c(\"cefotaxim\", \"cefotaxim hikma\", \"cefotaxima\", \"cefotaxime\", \"cefotaxime acid\", \"cefotaximum\", \"cephotaxime\", \"claforan\", \"omnatax\")" 4 "g" "c(\"25238-7\", \"3446-2\", \"80961-6\")"
|
||||
"CTC" 9575353 "Cefotaxime/clavulanic acid" "Cephalosporins (3rd gen.)" "c(\"cxcl\", \"xctl\")" "" ""
|
||||
"CTS" 9574753 "Cefotaxime/sulbactam" "Cephalosporins (3rd gen.)" "" "" ""
|
||||
"CTT" "J01DC05" 53025 "Cefotetan" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cftt\", \"cn\", \"cte\", \"ctn\", \"ctt\", \"tans\")" "c(\"apacef\", \"cefotetan\", \"cefotetan free acid\", \"cefotetanum\")" 4 "g" "c(\"25239-5\", \"3447-0\")"
|
||||
"CTF" "J01DC07" 43708 "Cefotiam" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "c(\"cefotiam\", \"cefotiam?\", \"cefotiamum\", \"ceradolan\", \"ceradon\", \"haloapor\")" 1.2 "g" 4 "g" "character(0)"
|
||||
"CHE" 125846 "Cefotiam hexetil" "Cephalosporins (3rd gen.)" "" "c(\"cefotiam cilexetil\", \"pansporin t\")" "character(0)"
|
||||
"FOV" 9578573 "Cefovecin" "Cephalosporins (3rd gen.)" "" "" ""
|
||||
"FOX" "J01DC01" 441199 "Cefoxitin" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cfox\", \"cfx\", \"cfxt\", \"cx\", \"fox\", \"fx\")" "c(\"cefoxitin\", \"cefoxitina\", \"cefoxitine\", \"cefoxitinum\", \"cefoxotin\", \"cephoxitin\", \"mefoxin\", \"mefoxitin\", \"rephoxitin\")" 6 "g" "c(\"25240-3\", \"3448-8\")"
|
||||
"FOX1" "Cefoxitin screening" "Cephalosporins (2nd gen.)" "cfsc" "" ""
|
||||
"ZOP" 9571080 "Cefozopran" "Cephalosporins (4th gen.)" "" "cefozopran" "character(0)"
|
||||
"CFZ" 68597 "Cefpimizole" "Cephalosporins (3rd gen.)" "" "c(\"cefpimizol\", \"cefpimizole\", \"cefpimizole sodium\", \"cefpimizolum\")" "character(0)"
|
||||
"CPM" "J01DD11" 636405 "Cefpiramide" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "c(\"cefpiramide\", \"cefpiramide acid\", \"cefpiramido\", \"cefpiramidum\")" 2 "g" "character(0)"
|
||||
"CPO" "J01DE02" 5479539 "Cefpirome" "Cephalosporins (4th gen.)" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "c(\"\", \"cfpr\")" "c(\"broact\", \"cefpiroma\", \"cefpirome\", \"cefpiromum\", \"cefrom\", \"cerfpirome\", \"keiten\")" 4 "g" "character(0)"
|
||||
"CPD" "J01DD13" 6335986 "Cefpodoxime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfpd\", \"cfpo\", \"cpd\", \"pod\", \"px\")" "c(\"cefpodoxim acid\", \"cefpodoxima\", \"cefpodoxime\", \"cefpodoxime acid\", \"cefpodoximum\", \"epoxim\")" 0.4 "g" "25241-1"
|
||||
"CPX" 6526396 "Cefpodoxime proxetil" "Cephalosporins (3rd gen.)" "" "c(\"cefodox\", \"cefoprox\", \"cefpodoxime proxetil\", \"cepodem\", \"orelox\", \"otreon\", \"podomexef\", \"simplicef\", \"vantin\")" "character(0)"
|
||||
"CDC" "Cefpodoxime/clavulanic acid" "Cephalosporins (3rd gen.)" "c(\"\", \"cecl\")" "" ""
|
||||
"CPR" "J01DC10" 5281006 "Cefprozil" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cpr\", \"cpz\", \"fp\")" "c(\"arzimol\", \"brisoral\", \"cefprozil\", \"cefprozil anhydrous\", \"cefprozil hydrate\", \"cefprozilo\", \"cefprozilum\", \"cefzil\", \"cronocef\", \"procef\", \"serozil\")" 1 "g" "character(0)"
|
||||
"CEQ" 5464355 "Cefquinome" "Cephalosporins (4th gen.)" "" "c(\"cefquinoma\", \"cefquinome\", \"cefquinomum\", \"cobactan\")" "character(0)"
|
||||
"CRD" "J01DB11" 5284529 "Cefroxadine" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"cefroxadine\", \"cefroxadino\", \"cefroxadinum\")" 2.1 "character(0)"
|
||||
"CFS" "J01DD03" 656575 "Cefsulodin" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfsl\", \"cfsu\")" "c(\"cefsulodin\", \"cefsulodine\", \"cefsulodino\", \"cefsulodinum\")" 4 "g" "c(\"131-3\", \"25242-9\")"
|
||||
"CSU" 68718 "Cefsumide" "Cephalosporins (unclassified gen.)" "" "c(\"cefsumide\", \"cefsumido\", \"cefsumidum\")" "character(0)"
|
||||
"CPT" "J01DI02" 56841980 "Ceftaroline" "Cephalosporins (5th gen.)" "c(\"\", \"cfro\")" "c(\"teflaro\", \"zinforo\")" 1.2 "character(0)"
|
||||
"CPA" "Ceftaroline/avibactam" "Cephalosporins (5th gen.)" "" "" ""
|
||||
"CAZ" "J01DD02" 5481173 "Ceftazidime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"caz\", \"cefta\", \"cfta\", \"cftz\", \"taz\", \"tz\", \"xtz\")" "c(\"ceftazidim\", \"ceftazidima\", \"ceftazidime\", \"ceftazidimum\", \"ceptaz\", \"fortaz\", \"fortum\", \"pentacef\", \"tazicef\", \"tazidime\")" 4 "g" "c(\"21151-6\", \"3449-6\", \"80960-8\")"
|
||||
"CZA" "J01DD52" 90643431 "Ceftazidime/avibactam" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"\", \"cfav\")" "c(\"avycaz\", \"zavicefta\")" 6 "g" ""
|
||||
"CCV" "J01DD52" 9575352 "Ceftazidime/clavulanic acid" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"czcl\", \"xtzl\")" "" 6 ""
|
||||
"CEM" 6537431 "Cefteram" "Cephalosporins (3rd gen.)" "" "c(\"cefteram\", \"cefterame\", \"cefteramum\", \"ceftetrame\")" "character(0)"
|
||||
"CPL" 5362114 "Cefteram pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefteram pivoxil\", \"tomiron\")" "character(0)"
|
||||
"CTL" "J01DB12" 65755 "Ceftezole" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"ceftezol\", \"ceftezole\", \"ceftezolo\", \"ceftezolum\", \"demethylcefazolin\")" 3 "g" "character(0)"
|
||||
"CTB" "J01DD14" 5282242 "Ceftibuten" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cb\", \"cfbu\", \"ctb\", \"tib\")" "c(\"ceftem\", \"ceftibuten\", \"ceftibuten hydrate\", \"ceftibutene\", \"ceftibuteno\", \"ceftibutenum\", \"cephem\", \"ceprifran\", \"isocef\", \"keimax\")" 0.4 "g" "character(0)"
|
||||
"TIO" 6328657 "Ceftiofur" "Cephalosporins (3rd gen.)" "" "c(\"ceftiofur\", \"ceftiofurum\", \"excede\", \"excenel\", \"naxcel\")" "character(0)"
|
||||
"CZX" "J01DD07" 6533629 "Ceftizoxime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfzx\", \"ctz\", \"cz\", \"czx\", \"tiz\", \"zox\")" "c(\"cefizox\", \"ceftisomin\", \"ceftix\", \"ceftizoxima\", \"ceftizoxime\", \"ceftizoximum\", \"epocelin\", \"eposerin\")" 4 "g" "c(\"25243-7\", \"3450-4\")"
|
||||
"CZP" 9578661 "Ceftizoxime alapivoxil" "Cephalosporins (3rd gen.)" "" "" ""
|
||||
"BPR" "J01DI01" 135413542 "Ceftobiprole" "Cephalosporins (5th gen.)" "" "ceftobiprole" 1.5 "character(0)"
|
||||
"CFM1" "J01DI01" 135413544 "Ceftobiprole medocaril" "Cephalosporins (5th gen.)" "Other beta-lactam antibacterials" "Other cephalosporins" "" "" 1.5 ""
|
||||
"CEI" "J01DI54" "Ceftolozane/enzyme inhibitor" "Cephalosporins (5th gen.)" "Other beta-lactam antibacterials" "Other cephalosporins" "" "" 3 ""
|
||||
"CZT" "Ceftolozane/tazobactam" "Cephalosporins (5th gen.)" "" "" ""
|
||||
"CRO" "J01DD04" 5479530 "Ceftriaxone" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"axo\", \"cax\", \"cftr\", \"cro\", \"ctr\", \"frx\", \"tx\")" "c(\"biotrakson\", \"cefatriaxone\", \"cefatriaxone hydrate\", \"ceftriaxon\", \"ceftriaxona\", \"ceftriaxone\", \"ceftriaxone sodium\", \"ceftriaxonum\", \"ceftriazone\", \"cephtriaxone\", \"longacef\", \"rocefin\", \"rocephalin\", \"rocephin\", \"rocephine\", \"rophex\")" 2 "g" "c(\"25244-5\", \"3451-2\", \"80957-4\")"
|
||||
"CXM" "J01DC02" 5479529 "Cefuroxime" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cfrx\", \"cfur\", \"cfx\", \"crm\", \"cxm\", \"fur\", \"rox\", \"xm\")" "c(\"biofuroksym\", \"cefuril\", \"cefuroxim\", \"cefuroxime\", \"cefuroximine\", \"cefuroximo\", \"cefuroximum\", \"cephuroxime\", \"kefurox\", \"sharox\", \"zinacef\", \"zinacef danmark\")" 0.5 "g" 3 "g" "c(\"25245-2\", \"3452-0\", \"80608-3\", \"80617-4\")"
|
||||
"CXA" 6321416 "Cefuroxime axetil" "Cephalosporins (2nd gen.)" "c(\"\", \"cfax\")" "c(\"altacef\", \"bioracef\", \"cefaks\", \"cefazine\", \"ceftin\", \"cefuroximaxetil\", \"cefuroxime axetil\", \"celocid\", \"cepazine\", \"cethixim\", \"cetoxil\", \"coliofossim\", \"elobact\", \"forcef\", \"furoxime\", \"kalcef\", \"maxitil\", \"medoxm\", \"nivador\", \"zinnat\")" "character(0)"
|
||||
"CFM2" "J01RA03" "Cefuroxime/metronidazole" "Other antibacterials" "Combinations of antibacterials" "Combinations of antibacterials" "" "" ""
|
||||
"ZON" 6336505 "Cefuzonam" "Other antibacterials" "" "c(\"cefuzonam\", \"cefuzonam sodium\", \"cefuzoname\", \"cefuzonamum\")" "character(0)"
|
||||
"LEX" "J01DB01" 27447 "Cephalexin" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"\", \"cflx\")" "c(\"alcephin\", \"alexin\", \"alsporin\", \"anhydrous cefalexin\", \"anhydrous cephalexin\", \"biocef\", \"carnosporin\", \"cefablan\", \"cefadal\", \"cefadin\", \"cefadina\", \"cefaleksin\", \"cefalessina\", \"cefalexin\", \"cefalexin anhydrous\", \"cefalexina\", \"cefalexine\", \"cefalexinum\", \"cefalin\", \"cefaloto\", \"cefaseptin\", \"ceflax\", \"ceforal\", \"cefovit\", \"celexin\", \"cepastar\", \"cepexin\", \"cephacillin\", \"cephalexin\", \"cephalexin anhydrous\", \"cephalexine\", \"cephalexinum\", \"cephanasten\", \"cephaxin\", \"cephin\", \"ceporex\", \"ceporex forte\",
|
||||
"BES" 10178705 "Besifloxacin" "Quinolones" "S01AE08" "" "besifloxacin" "character(0)"
|
||||
"BIA" 71339 "Biapenem" "Carbapenems" "J01DH05" "" "c(\"biapenem\", \"biapenern\", \"bipenem\", \"omegacin\")" 1.2 "g" "character(0)"
|
||||
"BCZ" 65807 "Bicyclomycin (Bicozamycin)" "Other antibacterials" "" "c(\"aizumycin\", \"bacfeed\", \"bacteron\", \"bicozamicina\", \"bicozamycin\", \"bicozamycine\", \"bicozamycinum\")" "character(0)"
|
||||
"BDP" 68760 "Brodimoprim" "Trimethoprims" "J01EA02" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "" "c(\"brodimoprim\", \"brodimoprima\", \"brodimoprime\", \"brodimoprimum\", \"bromdimoprim\", \"hyprim\", \"unitrim\")" 0.2 "g" "character(0)"
|
||||
"BUT" 47472 "Butoconazole" "Antifungals/antimycotics" "G01AF15" "" "c(\"butaconazole\", \"butoconazol\", \"butoconazole\", \"butoconazolum\", \"compositenstarke\", \"dahlin\", \"femstat\", \"gynofort\", \"polyfructosanum\")" "character(0)"
|
||||
"CDZ" 44242317 "Cadazolid" "Oxazolidinones" "" "cadazolid" "character(0)"
|
||||
"CLA" "Calcium aminosalicylate" "Antimycobacterials" "J04AA03" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" "" "" 15 "g" ""
|
||||
"CAP" 135565060 "Capreomycin" "Antimycobacterials" "J04AB30" "Drugs for treatment of tuberculosis" "Antibiotics" "c(\"\", \"capr\")" "" 1 "g" ""
|
||||
"CRB" 20824 "Carbenicillin" "Beta-lactams/penicillins" "J01CA03" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"bar\", \"carb\", \"cb\")" "c(\"anabactyl\", \"carbenicilina\", \"carbenicillin\", \"carbenicillina\", \"carbenicilline\", \"carbenicillinum\", \"geopen\", \"pyopen\")" 12 "g" "3434-8"
|
||||
"CRN" 93184 "Carindacillin" "Beta-lactams/penicillins" "J01CA05" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"carindacilina\", \"carindacillin\", \"carindacilline\", \"carindacillinum\")" 4 "g" "character(0)"
|
||||
"CAR" 6540466 "Carumonam" "Other antibacterials" "J01DF02" "" "c(\"carumonam\", \"carumonamum\")" 2 "g" "character(0)"
|
||||
"CAS" 2826718 "Caspofungin" "Antifungals/antimycotics" "J02AX04" "Antimycotics for systemic use" "Other antimycotics for systemic use" "casp" "c(\"cancidas\", \"capsofungin\", \"caspofungin\")" 50 "mg" "58419-3"
|
||||
"CAC" 91562 "Cefacetrile" "Cephalosporins (1st gen.)" "J01DB10" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"cefacetril\", \"cefacetrile\", \"cefacetrilo\", \"cefacetrilum\", \"celospor\", \"celtol\", \"cephacetrile\", \"cristacef\", \"vetrimast\")" "character(0)"
|
||||
"CEC" 51039 "Cefaclor" "Cephalosporins (2nd gen.)" "J01DC04" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"ccl\", \"cec\", \"cf\", \"cfac\", \"cfc\", \"cfcl\", \"cfr\", \"fac\")" "c(\"alenfral\", \"alfacet\", \"ceclor\", \"ceclor cd\", \"cefaclor\", \"cefaclor anhydrous\", \"cefaclor monohydrate\", \"cefacloro\", \"cefaclorum\", \"cefeaclor\", \"cephaclor\", \"dystaclor mr\", \"keflor\", \"kefral\", \"raniclor\")" 1 "g" "c(\"16564-7\", \"21149-0\")"
|
||||
"CFR" 47965 "Cefadroxil" "Cephalosporins (1st gen.)" "J01DB05" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"cfdx\", \"cfr\", \"fad\")" "c(\"cefadrops\", \"cefadroxil\", \"cefadroxil anhydrous\", \"cefadroxilo\", \"cefadroxilum\", \"cefradroxil\", \"cephadroxil\", \"duricef\", \"sumacef\", \"ultracef\")" 2 "g" "16565-4"
|
||||
"RID" 5773 "Cefaloridine" "Cephalosporins (1st gen.)" "J01DB02" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cefa" "c(\"aliporina\", \"ampligram\", \"cefaloridin\", \"cefaloridina\", \"cefaloridine\", \"cefaloridinum\", \"cefalorizin\", \"ceflorin\", \"cepaloridin\", \"cepalorin\", \"cephalomycine\", \"cephaloridin\", \"cephaloridine\", \"cephaloridinum\", \"ceporan\", \"ceporin\", \"ceporine\", \"cilifor\", \"deflorin\", \"faredina\", \"floridin\", \"glaxoridin\", \"intrasporin\", \"keflodin\", \"keflordin\", \"kefloridin\", \"kefspor\", \"lloncefal\", \"loridine\", \"sasperin\", \"sefacin\", \"verolgin\", \"vioviantine\")" 3 "g" "character(0)"
|
||||
"MAN" 456255 "Cefamandole" "Cephalosporins (2nd gen.)" "J01DC03" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cfam\", \"cfmn\")" "c(\"cefadole\", \"cefamandol\", \"cefamandole\", \"cefamandolum\", \"cephadole\", \"cephamandole\", \"kefamandol\", \"kefdole\", \"mancef\")" 6 "g" "3441-3"
|
||||
"CTZ" 6410758 "Cefatrizine" "Cephalosporins (1st gen.)" "J01DB07" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"bricef\", \"cefatrix\", \"cefatrizine\", \"cefatrizino\", \"cefatrizinum\", \"cepticol\", \"cetrazil\", \"latocef\", \"orosporina\", \"trizina\")" 1 "g" "character(0)"
|
||||
"CZD" 71736 "Cefazedone" "Cephalosporins (1st gen.)" "J01DB06" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"cefazedon\", \"cefazedona\", \"cefazedone\", \"cefazedone acid\", \"cefazedonum\", \"refosporen\", \"refosporene\", \"refosporin\")" 3 "g" "character(0)"
|
||||
"CZO" 33255 "Cefazolin" "Cephalosporins (1st gen.)" "J01DB04" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"cfz\", \"cfzl\", \"cz\", \"czol\", \"faz\", \"kz\")" "c(\"atirin\", \"cefamezin\", \"cefamezine\", \"cefazina\", \"cefazolin\", \"cefazolin acid\", \"cefazolina\", \"cefazoline\", \"cefazolinum\", \"cephamezine\", \"cephazolidin\", \"cephazolin\", \"cephazoline\", \"elzogram\", \"firmacef\", \"kefzol\", \"liviclina\", \"totacef\")" 3 "g" "c(\"16566-2\", \"25235-3\", \"3442-1\", \"3443-9\", \"80962-4\")"
|
||||
"CFB" 127527 "Cefbuperazone" "Other antibacterials" "J01DC13" "" "c(\"cefbuperazona\", \"cefbuperazone\", \"cefbuperazonum\", \"cefbuperzaone\", \"cerbuperazone\", \"tomiporan\")" 2 "g" "character(0)"
|
||||
"CCP" 6436055 "Cefcapene" "Cephalosporins (3rd gen.)" "J01DD17" "" "c(\"cefcamate\", \"cefcapene\")" 0.45 "g" "character(0)"
|
||||
"CCX" 5282438 "Cefcapene pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefcamate pivoxil\", \"cefcapene piroxil\")" "character(0)"
|
||||
"CDR" 6915944 "Cefdinir" "Cephalosporins (3rd gen.)" "J01DD15" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cd\", \"cdn\", \"cdr\", \"cfd\", \"din\")" "c(\"cefdinir\", \"cefdinirum\", \"cefdinyl\", \"cefdirnir\", \"ceftinex\", \"cefzon\", \"omnicef\")" 0.6 "g" "character(0)"
|
||||
"DIT" 9870843 "Cefditoren" "Cephalosporins (3rd gen.)" "J01DD16" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cdn" "cefditoren" 0.4 "g" "character(0)"
|
||||
"DIX" 6437877 "Cefditoren pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefditoren\", \"cefditoren pi voxil\", \"cefditoren pivoxil\", \"cefditorin\", \"cefditorin pivoxil\", \"meiact\", \"spectracef\")" "character(0)"
|
||||
"FEP" 5479537 "Cefepime" "Cephalosporins (4th gen.)" "J01DE01" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "c(\"cfep\", \"cfpi\", \"cpe\", \"cpm\", \"fep\", \"pm\", \"xpm\")" "c(\"axepim\", \"cefepima\", \"cefepime\", \"cefepimum\", \"cepimax\", \"cepimex\", \"maxcef\", \"maxipime\")" 4 "g" "38363-8"
|
||||
"CPC" 9567559 "Cefepime/clavulanic acid" "Cephalosporins (4th gen.)" "c(\"cicl\", \"xpml\")" "" ""
|
||||
"FPT" 9567558 "Cefepime/tazobactam" "Cephalosporins (4th gen.)" "" "" ""
|
||||
"FPZ" "Cefepime/zidebactam" "Other antibacterials" "" "" ""
|
||||
"CAT" 5487888 "Cefetamet" "Cephalosporins (3rd gen.)" "J01DD10" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "c(\"cefetamet\", \"cefetametum\", \"cepime o\", \"deacetoxycefotaxime\")" 1 "g" "character(0)"
|
||||
"CPI" 5486182 "Cefetamet pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefetamet pivoxyl\", \"globocef\")" "character(0)"
|
||||
"CCL" 71719688 "Cefetecol (Cefcatacol)" "Cephalosporins (4th gen.)" "" "" ""
|
||||
"CZL" 193956 "Cefetrizole" "Cephalosporins (unclassified gen.)" "" "c(\"cefetrizole\", \"cefetrizolum\")" "character(0)"
|
||||
"FDC" 77843966 "Cefiderocol" "Other antibacterials" "J01DI04" "" "cefiderocol" "character(0)"
|
||||
"CFM" 5362065 "Cefixime" "Cephalosporins (3rd gen.)" "J01DD08" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfe\", \"cfix\", \"cfxm\", \"dcfm\", \"fix\", \"ix\")" "c(\"cefixim\", \"cefixima\", \"cefixime\", \"cefixime anhydrous\", \"cefiximum\", \"cefixoral\", \"cefspan\", \"cephoral\", \"denvar\", \"necopen\", \"suprax\", \"tricef\", \"unixime\")" 0.4 "g" "c(\"16567-0\", \"25236-1\")"
|
||||
"CMX" 9570757 "Cefmenoxime" "Cephalosporins (3rd gen.)" "J01DD05" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "c(\"bestron\", \"cefmax\", \"cefmenoxima\", \"cefmenoxime\", \"cefmenoximum\")" 2 "g" "character(0)"
|
||||
"CMZ" 42008 "Cefmetazole" "Cephalosporins (2nd gen.)" "J01DC09" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "c(\"cefmetazole\", \"cefmetazolo\", \"cefmetazolum\")" 4 "g" "character(0)"
|
||||
"CNX" 71141 "Cefminox" "Other antibacterials" "J01DC12" "" "c(\"cefminox\", \"cefminoxum\")" 4 "g" "character(0)"
|
||||
"DIZ" 5361871 "Cefodizime" "Cephalosporins (3rd gen.)" "J01DD09" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "c(\"cefodizima\", \"cefodizime\", \"cefodizime acid\", \"cefodizimum\", \"cefodizme\", \"diezime\", \"modivid\", \"neucef\", \"timecef\")" 2 "g" "character(0)"
|
||||
"CID" 43594 "Cefonicid" "Cephalosporins (2nd gen.)" "J01DC06" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "c(\"cefonicid\", \"cefonicido\", \"cefonicidum\", \"monocef\")" 1 "g" "c(\"25237-9\", \"3444-7\")"
|
||||
"CFP" 44187 "Cefoperazone" "Cephalosporins (3rd gen.)" "J01DD12" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfp\", \"cfpz\", \"cp\", \"cpz\", \"fop\", \"per\")" "c(\"bioperazone\", \"cefobid\", \"cefoperazine\", \"cefoperazon\", \"cefoperazone\", \"cefoperazone acid\", \"cefoperazono\", \"cefoperazonum\", \"cefozon\", \"medocef\", \"myticef\", \"pathozone\", \"peracef\")" 4 "g" "3445-4"
|
||||
"CSL" "Cefoperazone/sulbactam" "Cephalosporins (3rd gen.)" "J01DD62" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "" 4 "g" ""
|
||||
"CND" 43507 "Ceforanide" "Cephalosporins (2nd gen.)" "J01DC11" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "c(\"ceforanide\", \"ceforanido\", \"ceforanidum\", \"precef\", \"radacef\")" 4 "g" "character(0)"
|
||||
"CSE" 9830519 "Cefoselis" "Cephalosporins (4th gen.)" "" "c(\"cefoselis\", \"cefoselis sulfate\", \"winsef\")" "character(0)"
|
||||
"CTX" 5742673 "Cefotaxime" "Cephalosporins (3rd gen.)" "J01DD01" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfot\", \"cft\", \"cftx\", \"ct\", \"ctx\", \"fot\", \"tax\", \"xct\")" "c(\"cefotaxim\", \"cefotaxim hikma\", \"cefotaxima\", \"cefotaxime\", \"cefotaxime acid\", \"cefotaximum\", \"cephotaxime\", \"claforan\", \"omnatax\")" 4 "g" "c(\"25238-7\", \"3446-2\", \"80961-6\")"
|
||||
"CTC" 9575353 "Cefotaxime/clavulanic acid" "Cephalosporins (3rd gen.)" "c(\"cxcl\", \"xctl\")" "" ""
|
||||
"CTS" 9574753 "Cefotaxime/sulbactam" "Cephalosporins (3rd gen.)" "" "" ""
|
||||
"CTT" 53025 "Cefotetan" "Cephalosporins (2nd gen.)" "J01DC05" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cftt\", \"cn\", \"cte\", \"ctn\", \"ctt\", \"tans\")" "c(\"apacef\", \"cefotetan\", \"cefotetan free acid\", \"cefotetanum\")" 4 "g" "c(\"25239-5\", \"3447-0\")"
|
||||
"CTF" 43708 "Cefotiam" "Cephalosporins (2nd gen.)" "J01DC07" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "c(\"cefotiam\", \"cefotiam?\", \"cefotiamum\", \"ceradolan\", \"ceradon\", \"haloapor\")" 1.2 "g" 4 "g" "character(0)"
|
||||
"CHE" 125846 "Cefotiam hexetil" "Cephalosporins (3rd gen.)" "" "c(\"cefotiam cilexetil\", \"pansporin t\")" "character(0)"
|
||||
"FOV" 9578573 "Cefovecin" "Cephalosporins (3rd gen.)" "" "" ""
|
||||
"FOX" 441199 "Cefoxitin" "Cephalosporins (2nd gen.)" "J01DC01" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cfox\", \"cfx\", \"cfxt\", \"cx\", \"fox\", \"fx\")" "c(\"cefoxitin\", \"cefoxitina\", \"cefoxitine\", \"cefoxitinum\", \"cefoxotin\", \"cephoxitin\", \"mefoxin\", \"mefoxitin\", \"rephoxitin\")" 6 "g" "c(\"25240-3\", \"3448-8\")"
|
||||
"FOX1" "Cefoxitin screening" "Cephalosporins (2nd gen.)" "cfsc" "" ""
|
||||
"ZOP" 9571080 "Cefozopran" "Cephalosporins (4th gen.)" "J01DE03" "" "cefozopran" 4 "g" "character(0)"
|
||||
"CFZ" 68597 "Cefpimizole" "Cephalosporins (3rd gen.)" "" "c(\"cefpimizol\", \"cefpimizole\", \"cefpimizole sodium\", \"cefpimizolum\")" "character(0)"
|
||||
"CPM" 636405 "Cefpiramide" "Cephalosporins (3rd gen.)" "J01DD11" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "c(\"cefpiramide\", \"cefpiramide acid\", \"cefpiramido\", \"cefpiramidum\")" 2 "g" "character(0)"
|
||||
"CPO" 5479539 "Cefpirome" "Cephalosporins (4th gen.)" "J01DE02" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "c(\"\", \"cfpr\")" "c(\"broact\", \"cefpiroma\", \"cefpirome\", \"cefpiromum\", \"cefrom\", \"cerfpirome\", \"keiten\")" 4 "g" "character(0)"
|
||||
"CPD" 6335986 "Cefpodoxime" "Cephalosporins (3rd gen.)" "J01DD13" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfpd\", \"cfpo\", \"cpd\", \"pod\", \"px\")" "c(\"cefpodoxim acid\", \"cefpodoxima\", \"cefpodoxime\", \"cefpodoxime acid\", \"cefpodoximum\", \"epoxim\")" 0.4 "g" "25241-1"
|
||||
"CPX" 6526396 "Cefpodoxime proxetil" "Cephalosporins (3rd gen.)" "" "c(\"cefodox\", \"cefoprox\", \"cefpodoxime proxetil\", \"cepodem\", \"orelox\", \"otreon\", \"podomexef\", \"simplicef\", \"vantin\")" "character(0)"
|
||||
"CDC" "Cefpodoxime/clavulanic acid" "Cephalosporins (3rd gen.)" "c(\"\", \"cecl\")" "" ""
|
||||
"CPR" 5281006 "Cefprozil" "Cephalosporins (2nd gen.)" "J01DC10" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cpr\", \"cpz\", \"fp\")" "c(\"arzimol\", \"brisoral\", \"cefprozil\", \"cefprozil anhydrous\", \"cefprozil hydrate\", \"cefprozilo\", \"cefprozilum\", \"cefzil\", \"cronocef\", \"procef\", \"serozil\")" 1 "g" "character(0)"
|
||||
"CEQ" 5464355 "Cefquinome" "Cephalosporins (4th gen.)" "" "c(\"cefquinoma\", \"cefquinome\", \"cefquinomum\", \"cobactan\")" "character(0)"
|
||||
"CRD" 5284529 "Cefroxadine" "Cephalosporins (1st gen.)" "J01DB11" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"cefroxadine\", \"cefroxadino\", \"cefroxadinum\")" 2.1 "g" "character(0)"
|
||||
"CFS" 656575 "Cefsulodin" "Cephalosporins (3rd gen.)" "J01DD03" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfsl\", \"cfsu\")" "c(\"cefsulodin\", \"cefsulodine\", \"cefsulodino\", \"cefsulodinum\")" 4 "g" "c(\"131-3\", \"25242-9\")"
|
||||
"CSU" 68718 "Cefsumide" "Cephalosporins (unclassified gen.)" "" "c(\"cefsumide\", \"cefsumido\", \"cefsumidum\")" "character(0)"
|
||||
"CPT" 56841980 "Ceftaroline" "Cephalosporins (5th gen.)" "J01DI02" "c(\"\", \"cfro\")" "c(\"teflaro\", \"zinforo\")" 1.2 "g" "character(0)"
|
||||
"CPA" "Ceftaroline/avibactam" "Cephalosporins (5th gen.)" "" "" ""
|
||||
"CAZ" 5481173 "Ceftazidime" "Cephalosporins (3rd gen.)" "J01DD02" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"caz\", \"cefta\", \"cfta\", \"cftz\", \"taz\", \"tz\", \"xtz\")" "c(\"ceftazidim\", \"ceftazidima\", \"ceftazidime\", \"ceftazidimum\", \"ceptaz\", \"fortaz\", \"fortum\", \"pentacef\", \"tazicef\", \"tazidime\")" 4 "g" "c(\"21151-6\", \"3449-6\", \"80960-8\")"
|
||||
"CZA" 90643431 "Ceftazidime/avibactam" "Cephalosporins (3rd gen.)" "c(\"\", \"cfav\")" "c(\"avycaz\", \"zavicefta\")" ""
|
||||
"CCV" 9575352 "Ceftazidime/clavulanic acid" "Cephalosporins (3rd gen.)" "J01DD52" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"czcl\", \"xtzl\")" "" 6 "g" ""
|
||||
"CEM" 6537431 "Cefteram" "Cephalosporins (3rd gen.)" "J01DD18" "" "c(\"cefteram\", \"cefterame\", \"cefteramum\", \"ceftetrame\")" 0.4 "g" "character(0)"
|
||||
"CPL" 5362114 "Cefteram pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefteram pivoxil\", \"tomiron\")" "character(0)"
|
||||
"CTL" 65755 "Ceftezole" "Cephalosporins (1st gen.)" "J01DB12" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"ceftezol\", \"ceftezole\", \"ceftezolo\", \"ceftezolum\", \"demethylcefazolin\")" 3 "g" "character(0)"
|
||||
"CTB" 5282242 "Ceftibuten" "Cephalosporins (3rd gen.)" "J01DD14" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cb\", \"cfbu\", \"ctb\", \"tib\")" "c(\"ceftem\", \"ceftibuten\", \"ceftibuten hydrate\", \"ceftibutene\", \"ceftibuteno\", \"ceftibutenum\", \"cephem\", \"ceprifran\", \"isocef\", \"keimax\")" 0.4 "g" "character(0)"
|
||||
"TIO" 6328657 "Ceftiofur" "Cephalosporins (3rd gen.)" "" "c(\"ceftiofur\", \"ceftiofurum\", \"excede\", \"excenel\", \"naxcel\")" "character(0)"
|
||||
"CZX" 6533629 "Ceftizoxime" "Cephalosporins (3rd gen.)" "J01DD07" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfzx\", \"ctz\", \"cz\", \"czx\", \"tiz\", \"zox\")" "c(\"cefizox\", \"ceftisomin\", \"ceftix\", \"ceftizoxima\", \"ceftizoxime\", \"ceftizoximum\", \"epocelin\", \"eposerin\")" 4 "g" "c(\"25243-7\", \"3450-4\")"
|
||||
"CZP" 9578661 "Ceftizoxime alapivoxil" "Cephalosporins (3rd gen.)" "" "" ""
|
||||
"BPR" 135413542 "Ceftobiprole" "Cephalosporins (5th gen.)" "" "ceftobiprole" "character(0)"
|
||||
"CFM1" 135413544 "Ceftobiprole medocaril" "Cephalosporins (5th gen.)" "J01DI01" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "" "" 1.5 "g" ""
|
||||
"CEI" "Ceftolozane/enzyme inhibitor" "Cephalosporins (5th gen.)" "J01DI54" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "" "" 3 "g" ""
|
||||
"CZT" "Ceftolozane/tazobactam" "Cephalosporins (5th gen.)" "" "" ""
|
||||
"CRO" 5479530 "Ceftriaxone" "Cephalosporins (3rd gen.)" "J01DD04" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"axo\", \"cax\", \"cftr\", \"cro\", \"ctr\", \"frx\", \"tx\")" "c(\"biotrakson\", \"cefatriaxone\", \"cefatriaxone hydrate\", \"ceftriaxon\", \"ceftriaxona\", \"ceftriaxone\", \"ceftriaxone sodium\", \"ceftriaxonum\", \"ceftriazone\", \"cephtriaxone\", \"longacef\", \"rocefin\", \"rocephalin\", \"rocephin\", \"rocephine\", \"rophex\")" 2 "g" "c(\"25244-5\", \"3451-2\", \"80957-4\")"
|
||||
"CXM" 5479529 "Cefuroxime" "Cephalosporins (2nd gen.)" "c(\"J01DC02\", \"S01AA27\")" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cfrx\", \"cfur\", \"cfx\", \"crm\", \"cxm\", \"fur\", \"rox\", \"xm\")" "c(\"biofuroksym\", \"cefuril\", \"cefuroxim\", \"cefuroxime\", \"cefuroximine\", \"cefuroximo\", \"cefuroximum\", \"cephuroxime\", \"kefurox\", \"sharox\", \"zinacef\", \"zinacef danmark\")" 0.5 "g" 3 "g" "c(\"25245-2\", \"3452-0\", \"80608-3\", \"80617-4\")"
|
||||
"CXA" 6321416 "Cefuroxime axetil" "Cephalosporins (2nd gen.)" "c(\"\", \"cfax\")" "c(\"altacef\", \"bioracef\", \"cefaks\", \"cefazine\", \"ceftin\", \"cefuroximaxetil\", \"cefuroxime axetil\", \"celocid\", \"cepazine\", \"cethixim\", \"cetoxil\", \"coliofossim\", \"elobact\", \"forcef\", \"furoxime\", \"kalcef\", \"maxitil\", \"medoxm\", \"nivador\", \"zinnat\")" "character(0)"
|
||||
"CFM2" "Cefuroxime/metronidazole" "Other antibacterials" "J01RA03" "Combinations of antibacterials" "Combinations of antibacterials" "" "" ""
|
||||
"ZON" 6336505 "Cefuzonam" "Other antibacterials" "" "c(\"cefuzonam\", \"cefuzonam sodium\", \"cefuzoname\", \"cefuzonamum\")" "character(0)"
|
||||
"LEX" 27447 "Cephalexin" "Cephalosporins (1st gen.)" "J01DB01" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"\", \"cflx\")" "c(\"alcephin\", \"alexin\", \"alsporin\", \"anhydrous cefalexin\", \"anhydrous cephalexin\", \"biocef\", \"carnosporin\", \"cefablan\", \"cefadal\", \"cefadin\", \"cefadina\", \"cefaleksin\", \"cefalessina\", \"cefalexin\", \"cefalexin anhydrous\", \"cefalexina\", \"cefalexine\", \"cefalexinum\", \"cefalin\", \"cefaloto\", \"cefaseptin\", \"ceflax\", \"ceforal\", \"cefovit\", \"celexin\", \"cepastar\", \"cepexin\", \"cephacillin\", \"cephalexin\", \"cephalexin anhydrous\", \"cephalexine\", \"cephalexinum\", \"cephanasten\", \"cephaxin\", \"cephin\", \"ceporex\", \"ceporex forte\",
|
||||
\"ceporexin\", \"ceporexine\", \"cerexin\", \"cerexins\", \"cophalexin\", \"durantel\", \"durantel ds\", \"erocetin\", \"factagard\", \"felexin\", \"ibilex\", \"ibrexin\", \"inphalex\", \"kefalospes\", \"keflet\", \"keflex\", \"kefolan\", \"keforal\", \"keftab\", \"kekrinal\", \"kidolex\", \"lafarine\", \"larixin\", \"lenocef\", \"lexibiotico\", \"lonflex\", \"lopilexin\", \"madlexin\", \"mamalexin\", \"mamlexin\", \"medoxine\", \"neokef\", \"neolexina\", \"novolexin\", \"optocef\", \"oracef\", \"oriphex\", \"oroxin\", \"ortisporina\", \"ospexin\", \"palitrex\", \"panixine disperdose\",
|
||||
\"pectril\", \"pyassan\", \"roceph\", \"roceph distab\", \"sanaxin\", \"sartosona\", \"sencephalin\", \"sepexin\", \"servispor\", \"sialexin\", \"sinthecillin\", \"sporicef\", \"sporidex\", \"syncle\", \"synecl\", \"tepaxin\", \"tokiolexin\", \"uphalexin\", \"voxxim\", \"winlex\", \"zozarine\")" 2 "g" "c(\"21175-5\", \"3453-8\")"
|
||||
"CEP" "J01DB03" 6024 "Cephalothin" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"cfal\", \"cflt\")" "c(\"cefalothin\", \"cefalotin\", \"cefalotina\", \"cefalotina fabra\", \"cefalotine\", \"cefalotinum\", \"cemastin\", \"cephalothinum\", \"cephalotin\", \"coaxin\", \"keflin\", \"seffin\")" 4 "g" "c(\"25246-0\", \"3454-6\")"
|
||||
"HAP" "J01DB08" 30699 "Cephapirin" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"ambrocef\", \"cefadyl\", \"cefapilin\", \"cefapirin\", \"cefapirina\", \"cefapirine\", \"cefapirinum\", \"cefaprin\", \"cefaprin sodium\", \"cefatrex\", \"cefatrexyl\", \"cephapirine\", \"metricure\")" 4 "g" "10980-1"
|
||||
"CED" "J01DB09" 38103 "Cephradine" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"cfra\", \"cfrd\")" "c(\"anspor\", \"cefradin\", \"cefradina\", \"cefradine\", \"cefradinum\", \"cekodin\", \"cephradin\", \"cephradine\", \"eskacef\", \"infexin\", \"megace f\", \"megacef\", \"sefril\", \"velocef\", \"velosef\")" 2 "g" 2 "g" "character(0)"
|
||||
"CTO" 71402 "Cetocycline" "Tetracyclines" "" "c(\"cetocycline\", \"cetocyline\", \"cetotetrine\")" "character(0)"
|
||||
"CHL" "J01BA01" 5959 "Chloramphenicol" "Amphenicols" "Amphenicols" "Amphenicols" "c(\"c\", \"chl\", \"chlo\", \"cl\")" "c(\"alficetyn\", \"ambofen\", \"amphenicol\", \"amphicol\", \"amseclor\", \"anacetin\", \"aquamycetin\", \"austracil\", \"austracol\", \"biocetin\", \"biophenicol\", \"catilan\", \"ch loramex\", \"chemiceticol\", \"chemicetin\", \"chemicetina\", \"chlomin\", \"chlomycol\", \"chloramex\", \"chloramfenikol\", \"chloramficin\", \"chloramfilin\", \"chloramphenicol\", \"chloramphenicole\", \"chloramphenicolum\", \"chloramsaar\", \"chlorasol\", \"chlorbiotic\", \"chloricol\", \"chlormycetin r\", \"chlornitromycin\", \"chloroamphenicol\", \"chlorocaps\", \"chlorocid\",
|
||||
"CEP" 6024 "Cephalothin" "Cephalosporins (1st gen.)" "J01DB03" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"cfal\", \"cflt\")" "c(\"cefalothin\", \"cefalotin\", \"cefalotina\", \"cefalotina fabra\", \"cefalotine\", \"cefalotinum\", \"cemastin\", \"cephalothinum\", \"cephalotin\", \"coaxin\", \"keflin\", \"seffin\")" 4 "g" "c(\"25246-0\", \"3454-6\")"
|
||||
"HAP" 30699 "Cephapirin" "Cephalosporins (1st gen.)" "J01DB08" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"ambrocef\", \"cefadyl\", \"cefapilin\", \"cefapirin\", \"cefapirina\", \"cefapirine\", \"cefapirinum\", \"cefaprin\", \"cefaprin sodium\", \"cefatrex\", \"cefatrexyl\", \"cephapirine\", \"metricure\")" 4 "g" "10980-1"
|
||||
"CED" 38103 "Cephradine" "Cephalosporins (1st gen.)" "J01DB09" "Other beta-lactam antibacterials" "First-generation cephalosporins" "c(\"cfra\", \"cfrd\")" "c(\"anspor\", \"cefradin\", \"cefradina\", \"cefradine\", \"cefradinum\", \"cekodin\", \"cephradin\", \"cephradine\", \"eskacef\", \"infexin\", \"megace f\", \"megacef\", \"sefril\", \"velocef\", \"velosef\")" 2 "g" 2 "g" "character(0)"
|
||||
"CTO" 71402 "Cetocycline" "Tetracyclines" "" "c(\"cetocycline\", \"cetocyline\", \"cetotetrine\")" "character(0)"
|
||||
"CHL" 5959 "Chloramphenicol" "Amphenicols" "c(\"D06AX02\", \"D10AF03\", \"G01AA05\", \"J01BA01\", \"S01AA01\", \"S02AA01\", \"S03AA08\")" "Amphenicols" "Amphenicols" "c(\"c\", \"chl\", \"chlo\", \"cl\")" "c(\"alficetyn\", \"ambofen\", \"amphenicol\", \"amphicol\", \"amseclor\", \"anacetin\", \"aquamycetin\", \"austracil\", \"austracol\", \"biocetin\", \"biophenicol\", \"catilan\", \"ch loramex\", \"chemiceticol\", \"chemicetin\", \"chemicetina\", \"chlomin\", \"chlomycol\", \"chloramex\", \"chloramfenikol\", \"chloramficin\", \"chloramfilin\", \"chloramphenicol\", \"chloramphenicole\", \"chloramphenicolum\", \"chloramsaar\", \"chlorasol\", \"chlorbiotic\", \"chloricol\", \"chlormycetin r\", \"chlornitromycin\", \"chloroamphenicol\", \"chlorocaps\", \"chlorocid\",
|
||||
\"chlorocid s\", \"chlorocide\", \"chlorocidin c\", \"chlorocidin c tetran\", \"chlorocin\", \"chlorocol\", \"chlorofair\", \"chloroject l\", \"chloromax\", \"chloromycetin\", \"chloromycetny\", \"chloromyxin\", \"chloronitrin\", \"chloroptic\", \"chloroptic s.o.p\", \"chloroptic s.o.p.\", \"chlorovules\", \"chlorsig\", \"cidocetine\", \"ciplamycetin\", \"cloramfen\", \"cloramfenicol\", \"cloramfenicolo\", \"cloramficin\", \"cloramical\", \"cloramicol\", \"cloramidina\", \"cloranfenicol\", \"cloroamfenicolo\", \"clorocyn\", \"cloromisan\", \"cloromissan\", \"clorosintex\",
|
||||
\"comycetin\", \"cylphenicol\", \"desphen\", \"detreomycin\", \"detreomycine\", \"dextromycetin\", \"doctamicina\", \"duphenicol\", \"econochlor\", \"embacetin\", \"emetren\", \"enicol\", \"enteromycetin\", \"erbaplast\", \"ertilen\", \"f armicetina\", \"farmicetina\", \"fenicol\", \"globenicol\", \"glorous\", \"halomycetin\", \"hortfenicol\", \"interomycetine\", \"intramycetin\", \"intramyctin\", \"isicetin\", \"ismicetina\", \"isophenicol\", \"isopto fenicol\", \"juvamycetin\", \"kamaver\", \"kemicetina\", \"kemicetine\", \"kloramfenikol\", \"klorita\", \"klorocid s\",
|
||||
\"laevomycetinum\", \"leukamycin\", \"leukomyan\", \"leukomycin\", \"levocin\", \"levomicetina\", \"levomitsetin\", \"levomycetin\", \"levoplast\", \"levosin\", \"levovetin\", \"loromicetina\", \"loromisan\", \"loromisin\", \"mastiphen\", \"mediamycetine\", \"medichol\", \"micloretin\", \"micochlorine\", \"micoclorina\", \"microcetina\", \"mychel\", \"mycinol\", \"myclocin\", \"mycochlorin\", \"myscel\", \"normimycin v\", \"novochlorocap\", \"novomycetin\", \"novophenicol\", \"ocuphenicol\", \"oftalent\", \"oleomycetin\", \"opclor\", \"opelor\", \"ophthochlor\", \"ophthocort\",
|
||||
\"ophtochlor\", \"optomycin\", \"otachron\", \"otophen\", \"pantovernil\", \"paraxin\", \"pentamycetin\", \"quemicetina\", \"rivomycin\", \"romphenil\", \"ronfenil\", \"ronphenil\", \"septicol\", \"sificetina\", \"sintomicetina\", \"sintomicetine r\", \"sno phenicol\", \"soluthor\", \"stanomycetin\", \"synthomycetin\", \"synthomycetine\", \"synthomycine\", \"syntomycin\", \"tevcocin\", \"tevcosin\", \"tifomycin\", \"tifomycine\", \"tiromycetin\", \"treomicetina\", \"unimycetin\", \"veticol\", \"vice ton\", \"viceton\")" 3 "g" 3 "g" "c(\"15101-9\", \"16603-3\", \"16604-1\", \"25247-8\", \"29214-4\", \"29346-4\", \"29347-2\", \"3455-3\")"
|
||||
"CTE" "J01AA03" 54675777 "Chlortetracycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "" "c(\"acronize\", \"aueromycin\", \"aureocina\", \"aureomycin\", \"aureomykoin\", \"biomitsin\", \"biomycin\", \"biomycin a\", \"chlormax\", \"chlorotetracycline\", \"chlortetracycline\", \"chlortetracyclinum\", \"chrysomykine\", \"clortetraciclina\", \"duomycin\", \"flamycin\", \"uromycin\")" 1 "g" "87600-3"
|
||||
"CIC" 19003 "Ciclacillin" "Beta-lactams/penicillins" "" "c(\"bastcillin\", \"calthor\", \"ciclacilina\", \"ciclacillin\", \"ciclacilline\", \"ciclacillinum\", \"ciclacillum\", \"citosarin\", \"cyclacillin\", \"cyclapen\", \"noblicil\", \"orfilina\", \"peamezin\", \"syngacillin\", \"ultracillin\", \"vastcillin\", \"vipicil\", \"wyvital\")" "character(0)"
|
||||
"CIX" "D01AE14" 47472 "Ciclopirox" "Antifungals/antimycotics" "Antifungals for topical use" "Other antifungals for topical use" "cipx" "c(\"butaconazole\", \"butoconazol\", \"butoconazole\", \"butoconazolum\", \"compositenstarke\", \"dahlin\", \"femstat\", \"gynofort\", \"polyfructosanum\")" "character(0)"
|
||||
"CIN" "J01MB06" 2762 "Cinoxacin" "Quinolones" "Quinolone antibacterials" "Other quinolones" "c(\"cino\", \"cnox\")" "c(\"azolinic acid\", \"cinobac\", \"cinobactin\", \"cinoxacin\", \"cinoxacine\", \"cinoxacino\", \"cinoxacinum\", \"clinoxacin\", \"noxigram\", \"uronorm\")" 1 "g" "character(0)"
|
||||
"CIP" "J01MA02" 2764 "Ciprofloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"ci\", \"cip\", \"cipr\", \"cp\")" "c(\"alcon cilox\", \"auripro\", \"bacquinor\", \"baflox\", \"baycip\", \"bernoflox\", \"cetraxal\", \"ciflox\", \"cifloxin\", \"ciloxan\", \"ciplus\", \"ciprecu\", \"ciprine\", \"ciprinol\", \"cipro i.v.\", \"cipro iv\", \"cipro xl\", \"cipro xr\", \"ciprobay\", \"ciprobay uro\", \"ciprocinol\", \"ciprodar\", \"ciproflox\", \"ciprofloxacin\", \"ciprofloxacina\", \"ciprofloxacine\", \"ciprofloxacino\", \"ciprofloxacinum\", \"ciprogis\", \"ciprolin\", \"ciprolon\", \"cipromycin\", \"ciproquinol\", \"ciprowin\", \"ciproxan\", \"ciproxin\", \"ciproxina\", \"ciproxine\", \"ciriax\",
|
||||
"CTE" 54675777 "Chlortetracycline" "Tetracyclines" "c(\"A01AB21\", \"D06AA02\", \"J01AA03\", \"S01AA02\")" "Tetracyclines" "Tetracyclines" "" "c(\"acronize\", \"aueromycin\", \"aureocina\", \"aureomycin\", \"aureomykoin\", \"biomitsin\", \"biomycin\", \"biomycin a\", \"chlormax\", \"chlorotetracycline\", \"chlortetracycline\", \"chlortetracyclinum\", \"chrysomykine\", \"clortetraciclina\", \"duomycin\", \"flamycin\", \"uromycin\")" 1 "g" "87600-3"
|
||||
"CIC" 19003 "Ciclacillin" "Beta-lactams/penicillins" "" "c(\"bastcillin\", \"calthor\", \"ciclacilina\", \"ciclacillin\", \"ciclacilline\", \"ciclacillinum\", \"ciclacillum\", \"citosarin\", \"cyclacillin\", \"cyclapen\", \"noblicil\", \"orfilina\", \"peamezin\", \"syngacillin\", \"ultracillin\", \"vastcillin\", \"vipicil\", \"wyvital\")" "character(0)"
|
||||
"CIX" 47472 "Ciclopirox" "Antifungals/antimycotics" "c(\"D01AE14\", \"G01AX12\")" "Antifungals for topical use" "Other antifungals for topical use" "cipx" "c(\"butaconazole\", \"butoconazol\", \"butoconazole\", \"butoconazolum\", \"compositenstarke\", \"dahlin\", \"femstat\", \"gynofort\", \"polyfructosanum\")" "character(0)"
|
||||
"CIN" 2762 "Cinoxacin" "Quinolones" "J01MB06" "Quinolone antibacterials" "Other quinolones" "c(\"cino\", \"cnox\")" "c(\"azolinic acid\", \"cinobac\", \"cinobactin\", \"cinoxacin\", \"cinoxacine\", \"cinoxacino\", \"cinoxacinum\", \"clinoxacin\", \"noxigram\", \"uronorm\")" 1 "g" "character(0)"
|
||||
"CIP" 2764 "Ciprofloxacin" "Quinolones" "c(\"J01MA02\", \"S01AE03\", \"S02AA15\", \"S03AA07\")" "Quinolone antibacterials" "Fluoroquinolones" "c(\"ci\", \"cip\", \"cipr\", \"cp\")" "c(\"alcon cilox\", \"auripro\", \"bacquinor\", \"baflox\", \"baycip\", \"bernoflox\", \"cetraxal\", \"ciflox\", \"cifloxin\", \"ciloxan\", \"ciplus\", \"ciprecu\", \"ciprine\", \"ciprinol\", \"cipro i.v.\", \"cipro iv\", \"cipro xl\", \"cipro xr\", \"ciprobay\", \"ciprobay uro\", \"ciprocinol\", \"ciprodar\", \"ciproflox\", \"ciprofloxacin\", \"ciprofloxacina\", \"ciprofloxacine\", \"ciprofloxacino\", \"ciprofloxacinum\", \"ciprogis\", \"ciprolin\", \"ciprolon\", \"cipromycin\", \"ciproquinol\", \"ciprowin\", \"ciproxan\", \"ciproxin\", \"ciproxina\", \"ciproxine\", \"ciriax\",
|
||||
\"citopcin\", \"corsacin\", \"cyprobay\", \"fimoflox\", \"flociprin\", \"ipiflox\", \"italnik\", \"linhaliq\", \"otiprio\", \"probiox\", \"proflaxin\", \"quinolid\", \"quintor\", \"rancif\", \"roxytal\", \"septicide\", \"sophixin ofteno\", \"spitacin\", \"superocin\", \"velmonit\", \"velomonit\", \"zumaflox\")" 1 "g" 0.8 "g" "c(\"14031-9\", \"14032-7\", \"14058-2\", \"14059-0\", \"25248-6\", \"34636-1\", \"3484-3\")"
|
||||
"CLR" "J01FA09" 84029 "Clarithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"ch\", \"cla\", \"clar\", \"clm\", \"clr\")" "c(\"abbotic\", \"astromen\", \"biaxin\", \"biaxin filmtab\", \"biaxin hp\", \"biaxin xl\", \"biaxin xl filmtab\", \"bicrolid\", \"clacee\", \"clacid\", \"clacine\", \"clambiotic\", \"clarem\", \"claribid\", \"claricide\", \"claridar\", \"claripen\", \"clarith\", \"clarithromycin\", \"clarithromycine\", \"clarithromycinum\", \"claritromicina\", \"clathromycin\", \"crixan\", \"cyllid\", \"cyllind\", \"fromilid\", \"heliclar\", \"klabax\", \"klacid\", \"klaciped\", \"klaricid\", \"klaricid h.p\", \"klaricid h.p.\", \"klaricid pediatric\", \"klaricid xl\", \"klarid\", \"klarin\",
|
||||
"CLR" 84029 "Clarithromycin" "Macrolides/lincosamides" "J01FA09" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"ch\", \"cla\", \"clar\", \"clm\", \"clr\")" "c(\"abbotic\", \"astromen\", \"biaxin\", \"biaxin filmtab\", \"biaxin hp\", \"biaxin xl\", \"biaxin xl filmtab\", \"bicrolid\", \"clacee\", \"clacid\", \"clacine\", \"clambiotic\", \"clarem\", \"claribid\", \"claricide\", \"claridar\", \"claripen\", \"clarith\", \"clarithromycin\", \"clarithromycine\", \"clarithromycinum\", \"claritromicina\", \"clathromycin\", \"crixan\", \"cyllid\", \"cyllind\", \"fromilid\", \"heliclar\", \"klabax\", \"klacid\", \"klaciped\", \"klaricid\", \"klaricid h.p\", \"klaricid h.p.\", \"klaricid pediatric\", \"klaricid xl\", \"klarid\", \"klarin\",
|
||||
\"kofron\", \"mabicrol\", \"macladin\", \"maclar\", \"veclam\", \"vikrol\", \"zeclar\")" 0.5 "g" 1 "g" "c(\"16619-9\", \"25253-6\", \"34638-7\", \"80559-8\")"
|
||||
"CLA1" 5280980 "Clavulanic acid" "Other antibacterials" "" "c(\"acide clavulanique\", \"acido clavulanico\", \"acidum clavulanicum\", \"clavulanate\", \"clavulanate acid\", \"clavulanate lithium\", \"clavulanic acid\", \"clavulansaeure\", \"clavulansaure\", \"clavulinic acid\", \"clavulox\", \"sodium clavulanate\")" "character(0)"
|
||||
"CLX" 60063 "Clinafloxacin" "Quinolones" "" "clinafloxacin" "character(0)"
|
||||
"CLI" "J01FF01" 446598 "Clindamycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Lincosamides" "c(\"cc\", \"cd\", \"cli\", \"clin\", \"cm\", \"da\")" "c(\"antirobe\", \"chlolincocin\", \"clindaderm\", \"clindamicina\", \"clindamycin\", \"clindamycine\", \"clindamycinum\", \"clinimycin\", \"dalacin c\", \"dalacine\", \"klimicin\", \"sobelin\")" 1.2 "g" 1.8 "g" "c(\"16621-5\", \"16622-3\", \"25249-4\", \"3486-8\")"
|
||||
"CLF" "J04BA01" 2794 "Clofazimine" "Antimycobacterials" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "clof" "c(\"chlofazimine\", \"clofazimin\", \"clofazimina\", \"clofazimine\", \"clofaziminum\", \"lampren\", \"lamprene\", \"riminophenazine\")" 0.1 "g" "character(0)"
|
||||
"CLF1" "J01XX03" 2799 "Clofoctol" "Other antibacterials" "Other antibacterials" "Other antibacterials" "" "c(\"clofoctol\", \"clofoctolo\", \"clofoctolum\", \"gramplus\", \"octofene\")" "character(0)"
|
||||
"CLM" "J01CE07" 71807 "Clometocillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"chlomethocillin\", \"clometacillin\", \"clometocilina\", \"clometocillin\", \"clometocilline\", \"clometocillinum\", \"rixapen\")" 1 "g" "character(0)"
|
||||
"CLM1" "J01AA11" 54680675 "Clomocycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "" "c(\"chlormethylencycline\", \"clomociclina\", \"clomocyclin\", \"clomocycline\", \"clomocyclinum\", \"megaclor\")" 1 "g" "character(0)"
|
||||
"CTR" "G01AF02" 2812 "Clotrimazole" "Antifungals/antimycotics" "clot" "c(\"canesten\", \"canesten cream\", \"canesten solution\", \"canestene\", \"canestine\", \"canifug\", \"chlotrimazole\", \"cimitidine\", \"clomatin\", \"clotrimaderm\", \"clotrimaderm cream\", \"clotrimazol\", \"clotrimazole\", \"clotrimazolum\", \"cutistad\", \"desamix f\", \"diphenylmethane\", \"empecid\", \"esparol\", \"fem care\", \"femcare\", \"gyne lotrimin\", \"jidesheng\", \"kanesten\", \"klotrimazole\", \"lotrimax\", \"lotrimin\", \"lotrimin af\", \"lotrimin af cream\", \"lotrimin af lotion\", \"lotrimin af solution\", \"lotrimin cream\", \"lotrimin lotion\",
|
||||
"CLA1" 5280980 "Clavulanic acid" "Other antibacterials" "" "c(\"acide clavulanique\", \"acido clavulanico\", \"acidum clavulanicum\", \"clavulanate\", \"clavulanate acid\", \"clavulanate lithium\", \"clavulanic acid\", \"clavulansaeure\", \"clavulansaure\", \"clavulinic acid\", \"clavulox\", \"sodium clavulanate\")" "character(0)"
|
||||
"CLX" 60063 "Clinafloxacin" "Quinolones" "" "clinafloxacin" "character(0)"
|
||||
"CLI" 446598 "Clindamycin" "Macrolides/lincosamides" "c(\"D10AF01\", \"G01AA10\", \"J01FF01\")" "Macrolides, lincosamides and streptogramins" "Lincosamides" "c(\"cc\", \"cd\", \"cli\", \"clin\", \"cm\", \"da\")" "c(\"antirobe\", \"chlolincocin\", \"clindaderm\", \"clindamicina\", \"clindamycin\", \"clindamycine\", \"clindamycinum\", \"clinimycin\", \"dalacin c\", \"dalacine\", \"klimicin\", \"sobelin\")" 1.2 "g" 1.8 "g" "c(\"16621-5\", \"16622-3\", \"25249-4\", \"3486-8\")"
|
||||
"CLF" 2794 "Clofazimine" "Antimycobacterials" "J04BA01" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "clof" "c(\"chlofazimine\", \"clofazimin\", \"clofazimina\", \"clofazimine\", \"clofaziminum\", \"lampren\", \"lamprene\", \"riminophenazine\")" 0.1 "g" "character(0)"
|
||||
"CLF1" 2799 "Clofoctol" "Other antibacterials" "J01XX03" "Other antibacterials" "Other antibacterials" "" "c(\"clofoctol\", \"clofoctolo\", \"clofoctolum\", \"gramplus\", \"octofene\")" "character(0)"
|
||||
"CLM" 71807 "Clometocillin" "Beta-lactams/penicillins" "J01CE07" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"chlomethocillin\", \"clometacillin\", \"clometocilina\", \"clometocillin\", \"clometocilline\", \"clometocillinum\", \"rixapen\")" 1 "g" "character(0)"
|
||||
"CLM1" 54680675 "Clomocycline" "Tetracyclines" "J01AA11" "Tetracyclines" "Tetracyclines" "" "c(\"chlormethylencycline\", \"clomociclina\", \"clomocyclin\", \"clomocycline\", \"clomocyclinum\", \"megaclor\")" 1 "g" "character(0)"
|
||||
"CTR" 2812 "Clotrimazole" "Antifungals/antimycotics" "c(\"A01AB18\", \"D01AC01\", \"G01AF02\")" "clot" "c(\"canesten\", \"canesten cream\", \"canesten solution\", \"canestene\", \"canestine\", \"canifug\", \"chlotrimazole\", \"cimitidine\", \"clomatin\", \"clotrimaderm\", \"clotrimaderm cream\", \"clotrimazol\", \"clotrimazole\", \"clotrimazolum\", \"cutistad\", \"desamix f\", \"diphenylmethane\", \"empecid\", \"esparol\", \"fem care\", \"femcare\", \"gyne lotrimin\", \"jidesheng\", \"kanesten\", \"klotrimazole\", \"lotrimax\", \"lotrimin\", \"lotrimin af\", \"lotrimin af cream\", \"lotrimin af lotion\", \"lotrimin af solution\", \"lotrimin cream\", \"lotrimin lotion\",
|
||||
\"lotrimin solution\", \"monobaycuten\", \"mycelax\", \"mycelex\", \"mycelex cream\", \"mycelex g\", \"mycelex otc\", \"mycelex solution\", \"mycelex troches\", \"mycelex twin pack\", \"myclo cream\", \"myclo solution\", \"myclo spray solution\", \"mycofug\", \"mycosporin\", \"mykosporin\", \"nalbix\", \"otomax\", \"pedisafe\", \"rimazole\", \"stiemazol\", \"tibatin\", \"trimysten\", \"veltrim\")" "character(0)"
|
||||
"CLO" "J01CF02" 6098 "Cloxacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "c(\"\", \"clox\")" "c(\"chloroxacillin\", \"clossacillina\", \"cloxacilina\", \"cloxacillin\", \"cloxacillin sodium\", \"cloxacilline\", \"cloxacillinna\", \"cloxacillinum\", \"cloxapen\", \"methocillin s\", \"orbenin\", \"syntarpen\", \"tegopen\")" 2 "g" 2 "g" "c(\"16628-0\", \"25250-2\")"
|
||||
"COL" "J01XB01" 5311054 "Colistin" "Polymyxins" "Other antibacterials" "Polymyxins" "c(\"cl\", \"coli\", \"cs\", \"cst\", \"ct\")" "c(\"belcomycine\", \"colimycin\", \"colimycin sulphate\", \"colisticin\", \"colistimethate\", \"colistimethate sodium\", \"colistin sulfate\", \"colistin sulphate\", \"colomycin\", \"coly-mycin\", \"polymyxin e\", \"polymyxin e. sulfate\", \"promixin\", \"totazina\")" 9 "MU" "c(\"16645-4\", \"29493-4\")"
|
||||
"COP" "Colistin/polysorbate" "Other antibacterials" "" "" ""
|
||||
"CYC" "J04AB01" 6234 "Cycloserine" "Oxazolidinones" "Drugs for treatment of tuberculosis" "Antibiotics" "cycl" "c(\"cicloserina\", \"closerin\", \"closina\", \"cyclorin\", \"cycloserin\", \"cycloserine\", \"cycloserinum\", \"farmiserina\", \"micoserina\", \"miroserina\", \"miroseryn\", \"novoserin\", \"oxamicina\", \"oxamycin\", \"seromycin\", \"tebemicina\", \"tisomycin\", \"wasserina\")" 0.75 "g" "c(\"16702-3\", \"25251-0\", \"3519-6\")"
|
||||
"DAL" "J01XA04" 23724878 "Dalbavancin" "Glycopeptides" "Other antibacterials" "Glycopeptide antibacterials" "dalb" "c(\"dalbavancin\", \"dalvance\")" 1.5 "character(0)"
|
||||
"DAN" 71335 "Danofloxacin" "Quinolones" "" "c(\"advocin\", \"danofloxacin\", \"danofloxacine\", \"danofloxacino\", \"danofloxacinum\")" "character(0)"
|
||||
"DPS" "J04BA02" 2955 "Dapsone" "Other antibacterials" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "" "c(\"aczone\", \"araldite ht\", \"atrisone\", \"avlosulfon\", \"avlosulfone\", \"avlosulphone\", \"avsulfor\", \"bis sulfone\", \"bissulfone\", \"bissulphone\", \"croysulfone\", \"croysulphone\", \"dapson\", \"dapsona\", \"dapsone\", \"dapsonum\", \"di sulfone\", \"diaphenyl sulfone\", \"diaphenylsulfon\", \"diaphenylsulfone\", \"diaphenylsulphon\", \"diaphenylsulphone\", \"dimitone\", \"diphenasone\", \"diphone\", \"disulfone\", \"disulone\", \"disulphone\", \"dubronax\", \"dubronaz\", \"dumitone\", \"eporal\", \"metabolite c\", \"novophone\", \"protogen\", \"servidapson\",
|
||||
"CLO" 6098 "Cloxacillin" "Beta-lactams/penicillins" "J01CF02" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "c(\"\", \"clox\")" "c(\"chloroxacillin\", \"clossacillina\", \"cloxacilina\", \"cloxacillin\", \"cloxacillin sodium\", \"cloxacilline\", \"cloxacillinna\", \"cloxacillinum\", \"cloxapen\", \"methocillin s\", \"orbenin\", \"syntarpen\", \"tegopen\")" 2 "g" 2 "g" "c(\"16628-0\", \"25250-2\")"
|
||||
"COL" 5311054 "Colistin" "Polymyxins" "c(\"A07AA10\", \"J01XB01\")" "Other antibacterials" "Polymyxins" "c(\"cl\", \"coli\", \"cs\", \"cst\", \"ct\")" "c(\"belcomycine\", \"colimycin\", \"colimycin sulphate\", \"colisticin\", \"colistimethate\", \"colistimethate sodium\", \"colistin sulfate\", \"colistin sulphate\", \"colomycin\", \"coly-mycin\", \"polymyxin e\", \"polymyxin e. sulfate\", \"promixin\", \"totazina\")" 9 "MU" 9 "MU" "c(\"16645-4\", \"29493-4\")"
|
||||
"COP" "Colistin/polysorbate" "Other antibacterials" "" "" ""
|
||||
"CYC" 6234 "Cycloserine" "Oxazolidinones" "J04AB01" "Drugs for treatment of tuberculosis" "Antibiotics" "cycl" "c(\"cicloserina\", \"closerin\", \"closina\", \"cyclorin\", \"cycloserin\", \"cycloserine\", \"cycloserinum\", \"farmiserina\", \"micoserina\", \"miroserina\", \"miroseryn\", \"novoserin\", \"oxamicina\", \"oxamycin\", \"seromycin\", \"tebemicina\", \"tisomycin\", \"wasserina\")" 0.75 "g" "c(\"16702-3\", \"25251-0\", \"3519-6\")"
|
||||
"DAL" 23724878 "Dalbavancin" "Glycopeptides" "J01XA04" "Other antibacterials" "Glycopeptide antibacterials" "dalb" "c(\"dalbavancin\", \"dalvance\")" 1.5 "g" "character(0)"
|
||||
"DAN" 71335 "Danofloxacin" "Quinolones" "" "c(\"advocin\", \"danofloxacin\", \"danofloxacine\", \"danofloxacino\", \"danofloxacinum\")" "character(0)"
|
||||
"DPS" 2955 "Dapsone" "Other antibacterials" "c(\"D10AX05\", \"J04BA02\")" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "" "c(\"aczone\", \"araldite ht\", \"atrisone\", \"avlosulfon\", \"avlosulfone\", \"avlosulphone\", \"avsulfor\", \"bis sulfone\", \"bissulfone\", \"bissulphone\", \"croysulfone\", \"croysulphone\", \"dapson\", \"dapsona\", \"dapsone\", \"dapsonum\", \"di sulfone\", \"diaphenyl sulfone\", \"diaphenylsulfon\", \"diaphenylsulfone\", \"diaphenylsulphon\", \"diaphenylsulphone\", \"dimitone\", \"diphenasone\", \"diphone\", \"disulfone\", \"disulone\", \"disulphone\", \"dubronax\", \"dubronaz\", \"dumitone\", \"eporal\", \"metabolite c\", \"novophone\", \"protogen\", \"servidapson\",
|
||||
\"slphadione\", \"sulfadione\", \"sulfona\", \"sulfone ucb\", \"sulfonyldianiline\", \"sulphadione\", \"sulphonyldianiline\", \"sumicure s\", \"tarimyl\", \"udolac\", \"wln: zr dswr dz\")" 50 "mg" "9747-7"
|
||||
"DAP" "J01XX09" 16134395 "Daptomycin" "Other antibacterials" "Other antibacterials" "Other antibacterials" "c(\"dap\", \"dapt\")" "c(\"cidecin\", \"cubicin\", \"dapcin\", \"daptomicina\", \"daptomycine\", \"daptomycinum\")" 0.28 "g" "character(0)"
|
||||
"DFX" 487101 "Delafloxacin" "Quinolones" "" "c(\"baxdela\", \"delafloxacin\", \"delafloxacinum\")" "character(0)"
|
||||
"DLM" "J04AK06" 6480466 "Delamanid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "dela" "c(\"delamanid\", \"deltyba\")" 0.2 "character(0)"
|
||||
"DEM" "J01AA01" 54680690 "Demeclocycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "" "c(\"bioterciclin\", \"clortetrin\", \"deganol\", \"demeclociclina\", \"demeclocycline\", \"demeclocyclinum\", \"demeclor\", \"demetraclin\", \"diuciclin\", \"elkamicina\", \"ledermycin\", \"mexocine\", \"novotriclina\", \"perciclina\", \"sumaclina\")" 0.6 "g" "c(\"10982-7\", \"29494-2\")"
|
||||
"DKB" "J01GB09" 470999 "Dibekacin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "" "c(\"debecacin\", \"dibekacin\", \"dibekacin sulfate\", \"dibekacina\", \"dibekacine\", \"dibekacinum\", \"dideoxykanamycin b\", \"kappati\", \"orbicin\", \"panamicin\")" 0.14 "g" "character(0)"
|
||||
"DIC" "J01CF01" 18381 "Dicloxacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "c(\"\", \"dicl\")" "c(\"dichloroxacillin\", \"diclossacillina\", \"dicloxaciclin\", \"dicloxacilin\", \"dicloxacilina\", \"dicloxacillin\", \"dicloxacillin sodium\", \"dicloxacillina\", \"dicloxacilline\", \"dicloxacillinum\", \"dicloxacycline\", \"dycill\", \"dynapen\", \"maclicine\", \"nm|| dicloxacillin\", \"pathocil\")" 2 "g" 2 "g" "c(\"10984-3\", \"16769-2\", \"25252-8\")"
|
||||
"DIF" 56206 "Difloxacin" "Quinolones" "" "difloxacin" "character(0)"
|
||||
"DIR" "J01FA13" 6473883 "Dirithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"dirithromycin\", \"dirithromycine\", \"dirithromycinum\", \"diritromicina\", \"divitross\", \"dynabac\", \"noriclan\", \"valodin\")" 0.5 "g" "character(0)"
|
||||
"DOR" "J01DH04" 73303 "Doripenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "dori" "c(\"doribax\", \"doripenem\", \"doripenem hydrate\", \"finibax\")" 1.5 "character(0)"
|
||||
"DOX" "J01AA02" 54671203 "Doxycycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "c(\"dox\", \"doxy\")" "c(\"atridox\", \"azudoxat\", \"deoxymykoin\", \"dossiciclina\", \"doxcycline anhydrous\", \"doxiciclina\", \"doxitard\", \"doxivetin\", \"doxycen\", \"doxychel\", \"doxycin\", \"doxycyclin\", \"doxycycline\", \"doxycycline calcium\", \"doxycycline hyclate\", \"doxycyclinum\", \"doxylin\", \"doxysol\", \"doxytec\", \"doxytetracycline\", \"hydramycin\", \"investin\", \"jenacyclin\", \"liviatin\", \"monodox\", \"oracea\", \"periostat\", \"ronaxan\", \"spanor\", \"supracyclin\", \"vibramycin\", \"vibramycin novum\", \"vibramycine\", \"vibravenos\", \"zenavod\")" 0.1 "g" 0.1 "g" "c(\"10986-8\", \"21250-6\", \"26902-7\")"
|
||||
"ECO" "J01XDXX" 3198 "Econazole" "Antifungals/antimycotics" "econ" "c(\"econazol\", \"econazole\", \"econazolum\", \"ecostatin\", \"ecostatin cream\", \"palavale\", \"pevaryl\", \"spectazole\", \"spectazole cream\")" "character(0)"
|
||||
"ENX" "J01MA04" 3229 "Enoxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"enox\")" "c(\"almitil\", \"bactidan\", \"bactidron\", \"comprecin\", \"enofloxacine\", \"enoksetin\", \"enoram\", \"enoxacin\", \"enoxacina\", \"enoxacine\", \"enoxacino\", \"enoxacinum\", \"enoxen\", \"enoxin\", \"enoxor\", \"flumark\", \"penetrex\")" 0.8 "g" "c(\"16816-1\", \"3590-7\")"
|
||||
"ENR" 71188 "Enrofloxacin" "Quinolones" "" "c(\"baytril\", \"enrofloxacin\", \"enrofloxacine\", \"enrofloxacino\", \"enrofloxacinum\")" "character(0)"
|
||||
"ENV" 135565326 "Enviomycin (Tuberactinomycin)" "Antimycobacterials" "" "c(\"enviomicina\", \"enviomycin\", \"enviomycina\", \"enviomycinum\")" "character(0)"
|
||||
"EPE" "Eperozolid" "Other antibacterials" "" "" ""
|
||||
"EPC" "J01CA07" 71392 "Epicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"dexacillin\", \"dihydroampicillin\", \"epicilina\", \"epicillin\", \"epicilline\", \"epicillinum\")" 2 "g" 2 "g" "character(0)"
|
||||
"EPP" 68916 "Epiroprim" "Other antibacterials" "" "c(\"epiroprim\", \"epiroprima\", \"epiroprime\", \"epiroprimum\")" "character(0)"
|
||||
"ERV" "J01AA13" 54726192 "Eravacycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "erav" "eravacycline" "character(0)"
|
||||
"ETP" "J01DH03" 150610 "Ertapenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "c(\"erta\", \"etp\")" "c(\"ertapenem\", \"invanz\")" 1 "g" "character(0)"
|
||||
"ERY" "J01FA01" 12560 "Erythromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"e\", \"em\", \"ery\", \"eryt\")" "c(\"abboticin\", \"abomacetin\", \"acneryne\", \"acnesol\", \"akne cordes losung\", \"aknederm ery gel\", \"aknemycin\", \"austrias\", \"benzamycin\", \"derimer\", \"deripil\", \"dotycin\", \"dumotrycin\", \"emuvin\", \"emycin\", \"endoeritrin\", \"erecin\", \"erisone\", \"eritomicina\", \"eritrocina\", \"eritromicina\", \"ermycin\", \"eryacne\", \"eryacnen\", \"eryc sprinkles\", \"erycen\", \"erycette\", \"erycin\", \"erycinum\", \"eryderm\", \"erydermer\", \"erygel\", \"eryhexal\", \"erymax\", \"erymed\", \"erysafe\", \"erytab\", \"erythrocin\", \"erythrocin stearate\",
|
||||
"DAP" 16134395 "Daptomycin" "Other antibacterials" "J01XX09" "Other antibacterials" "Other antibacterials" "c(\"dap\", \"dapt\")" "c(\"cidecin\", \"cubicin\", \"dapcin\", \"daptomicina\", \"daptomycine\", \"daptomycinum\")" 0.28 "g" "character(0)"
|
||||
"DFX" 487101 "Delafloxacin" "Quinolones" "J01MA23" "" "c(\"baxdela\", \"delafloxacin\", \"delafloxacinum\")" 0.9 "g" 0.6 "g" "character(0)"
|
||||
"DLM" 6480466 "Delamanid" "Antimycobacterials" "J04AK06" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "dela" "c(\"delamanid\", \"deltyba\")" 0.2 "g" "character(0)"
|
||||
"DEM" 54680690 "Demeclocycline" "Tetracyclines" "c(\"D06AA01\", \"J01AA01\")" "Tetracyclines" "Tetracyclines" "" "c(\"bioterciclin\", \"clortetrin\", \"deganol\", \"demeclociclina\", \"demeclocycline\", \"demeclocyclinum\", \"demeclor\", \"demetraclin\", \"diuciclin\", \"elkamicina\", \"ledermycin\", \"mexocine\", \"novotriclina\", \"perciclina\", \"sumaclina\")" 0.6 "g" "c(\"10982-7\", \"29494-2\")"
|
||||
"DKB" 470999 "Dibekacin" "Aminoglycosides" "J01GB09" "Aminoglycoside antibacterials" "Other aminoglycosides" "" "c(\"debecacin\", \"dibekacin\", \"dibekacin sulfate\", \"dibekacina\", \"dibekacine\", \"dibekacinum\", \"dideoxykanamycin b\", \"kappati\", \"orbicin\", \"panamicin\")" 0.14 "g" "character(0)"
|
||||
"DIC" 18381 "Dicloxacillin" "Beta-lactams/penicillins" "J01CF01" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "c(\"\", \"dicl\")" "c(\"dichloroxacillin\", \"diclossacillina\", \"dicloxaciclin\", \"dicloxacilin\", \"dicloxacilina\", \"dicloxacillin\", \"dicloxacillin sodium\", \"dicloxacillina\", \"dicloxacilline\", \"dicloxacillinum\", \"dicloxacycline\", \"dycill\", \"dynapen\", \"maclicine\", \"nm|| dicloxacillin\", \"pathocil\")" 2 "g" 2 "g" "c(\"10984-3\", \"16769-2\", \"25252-8\")"
|
||||
"DIF" 56206 "Difloxacin" "Quinolones" "" "difloxacin" "character(0)"
|
||||
"DIR" 6473883 "Dirithromycin" "Macrolides/lincosamides" "J01FA13" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"dirithromycin\", \"dirithromycine\", \"dirithromycinum\", \"diritromicina\", \"divitross\", \"dynabac\", \"noriclan\", \"valodin\")" 0.5 "g" "character(0)"
|
||||
"DOR" 73303 "Doripenem" "Carbapenems" "J01DH04" "Other beta-lactam antibacterials" "Carbapenems" "dori" "c(\"doribax\", \"doripenem\", \"doripenem hydrate\", \"finibax\")" 1.5 "g" "character(0)"
|
||||
"DOX" 54671203 "Doxycycline" "Tetracyclines" "c(\"A01AB22\", \"J01AA02\")" "Tetracyclines" "Tetracyclines" "c(\"dox\", \"doxy\")" "c(\"atridox\", \"azudoxat\", \"deoxymykoin\", \"dossiciclina\", \"doxcycline anhydrous\", \"doxiciclina\", \"doxitard\", \"doxivetin\", \"doxycen\", \"doxychel\", \"doxycin\", \"doxycyclin\", \"doxycycline\", \"doxycycline calcium\", \"doxycycline hyclate\", \"doxycyclinum\", \"doxylin\", \"doxysol\", \"doxytec\", \"doxytetracycline\", \"hydramycin\", \"investin\", \"jenacyclin\", \"liviatin\", \"monodox\", \"oracea\", \"periostat\", \"ronaxan\", \"spanor\", \"supracyclin\", \"vibramycin\", \"vibramycin novum\", \"vibramycine\", \"vibravenos\", \"zenavod\")" 0.1 "g" 0.1 "g" "c(\"10986-8\", \"21250-6\", \"26902-7\")"
|
||||
"ECO" 3198 "Econazole" "Antifungals/antimycotics" "c(\"D01AC03\", \"G01AF05\")" "Antifungals for topical use" "Imidazole and triazole derivatives" "econ" "c(\"econazol\", \"econazole\", \"econazolum\", \"ecostatin\", \"ecostatin cream\", \"palavale\", \"pevaryl\", \"spectazole\", \"spectazole cream\")" "character(0)"
|
||||
"ENX" 3229 "Enoxacin" "Quinolones" "J01MA04" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"enox\")" "c(\"almitil\", \"bactidan\", \"bactidron\", \"comprecin\", \"enofloxacine\", \"enoksetin\", \"enoram\", \"enoxacin\", \"enoxacina\", \"enoxacine\", \"enoxacino\", \"enoxacinum\", \"enoxen\", \"enoxin\", \"enoxor\", \"flumark\", \"penetrex\")" 0.8 "g" "c(\"16816-1\", \"3590-7\")"
|
||||
"ENR" 71188 "Enrofloxacin" "Quinolones" "" "c(\"baytril\", \"enrofloxacin\", \"enrofloxacine\", \"enrofloxacino\", \"enrofloxacinum\")" "character(0)"
|
||||
"ENV" 135565326 "Enviomycin (Tuberactinomycin)" "Antimycobacterials" "" "c(\"enviomicina\", \"enviomycin\", \"enviomycina\", \"enviomycinum\")" "character(0)"
|
||||
"EPE" "Eperozolid" "Other antibacterials" "" "" ""
|
||||
"EPC" 71392 "Epicillin" "Beta-lactams/penicillins" "J01CA07" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"dexacillin\", \"dihydroampicillin\", \"epicilina\", \"epicillin\", \"epicilline\", \"epicillinum\")" 2 "g" 2 "g" "character(0)"
|
||||
"EPP" 68916 "Epiroprim" "Other antibacterials" "" "c(\"epiroprim\", \"epiroprima\", \"epiroprime\", \"epiroprimum\")" "character(0)"
|
||||
"ERV" 54726192 "Eravacycline" "Tetracyclines" "J01AA13" "Tetracyclines" "Tetracyclines" "erav" "eravacycline" "character(0)"
|
||||
"ETP" 150610 "Ertapenem" "Carbapenems" "J01DH03" "Other beta-lactam antibacterials" "Carbapenems" "c(\"erta\", \"etp\")" "c(\"ertapenem\", \"invanz\")" 1 "g" "character(0)"
|
||||
"ERY" 12560 "Erythromycin" "Macrolides/lincosamides" "c(\"D10AF02\", \"J01FA01\", \"S01AA17\")" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"e\", \"em\", \"ery\", \"eryt\")" "c(\"abboticin\", \"abomacetin\", \"acneryne\", \"acnesol\", \"akne cordes losung\", \"aknederm ery gel\", \"aknemycin\", \"austrias\", \"benzamycin\", \"derimer\", \"deripil\", \"dotycin\", \"dumotrycin\", \"emuvin\", \"emycin\", \"endoeritrin\", \"erecin\", \"erisone\", \"eritomicina\", \"eritrocina\", \"eritromicina\", \"ermycin\", \"eryacne\", \"eryacnen\", \"eryc sprinkles\", \"erycen\", \"erycette\", \"erycin\", \"erycinum\", \"eryderm\", \"erydermer\", \"erygel\", \"eryhexal\", \"erymax\", \"erymed\", \"erysafe\", \"erytab\", \"erythrocin\", \"erythrocin stearate\",
|
||||
\"erythroderm\", \"erythrogran\", \"erythroguent\", \"erythromid\", \"erythromycin\", \"erythromycin a\", \"erythromycin base\", \"erythromycin lactate\", \"erythromycine\", \"erythromycines\", \"erythromycinum\", \"erytop\", \"erytrociclin\", \"ilocaps\", \"ilosone\", \"iloticina\", \"ilotycin\", \"ilotycin gluceptate\", \"ilotycin t.s.\", \"inderm\", \"inderm gel\", \"indermretcin\", \"latotryd\", \"lederpax\", \"mephamycin\", \"mercina\", \"oftamolets\", \"paediathrocin\", \"pantoderm\", \"pantodrin\", \"pantomicina\", \"pce dispertab\", \"pharyngocin\", \"primacine\",
|
||||
\"propiocine\", \"proterytrin\", \"retcin\", \"robimycin\", \"romycin\", \"sansac\", \"skid gel e\", \"staticin\", \"stiemicyn\", \"stiemycin\", \"theramycin z\", \"tiloryth\", \"tiprocin\", \"torlamicina\", \"udima ery gel\", \"wyamycin s\")" 2 "g" 1 "g" "c(\"12298-6\", \"16829-4\", \"25275-9\", \"3597-2\")"
|
||||
"ETH" "J04AK02" 14052 "Ethambutol" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "etha" "c(\"aethambutolum\", \"ebutol\", \"etambutol\", \"etambutolo\", \"etapiam\", \"ethambutol\", \"ethambutolum\", \"myambutol\", \"mycobutol\", \"purderal\", \"servambutol\")" 1.2 "g" 1.2 "g" "c(\"25404-5\", \"3607-9\")"
|
||||
"ETI" "J04AM03" 456476 "Ethambutol/isoniazid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "" ""
|
||||
"ETI1" "J04AD03" 2761171 "Ethionamide" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Thiocarbamide derivatives" "ethi" "c(\"aethionamidum\", \"aetina\", \"aetiva\", \"amidazin\", \"amidazine\", \"ethatyl\", \"ethimide\", \"ethina\", \"ethinamide\", \"ethionamide\", \"ethionamidum\", \"ethioniamide\", \"ethylisothiamide\", \"ethyonomide\", \"etimid\", \"etiocidan\", \"etionamid\", \"etionamida\", \"etionamide\", \"etioniamid\", \"etionid\", \"etionizin\", \"etionizina\", \"etionizine\", \"fatoliamid\", \"iridocin\", \"iridocin bayer\", \"iridozin\", \"isothin\", \"isotiamida\", \"itiocide\", \"nicotion\", \"nisotin\", \"nizotin\", \"rigenicid\", \"sertinon\", \"teberus\", \"thianid\", \"thianide\",
|
||||
"ETH" 14052 "Ethambutol" "Antimycobacterials" "J04AK02" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "etha" "c(\"aethambutolum\", \"ebutol\", \"etambutol\", \"etambutolo\", \"etapiam\", \"ethambutol\", \"ethambutolum\", \"myambutol\", \"mycobutol\", \"purderal\", \"servambutol\")" 1.2 "g" 1.2 "g" "c(\"25404-5\", \"3607-9\")"
|
||||
"ETI" 456476 "Ethambutol/isoniazid" "Antimycobacterials" "J04AM03" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "" ""
|
||||
"ETI1" 2761171 "Ethionamide" "Antimycobacterials" "J04AD03" "Drugs for treatment of tuberculosis" "Thiocarbamide derivatives" "ethi" "c(\"aethionamidum\", \"aetina\", \"aetiva\", \"amidazin\", \"amidazine\", \"ethatyl\", \"ethimide\", \"ethina\", \"ethinamide\", \"ethionamide\", \"ethionamidum\", \"ethioniamide\", \"ethylisothiamide\", \"ethyonomide\", \"etimid\", \"etiocidan\", \"etionamid\", \"etionamida\", \"etionamide\", \"etioniamid\", \"etionid\", \"etionizin\", \"etionizina\", \"etionizine\", \"fatoliamid\", \"iridocin\", \"iridocin bayer\", \"iridozin\", \"isothin\", \"isotiamida\", \"itiocide\", \"nicotion\", \"nisotin\", \"nizotin\", \"rigenicid\", \"sertinon\", \"teberus\", \"thianid\", \"thianide\",
|
||||
\"thioamide\", \"thiodine\", \"thiomid\", \"thioniden\", \"tianid\", \"tiomid\", \"trecator\", \"trecator sc\", \"trekator\", \"trescatyl\", \"trescazide\", \"tubenamide\", \"tubermin\", \"tuberoid\", \"tuberoson\")" 0.75 "g" "16845-0"
|
||||
"ETO" 6034 "Ethopabate" "Other antibacterials" "" "c(\"amprol plus\", \"ethopabat\", \"ethopabate\", \"ethyl pabate\")" "character(0)"
|
||||
"FAR" "J01DI03" 65894 "Faropenem" "Other antibacterials" "" "c(\"faropenem\", \"faropenem sodium\", \"fropenem\", \"fropenum sodium\")" 0.75 "character(0)"
|
||||
"FDX" 10034073 "Fidaxomicin" "Other antibacterials" "" "c(\"dificid\", \"dificlir\", \"difimicin\", \"fidaxomicin\", \"lipiarmycin\", \"tiacumicin b\")" "character(0)"
|
||||
"FIN" 11567473 "Finafloxacin" "Quinolones" "" "finafloxacin" "character(0)"
|
||||
"FLA" 46783781 "Flavomycin" "Other antibacterials" "" "moenomycin complex" "character(0)"
|
||||
"FLE" "J01MA08" 3357 "Fleroxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"fler\")" "c(\"fleroxacin\", \"fleroxacine\", \"fleroxacino\", \"fleroxacinum\", \"fleroxicin\", \"megalocin\", \"megalone\", \"megalosin\", \"quinodis\")" 0.4 "g" 0.4 "g" "character(0)"
|
||||
"FLO" 65864 "Flomoxef" "Other antibacterials" "" "c(\"flomoxef\", \"flomoxefo\", \"flomoxefum\")" "character(0)"
|
||||
"FLR" 114811 "Florfenicol" "Other antibacterials" "" "c(\"aquafen\", \"florfenicol\", \"nuflor\", \"nuflor gold\")" "87599-7"
|
||||
"FLC" "J01CF05" 21319 "Flucloxacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "c(\"clox\", \"flux\")" "c(\"floxacillin\", \"floxapen\", \"floxapen sodium salt\", \"fluclox\", \"flucloxacilina\", \"flucloxacillin\", \"flucloxacilline\", \"flucloxacillinum\", \"fluorochloroxacillin\")" 2 "g" 2 "g" "character(0)"
|
||||
"FLU" "J02AC01" 3365 "Fluconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives" "c(\"fluc\", \"fluz\", \"flz\")" "c(\"alflucoz\", \"alfumet\", \"biocanol\", \"biozole\", \"biozolene\", \"canzol\", \"cryptal\", \"diflazon\", \"diflucan\", \"dimycon\", \"elazor\", \"flucazol\", \"fluconazol\", \"fluconazole\", \"fluconazole capsules\", \"fluconazolum\", \"flucostat\", \"flukezol\", \"flunazol\", \"flunizol\", \"flusol\", \"fluzon\", \"fluzone\", \"forcan\", \"fuconal\", \"fungata\", \"loitin\", \"oxifugol\", \"pritenzol\", \"syscan\", \"trican\", \"triconal\", \"triflucan\", \"zoltec\")" 0.2 "g" 0.2 "g" "c(\"10987-6\", \"16870-8\", \"25255-1\", \"80530-9\")"
|
||||
"FLM" "J01MB07" 3374 "Flumequine" "Quinolones" "Quinolone antibacterials" "Other quinolones" "" "c(\"apurone\", \"fantacin\", \"flumequine\", \"flumequino\", \"flumequinum\", \"flumigal\", \"flumiquil\", \"flumisol\", \"flumix\", \"imequyl\")" 1.2 "g" "character(0)"
|
||||
"FLR1" "J01FA14" 71260 "Flurithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"flurithromicina\", \"flurithromycime\", \"flurithromycin\", \"flurithromycine\", \"flurithromycinum\", \"fluritromicina\", \"fluritromycinum\", \"flurizic\")" 0.75 "g" "character(0)"
|
||||
"FFL" 214356 "Fosfluconazole" "Antifungals/antimycotics" "" "c(\"fosfluconazole\", \"phosfluconazole\", \"procif\", \"prodif\")" "character(0)"
|
||||
"FOS" "J01XX01" 446987 "Fosfomycin" "Other antibacterials" "Other antibacterials" "Other antibacterials" "c(\"ff\", \"fm\", \"fo\", \"fof\", \"fos\", \"fosf\")" "c(\"fosfocina\", \"fosfomicina\", \"fosfomycin\", \"fosfomycin sodium\", \"fosfomycine\", \"fosfomycinum\", \"fosfonomycin\", \"monuril\", \"monurol\", \"phosphonemycin\", \"phosphonomycin\", \"veramina\")" 3 "g" 8 "g" "character(0)"
|
||||
"FMD" 572 "Fosmidomycin" "Other antibacterials" "" "c(\"fosmidomycin\", \"fosmidomycina\", \"fosmidomycine\", \"fosmidomycinum\")" "character(0)"
|
||||
"FRM" 8378 "Framycetin" "Aminoglycosides" "c(\"\", \"fram\")" "c(\"actilin\", \"actiline\", \"antibiotique\", \"bycomycin\", \"endomixin\", \"enterfram\", \"fradiomycin\", \"fradiomycin b\", \"fradiomycinum\", \"framicetina\", \"framycetin\", \"framycetin sulfate\", \"framycetine\", \"framycetinum\", \"framygen\", \"fraquinol\", \"jernadex\", \"myacine\", \"myacyne\", \"mycerin\", \"mycifradin\", \"neobrettin\", \"neolate\", \"neomas\", \"neomcin\", \"neomicina\", \"neomin\", \"neomycin\", \"neomycin b\", \"neomycin b sulfate\", \"neomycin solution\", \"neomycin sulfate\", \"neomycin sulphate\", \"neomycinb\", \"neomycine\", \"neomycinum\",
|
||||
"ETO" 6034 "Ethopabate" "Other antibacterials" "" "c(\"amprol plus\", \"ethopabat\", \"ethopabate\", \"ethyl pabate\")" "character(0)"
|
||||
"FAR" 65894 "Faropenem" "Other antibacterials" "J01DI03" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "" "c(\"faropenem\", \"faropenem sodium\", \"fropenem\", \"fropenum sodium\")" 0.75 "g" "character(0)"
|
||||
"FDX" 10034073 "Fidaxomicin" "Other antibacterials" "A07AA12" "" "c(\"dificid\", \"dificlir\", \"difimicin\", \"fidaxomicin\", \"lipiarmycin\", \"tiacumicin b\")" 0.4 "g" "character(0)"
|
||||
"FIN" 11567473 "Finafloxacin" "Quinolones" "" "finafloxacin" "character(0)"
|
||||
"FLA" 46783781 "Flavomycin" "Other antibacterials" "" "moenomycin complex" "character(0)"
|
||||
"FLE" 3357 "Fleroxacin" "Quinolones" "J01MA08" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"fler\")" "c(\"fleroxacin\", \"fleroxacine\", \"fleroxacino\", \"fleroxacinum\", \"fleroxicin\", \"megalocin\", \"megalone\", \"megalosin\", \"quinodis\")" 0.4 "g" 0.4 "g" "character(0)"
|
||||
"FLO" 65864 "Flomoxef" "Other antibacterials" "J01DC14" "" "c(\"flomoxef\", \"flomoxefo\", \"flomoxefum\")" 2 "g" "character(0)"
|
||||
"FLR" 114811 "Florfenicol" "Other antibacterials" "" "c(\"aquafen\", \"florfenicol\", \"nuflor\", \"nuflor gold\")" "87599-7"
|
||||
"FLC" 21319 "Flucloxacillin" "Beta-lactams/penicillins" "J01CF05" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "c(\"clox\", \"flux\")" "c(\"floxacillin\", \"floxapen\", \"floxapen sodium salt\", \"fluclox\", \"flucloxacilina\", \"flucloxacillin\", \"flucloxacilline\", \"flucloxacillinum\", \"fluorochloroxacillin\")" 2 "g" 2 "g" "character(0)"
|
||||
"FLU" 3365 "Fluconazole" "Antifungals/antimycotics" "c(\"D01AC15\", \"J02AC01\")" "Antimycotics for systemic use" "Triazole derivatives" "c(\"fluc\", \"fluz\", \"flz\")" "c(\"alflucoz\", \"alfumet\", \"biocanol\", \"biozole\", \"biozolene\", \"canzol\", \"cryptal\", \"diflazon\", \"diflucan\", \"dimycon\", \"elazor\", \"flucazol\", \"fluconazol\", \"fluconazole\", \"fluconazole capsules\", \"fluconazolum\", \"flucostat\", \"flukezol\", \"flunazol\", \"flunizol\", \"flusol\", \"fluzon\", \"fluzone\", \"forcan\", \"fuconal\", \"fungata\", \"loitin\", \"oxifugol\", \"pritenzol\", \"syscan\", \"trican\", \"triconal\", \"triflucan\", \"zoltec\")" 0.2 "g" 0.2 "g" "c(\"10987-6\", \"16870-8\", \"25255-1\", \"80530-9\")"
|
||||
"FLM" 3374 "Flumequine" "Quinolones" "J01MB07" "Quinolone antibacterials" "Other quinolones" "" "c(\"apurone\", \"fantacin\", \"flumequine\", \"flumequino\", \"flumequinum\", \"flumigal\", \"flumiquil\", \"flumisol\", \"flumix\", \"imequyl\")" 1.2 "g" "character(0)"
|
||||
"FLR1" 71260 "Flurithromycin" "Macrolides/lincosamides" "J01FA14" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"flurithromicina\", \"flurithromycime\", \"flurithromycin\", \"flurithromycine\", \"flurithromycinum\", \"fluritromicina\", \"fluritromycinum\", \"flurizic\")" 0.75 "g" "character(0)"
|
||||
"FFL" 214356 "Fosfluconazole" "Antifungals/antimycotics" "" "c(\"fosfluconazole\", \"phosfluconazole\", \"procif\", \"prodif\")" "character(0)"
|
||||
"FOS" 446987 "Fosfomycin" "Other antibacterials" "J01XX01" "Other antibacterials" "Other antibacterials" "c(\"ff\", \"fm\", \"fo\", \"fof\", \"fos\", \"fosf\")" "c(\"fosfocina\", \"fosfomicina\", \"fosfomycin\", \"fosfomycin sodium\", \"fosfomycine\", \"fosfomycinum\", \"fosfonomycin\", \"monuril\", \"monurol\", \"phosphonemycin\", \"phosphonomycin\", \"veramina\")" 3 "g" 8 "g" "character(0)"
|
||||
"FMD" 572 "Fosmidomycin" "Other antibacterials" "" "c(\"fosmidomycin\", \"fosmidomycina\", \"fosmidomycine\", \"fosmidomycinum\")" "character(0)"
|
||||
"FRM" 8378 "Framycetin" "Aminoglycosides" "c(\"D09AA01\", \"R01AX08\", \"S01AA07\")" "c(\"\", \"fram\")" "c(\"actilin\", \"actiline\", \"antibiotique\", \"bycomycin\", \"endomixin\", \"enterfram\", \"fradiomycin\", \"fradiomycin b\", \"fradiomycinum\", \"framicetina\", \"framycetin\", \"framycetin sulfate\", \"framycetine\", \"framycetinum\", \"framygen\", \"fraquinol\", \"jernadex\", \"myacine\", \"myacyne\", \"mycerin\", \"mycifradin\", \"neobrettin\", \"neolate\", \"neomas\", \"neomcin\", \"neomicina\", \"neomin\", \"neomycin\", \"neomycin b\", \"neomycin b sulfate\", \"neomycin solution\", \"neomycin sulfate\", \"neomycin sulphate\", \"neomycinb\", \"neomycine\", \"neomycinum\",
|
||||
\"nivemycin\", \"pimavecort\", \"soframycin\", \"soframycine\", \"tuttomycin\", \"vonamycin\", \"vonamycin powder v\")" "character(0)"
|
||||
"FRZ" 5323714 "Furazolidone" "Other antibacterials" "" "c(\"bifuron\", \"corizium\", \"coryzium\", \"diafuron\", \"enterotoxon\", \"furall\", \"furaxon\", \"furaxone\", \"furazol\", \"furazolidine\", \"furazolidon\", \"furazolidona\", \"furazolidone\", \"furazolidonum\", \"furazolum\", \"furazon\", \"furidon\", \"furovag\", \"furox aerosol powder\", \"furoxal\", \"furoxane\", \"furoxon\", \"furoxone\", \"furoxone liquid\", \"furoxone swine mix\", \"furozolidine\", \"giardil\", \"giarlam\", \"medaron\", \"neftin\", \"nicolen\", \"nifulidone\", \"nifuran\", \"nifurazolidone\", \"nifurazolidonum\", \"nitrofurazolidone\", \"nitrofurazolidonum\",
|
||||
"FRZ" 5323714 "Furazolidone" "Other antibacterials" "G01AX06" "" "c(\"bifuron\", \"corizium\", \"coryzium\", \"diafuron\", \"enterotoxon\", \"furall\", \"furaxon\", \"furaxone\", \"furazol\", \"furazolidine\", \"furazolidon\", \"furazolidona\", \"furazolidone\", \"furazolidonum\", \"furazolum\", \"furazon\", \"furidon\", \"furovag\", \"furox aerosol powder\", \"furoxal\", \"furoxane\", \"furoxon\", \"furoxone\", \"furoxone liquid\", \"furoxone swine mix\", \"furozolidine\", \"giardil\", \"giarlam\", \"medaron\", \"neftin\", \"nicolen\", \"nifulidone\", \"nifuran\", \"nifurazolidone\", \"nifurazolidonum\", \"nitrofurazolidone\", \"nitrofurazolidonum\",
|
||||
\"nitrofuroxon\", \"optazol\", \"ortazol\", \"puradin\", \"roptazol\", \"sclaventerol\", \"tikofuran\", \"topazone\", \"trichofuron\", \"tricofuron\", \"tricoron\", \"trifurox\", \"viofuragyn\")" "character(0)"
|
||||
"FUS" "J01XC01" 3000226 "Fusidic acid" "Other antibacterials" "Other antibacterials" "Steroid antibacterials" "c(\"fa\", \"fusi\")" "c(\"acide fusidique\", \"acido fusidico\", \"acidum fusidicum\", \"flucidin\", \"fucidate\", \"fucidate sodium\", \"fucidic acid\", \"fucidin\", \"fucidin acid\", \"fucithalmic\", \"fusidate\", \"fusidate acid\", \"fusidic acid\", \"fusidine\", \"fusidinic acid\", \"ramycin\")" 1.5 "g" 1.5 "g" "character(0)"
|
||||
"GAM" 59364992 "Gamithromycin" "Macrolides/lincosamides" "" "gamithromycin" "character(0)"
|
||||
"GRN" 124093 "Garenoxacin" "Quinolones" "" "c(\"ganefloxacin\", \"garenfloxacin\", \"garenoxacin\")" "character(0)"
|
||||
"GAT" "J01MA16" 5379 "Gatifloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"gati\")" "c(\"gatiflo\", \"gatifloxacin\", \"gatifloxacine\", \"gatifloxcin\", \"gatilox\", \"gatiquin\", \"gatispan\", \"tequin\", \"tequin and zymar\", \"zymaxid\")" 0.4 "g" 0.4 "g" "character(0)"
|
||||
"GEM" "J01MA15" 9571107 "Gemifloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "" "c(\"factiv\", \"factive\", \"gemifioxacin\", \"gemifloxacin\", \"gemifloxacine\", \"gemifloxacino\", \"gemifloxacinum\")" 0.32 "character(0)"
|
||||
"GEN" "J01GB03" 3467 "Gentamicin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "c(\"cn\", \"gen\", \"gent\", \"gm\")" "c(\"apogen\", \"centicin\", \"cidomycin\", \"garasol\", \"genoptic liquifilm\", \"genoptic s.o.p.\", \"gentacycol\", \"gentafair\", \"gentak\", \"gentamar\", \"gentamcin sulfate\", \"gentamicin\", \"gentamicina\", \"gentamicine\", \"gentamicins\", \"gentamicinum\", \"gentamycin\", \"gentamycins\", \"gentamycinum\", \"gentavet\", \"gentocin\", \"jenamicin\", \"lyramycin\", \"oksitselanim\", \"refobacin\", \"refobacin tm\", \"septigen\", \"uromycine\")" 0.24 "g" "c(\"13561-6\", \"13562-4\", \"15106-8\", \"22746-2\", \"22747-0\", \"31091-2\", \"31092-0\", \"31093-8\", \"35668-3\", \"3663-2\", \"3664-0\", \"3665-7\", \"39082-3\", \"47109-4\", \"59379-8\", \"80971-5\", \"88111-0\")"
|
||||
"GEH" "Gentamicin-high" "Aminoglycosides" "c(\"g_h\", \"gehl\", \"genta high\", \"gentamicin high\")" "" ""
|
||||
"GEP" 25101874 "Gepotidacin" "Other antibacterials" "" "gepotidacin" "character(0)"
|
||||
"GRX" "J01MA11" 72474 "Grepafloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"grep\")" "grepafloxacin" 0.4 "g" "character(0)"
|
||||
"GRI" 441140 "Griseofulvin" "Antifungals/antimycotics" "" "c(\"amudane\", \"curling factor\", \"delmofulvina\", \"fulcin\", \"fulcine\", \"fulvican grisactin\", \"fulvicin\", \"fulvicin bolus\", \"fulvidex\", \"fulvina\", \"fulvinil\", \"fulvistatin\", \"fungivin\", \"greosin\", \"gresfeed\", \"gricin\", \"grifulin\", \"grifulvin\", \"grifulvin v\", \"grisactin\", \"grisactin ultra\", \"grisactin v\", \"griscofulvin\", \"grise ostatin\", \"grisefuline\", \"griseo\", \"griseofulvin\", \"griseofulvin forte\", \"griseofulvina\", \"griseofulvine\", \"griseofulvinum\", \"griseomix\", \"griseostatin\", \"grisetin\", \"grisofulvin\",
|
||||
\"grisovin\", \"grisovin fp\", \"grizeofulvin\", \"grysio\", \"guservin\", \"lamoryl\", \"likuden\", \"likunden\", \"murfulvin\", \"poncyl\", \"spirofulvin\", \"sporostatin xan\", \"xuanjing\")" "12402-4"
|
||||
"HAB" 175989 "Habekacin" "Aminoglycosides" "" "c(\"arbekacin sulfate\", \"habekacin\", \"habekacin sulfate\", \"habekacin xsulfate\")" "character(0)"
|
||||
"HCH" "J02AA02" 11979956 "Hachimycin" "Antifungals/antimycotics" "Antimycotics for systemic use" "Antibiotics" "" "c(\"cabimicina\", \"hachimicina\", \"hachimycin\", \"hachimycine\", \"hachimycinum\", \"trichomycinum\", \"trichonat\")" "character(0)"
|
||||
"HET" "J01CA18" 443387 "Hetacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"etacillina\", \"hetacilina\", \"hetacillin\", \"hetacilline\", \"hetacillinum\", \"phenazacillin\", \"versapen\")" 2 "g" "character(0)"
|
||||
"HYG" 56928061 "Hygromycin" "Aminoglycosides" "" "c(\"antihelmycin\", \"hydromycin b\", \"hygrovetine\")" "character(0)"
|
||||
"ICL" 213043 "Iclaprim" "Other antibacterials" "" "c(\"iclaprim\", \"mersarex\")" "character(0)"
|
||||
"IPM" "J01DH51" 104838 "Imipenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "c(\"imci\", \"imi\", \"imip\", \"imp\")" "c(\"imipemide\", \"imipenem\", \"imipenem anhydrous\", \"imipenem/cilastatin\", \"imipenemum\", \"imipenen\", \"primaxin\", \"tienamycin\")" 2 "g" "c(\"17010-0\", \"25257-7\", \"27331-8\", \"3688-9\")"
|
||||
"IPE" "Imipenem/EDTA" "Carbapenems" "" "" ""
|
||||
"IMR" "Imipenem/relebactam" "Carbapenems" "" "" ""
|
||||
"ISV" 6918485 "Isavuconazole" "Antifungals/antimycotics" "c(\"\", \"isav\")" "isavuconazole" "character(0)"
|
||||
"ISE" "J01GB11" 3037209 "Isepamicin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "" "c(\"isepacin\", \"isepalline\", \"isepamicin\", \"isepamicina\", \"isepamicine\", \"isepamicinum\")" 0.4 "g" "character(0)"
|
||||
"ISO" "D01AC05" 3760 "Isoconazole" "Antifungals/antimycotics" "Antimycotics for topic use" "Triazole derivatives" "" "c(\"isoconazol\", \"isoconazole\", \"isoconazolum\", \"travogen\")" "character(0)"
|
||||
"INH" "J04AC01" 3767 "Isoniazid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Hydrazides" "inh" "c(\"abdizide\", \"andrazide\", \"anidrasona\", \"antimicina\", \"antituberkulosum\", \"armacide\", \"armazid\", \"armazide\", \"atcotibine\", \"azt + isoniazid\", \"azuren\", \"bacillin\", \"cemidon\", \"chemiazid\", \"chemidon\", \"continazine\", \"cortinazine\", \"cotinazin\", \"cotinizin\", \"defonin\", \"dibutin\", \"diforin\", \"dinacrin\", \"ditubin\", \"ebidene\", \"eralon\", \"ertuban\", \"eutizon\", \"evalon\", \"fetefu\", \"fimalene\", \"hid rasonil\", \"hidranizil\", \"hidrasonil\", \"hidrulta\", \"hidrun\", \"hycozid\", \"hydrazid\", \"hydrazide\", \"hyozid\", \"i.a.i.\",
|
||||
"FUS" 3000226 "Fusidic acid" "Other antibacterials" "c(\"D06AX01\", \"D09AA02\", \"J01XC01\", \"S01AA13\")" "Other antibacterials" "Steroid antibacterials" "c(\"fa\", \"fusi\")" "c(\"acide fusidique\", \"acido fusidico\", \"acidum fusidicum\", \"flucidin\", \"fucidate\", \"fucidate sodium\", \"fucidic acid\", \"fucidin\", \"fucidin acid\", \"fucithalmic\", \"fusidate\", \"fusidate acid\", \"fusidic acid\", \"fusidine\", \"fusidinic acid\", \"ramycin\")" 1.5 "g" 1.5 "g" "character(0)"
|
||||
"GAM" 59364992 "Gamithromycin" "Macrolides/lincosamides" "" "gamithromycin" "character(0)"
|
||||
"GRN" 124093 "Garenoxacin" "Quinolones" "J01MA19" "" "c(\"ganefloxacin\", \"garenfloxacin\", \"garenoxacin\")" 0.4 "g" "character(0)"
|
||||
"GAT" 5379 "Gatifloxacin" "Quinolones" "c(\"J01MA16\", \"S01AE06\")" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"gati\")" "c(\"gatiflo\", \"gatifloxacin\", \"gatifloxacine\", \"gatifloxcin\", \"gatilox\", \"gatiquin\", \"gatispan\", \"tequin\", \"tequin and zymar\", \"zymaxid\")" 0.4 "g" 0.4 "g" "character(0)"
|
||||
"GEM" 9571107 "Gemifloxacin" "Quinolones" "J01MA15" "Quinolone antibacterials" "Fluoroquinolones" "" "c(\"factiv\", \"factive\", \"gemifioxacin\", \"gemifloxacin\", \"gemifloxacine\", \"gemifloxacino\", \"gemifloxacinum\")" 0.32 "g" "character(0)"
|
||||
"GEN" 3467 "Gentamicin" "Aminoglycosides" "c(\"D06AX07\", \"J01GB03\", \"S01AA11\", \"S02AA14\", \"S03AA06\")" "Aminoglycoside antibacterials" "Other aminoglycosides" "c(\"cn\", \"gen\", \"gent\", \"gm\")" "c(\"apogen\", \"centicin\", \"cidomycin\", \"garasol\", \"genoptic liquifilm\", \"genoptic s.o.p.\", \"gentacycol\", \"gentafair\", \"gentak\", \"gentamar\", \"gentamcin sulfate\", \"gentamicin\", \"gentamicina\", \"gentamicine\", \"gentamicins\", \"gentamicinum\", \"gentamycin\", \"gentamycins\", \"gentamycinum\", \"gentavet\", \"gentocin\", \"jenamicin\", \"lyramycin\", \"oksitselanim\", \"refobacin\", \"refobacin tm\", \"septigen\", \"uromycine\")" 0.24 "g" "c(\"13561-6\", \"13562-4\", \"15106-8\", \"22746-2\", \"22747-0\", \"31091-2\", \"31092-0\", \"31093-8\", \"35668-3\", \"3663-2\", \"3664-0\", \"3665-7\", \"39082-3\", \"47109-4\", \"59379-8\", \"80971-5\", \"88111-0\")"
|
||||
"GEH" "Gentamicin-high" "Aminoglycosides" "c(\"gehi\", \"gehl\", \"genta high\", \"gentamicin high\")" "" ""
|
||||
"GEP" 25101874 "Gepotidacin" "Other antibacterials" "" "gepotidacin" "character(0)"
|
||||
"GRX" 72474 "Grepafloxacin" "Quinolones" "J01MA11" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"grep\")" "grepafloxacin" 0.4 "g" "character(0)"
|
||||
"GRI" 441140 "Griseofulvin" "Antifungals/antimycotics" "c(\"D01AA08\", \"D01BA01\")" "" "c(\"amudane\", \"curling factor\", \"delmofulvina\", \"fulcin\", \"fulcine\", \"fulvican grisactin\", \"fulvicin\", \"fulvicin bolus\", \"fulvidex\", \"fulvina\", \"fulvinil\", \"fulvistatin\", \"fungivin\", \"greosin\", \"gresfeed\", \"gricin\", \"grifulin\", \"grifulvin\", \"grifulvin v\", \"grisactin\", \"grisactin ultra\", \"grisactin v\", \"griscofulvin\", \"grise ostatin\", \"grisefuline\", \"griseo\", \"griseofulvin\", \"griseofulvin forte\", \"griseofulvina\", \"griseofulvine\", \"griseofulvinum\", \"griseomix\", \"griseostatin\", \"grisetin\", \"grisofulvin\",
|
||||
\"grisovin\", \"grisovin fp\", \"grizeofulvin\", \"grysio\", \"guservin\", \"lamoryl\", \"likuden\", \"likunden\", \"murfulvin\", \"poncyl\", \"spirofulvin\", \"sporostatin xan\", \"xuanjing\")" 0.5 "g" "12402-4"
|
||||
"HAB" 175989 "Habekacin" "Aminoglycosides" "" "c(\"arbekacin sulfate\", \"habekacin\", \"habekacin sulfate\", \"habekacin xsulfate\")" "character(0)"
|
||||
"HCH" 11979956 "Hachimycin" "Antifungals/antimycotics" "c(\"D01AA03\", \"G01AA06\", \"J02AA02\")" "Antimycotics for systemic use" "Antibiotics" "" "c(\"cabimicina\", \"hachimicina\", \"hachimycin\", \"hachimycine\", \"hachimycinum\", \"trichomycinum\", \"trichonat\")" "character(0)"
|
||||
"HET" 443387 "Hetacillin" "Beta-lactams/penicillins" "J01CA18" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"etacillina\", \"hetacilina\", \"hetacillin\", \"hetacilline\", \"hetacillinum\", \"phenazacillin\", \"versapen\")" 2 "g" "character(0)"
|
||||
"HYG" 56928061 "Hygromycin" "Aminoglycosides" "" "c(\"antihelmycin\", \"hydromycin b\", \"hygrovetine\")" "character(0)"
|
||||
"ICL" 213043 "Iclaprim" "Other antibacterials" "J01EA03" "" "c(\"iclaprim\", \"mersarex\")" "character(0)"
|
||||
"IPM" 104838 "Imipenem" "Carbapenems" "J01DH51" "Other beta-lactam antibacterials" "Carbapenems" "c(\"imci\", \"imi\", \"imip\", \"imp\")" "c(\"imipemide\", \"imipenem\", \"imipenem anhydrous\", \"imipenem/cilastatin\", \"imipenemum\", \"imipenen\", \"primaxin\", \"tienamycin\")" 2 "g" "c(\"17010-0\", \"25257-7\", \"27331-8\", \"3688-9\")"
|
||||
"IPE" "Imipenem/EDTA" "Carbapenems" "" "" ""
|
||||
"IMR" "Imipenem/relebactam" "Carbapenems" "" "" ""
|
||||
"ISV" 6918485 "Isavuconazole" "Antifungals/antimycotics" "J02AC05" "c(\"\", \"isav\")" "isavuconazole" 0.2 "g" 0.2 "g" "character(0)"
|
||||
"ISE" 3037209 "Isepamicin" "Aminoglycosides" "J01GB11" "Aminoglycoside antibacterials" "Other aminoglycosides" "" "c(\"isepacin\", \"isepalline\", \"isepamicin\", \"isepamicina\", \"isepamicine\", \"isepamicinum\")" 0.4 "g" "character(0)"
|
||||
"ISO" 3760 "Isoconazole" "Antifungals/antimycotics" "c(\"D01AC05\", \"G01AF07\")" "Antimycotics for topic use" "Triazole derivatives" "" "c(\"isoconazol\", \"isoconazole\", \"isoconazolum\", \"travogen\")" "character(0)"
|
||||
"INH" 3767 "Isoniazid" "Antimycobacterials" "J04AC01" "Drugs for treatment of tuberculosis" "Hydrazides" "inh" "c(\"abdizide\", \"andrazide\", \"anidrasona\", \"antimicina\", \"antituberkulosum\", \"armacide\", \"armazid\", \"armazide\", \"atcotibine\", \"azt + isoniazid\", \"azuren\", \"bacillin\", \"cemidon\", \"chemiazid\", \"chemidon\", \"continazine\", \"cortinazine\", \"cotinazin\", \"cotinizin\", \"defonin\", \"dibutin\", \"diforin\", \"dinacrin\", \"ditubin\", \"ebidene\", \"eralon\", \"ertuban\", \"eutizon\", \"evalon\", \"fetefu\", \"fimalene\", \"hid rasonil\", \"hidranizil\", \"hidrasonil\", \"hidrulta\", \"hidrun\", \"hycozid\", \"hydrazid\", \"hydrazide\", \"hyozid\", \"i.a.i.\",
|
||||
\"idrazil\", \"inizid\", \"iscotin\", \"isidrina\", \"ismazide\", \"isobicina\", \"isocid\", \"isocidene\", \"isocotin\", \"isohydrazide\", \"isokin\", \"isolyn\", \"isonerit\", \"isonex\", \"isoniacid\", \"isoniazid\", \"isoniazid sa\", \"isoniazida\", \"isoniazide\", \"isoniazidum\", \"isonicazide\", \"isonicid\", \"isonico\", \"isonicotan\", \"isonicotil\", \"isonicotinhydrazid\", \"isonicotinohydrazide\", \"isonide\", \"isonidrin\", \"isonikazid\", \"isonilex\", \"isonin\", \"isonindon\", \"isonirit\", \"isoniton\", \"isonizida\", \"isonizide\", \"isotamine\", \"isotebe\",
|
||||
\"isotebezid\", \"isotinyl\", \"isozid\", \"isozide\", \"isozyd\", \"laniazid\", \"laniozid\", \"lanizid\", \"mayambutol\", \"mybasan\", \"neoteben\", \"neoxin\", \"neumandin\", \"niadrin\", \"nicazide\", \"nicetal\", \"nicizina\", \"niconyl\", \"nicotibina\", \"nicotibine\", \"nicotisan\", \"nicozide\", \"nidaton\", \"nidrazid\", \"nikozid\", \"niplen\", \"nitadon\", \"niteban\", \"nydrazid\", \"nyscozid\", \"pelazid\", \"percin\", \"phthisen\", \"pycazide\", \"pyreazid\", \"pyricidin\", \"pyridicin\", \"pyrizidin\", \"raumanon\", \"razide\", \"retozide\", \"rifater\", \"rimicid\",
|
||||
\"rimifon\", \"rimiphone\", \"rimitsid\", \"robiselin\", \"robisellin\", \"roxifen\", \"sanohidrazina\", \"sauterazid\", \"sauterzid\", \"stanozide\", \"tebecid\", \"tebenic\", \"tebexin\", \"tebilon\", \"teebaconin\", \"tekazin\", \"tibazide\", \"tibemid\", \"tibiazide\", \"tibinide\", \"tibison\", \"tibivis\", \"tibizide\", \"tibusan\", \"tisiodrazida\", \"tizide\", \"tubazid\", \"tubazide\", \"tubeco\", \"tubecotubercid\", \"tuberian\", \"tubicon\", \"tubilysin\", \"tubizid\", \"tubomel\", \"unicocyde\", \"unicozyde\", \"vazadrine\", \"vederon\", \"zidafimia\", \"zinadon\",
|
||||
\"zonazide\")" 0.3 "g" 0.3 "g" "c(\"25451-6\", \"26756-7\", \"3697-0\", \"40371-7\")"
|
||||
"ITR" "J02AC02" 3793 "Itraconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives" "itra" "c(\"itraconazol\", \"itraconazole\", \"itraconazolum\", \"itraconzaole\", \"itrazole\", \"oriconazole\", \"sporanox\")" 0.2 "g" 0.2 "g" "c(\"10989-2\", \"12392-7\", \"25258-5\", \"27081-9\", \"32184-4\", \"32185-1\", \"80531-7\")"
|
||||
"JOS" "J01FA07" 5282165 "Josamycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"josacine\", \"josamicina\", \"josamycin\", \"josamycine\", \"josamycinum\")" 2 "g" "character(0)"
|
||||
"KAN" "J01GB04" 6032 "Kanamycin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "c(\"hlk\", \"k\", \"kan\", \"kana\", \"km\")" "c(\"kanamicina\", \"kanamycin\", \"kanamycin a\", \"kanamycin base\", \"kanamycine\", \"kanamycinum\", \"kantrex\", \"kenamycin a\", \"klebcil\", \"liposomal kanamycin\")" 1 "g" "c(\"23889-9\", \"3698-8\", \"3699-6\", \"3700-2\", \"47395-9\")"
|
||||
"KAH" "Kanamycin-high" "Aminoglycosides" "c(\"\", \"k_h\", \"kahl\")" "" ""
|
||||
"KAC" "Kanamycin/cephalexin" "Aminoglycosides" "" "" ""
|
||||
"KET" "J02AB02" 456201 "Ketoconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Imidazole derivatives" "c(\"keto\", \"ktc\")" "c(\"extina\", \"fungarest\", \"fungoral\", \"ketocanazole\", \"ketoconazol\", \"ketoconazole\", \"ketoconazolum\", \"ketoderm\", \"nizoral\", \"xolegel\")" 0.2 "g" "c(\"10990-0\", \"12393-5\", \"25259-3\", \"60091-6\", \"60092-4\")"
|
||||
"KIT" "Kitasamycin (Leucomycin)" "Macrolides/lincosamides" "" "" ""
|
||||
"LAS" 5360807 "Lasalocid" "Other antibacterials" "" "c(\"avatec\", \"lasalocid\", \"lasalocid a\", \"lasalocide\", \"lasalocide a\", \"lasalocido\", \"lasalocidum\")" "87598-9"
|
||||
"LTM" "J01DD06" 47499 "Latamoxef" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"mox\", \"moxa\")" "c(\"disodium moxalactam\", \"festamoxin\", \"lamoxactam\", \"latamoxef\", \"latamoxefum\", \"shiomarin\")" 4 "g" "character(0)"
|
||||
"LMU" 25185057 "Lefamulin" "Other antibacterials" "" "lefamulin" "character(0)"
|
||||
"LEN" 65646 "Lenampicillin" "Beta-lactams/penicillins" "" "c(\"lenampicilina\", \"lenampicillin\", \"lenampicillin hcl\", \"lenampicilline\", \"lenampicillinum\")" "character(0)"
|
||||
"LVX" "J01MA12" 149096 "Levofloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"le\", \"lev\", \"levo\", \"lvx\")" "c(\"aeroquin\", \"cravit\", \"cravit hydrate\", \"cravit iv\", \"cravit ophthalmic\", \"elequine\", \"floxacin\", \"floxel\", \"iquix hydrate\", \"leroxacin\", \"lesacin\", \"levaquin\", \"levaquin hydrate\", \"levo floxacin\", \"levofiexacin\", \"levofloxacin\", \"levofloxacin hydrate\", \"levofloxacine\", \"levofloxacino\", \"levofloxacinum\", \"levokacin\", \"levoxacin\", \"mosardal\", \"nofaxin\", \"oftaquix\", \"quixin\", \"reskuin\", \"tavanic\", \"unibiotic\", \"venaxan\", \"volequin\")" 0.5 "g" 0.5 "g" "c(\"21368-6\", \"30532-6\", \"30533-4\")"
|
||||
"LND" 9850038 "Levonadifloxacin" "Quinolones" "" "levonadifloxacin" "character(0)"
|
||||
"LSP" "Linco-spectin (lincomycin/spectinomycin)" "Other antibacterials" "" "" ""
|
||||
"LIN" "J01FF02" 3000540 "Lincomycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Lincosamides" "linc" "c(\"cillimycin\", \"jiemycin\", \"lincolcina\", \"lincolnensin\", \"lincomicina\", \"lincomycin\", \"lincomycin a\", \"lincomycine\", \"lincomycinum\")" 1.8 "g" 1.8 "g" "87597-1"
|
||||
"LNZ" "J01XX08" 441401 "Linezolid" "Oxazolidinones" "Other antibacterials" "Other antibacterials" "c(\"line\", \"lnz\", \"lz\", \"lzd\")" "c(\"linezlid\", \"linezoid\", \"linezolid\", \"linezolide\", \"linezolidum\", \"zivoxid\", \"zyvoxa\", \"zyvoxam\", \"zyvoxid\")" 1.2 "g" 1.2 "g" "c(\"34202-2\", \"80609-1\")"
|
||||
"LFE" "Linoprist-flopristin" "Other antibacterials" "" "" ""
|
||||
"LOM" "J01MA07" 3948 "Lomefloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"lmf\", \"lom\", \"lome\")" "c(\"lomefloxacin\", \"lomefloxacine\", \"lomefloxacino\", \"lomefloxacinum\", \"maxaquin\")" 0.4 "character(0)"
|
||||
"LOR" "J01DC08" 5284585 "Loracarbef" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"\", \"lora\")" "c(\"anhydrous loracarbef\", \"lorabid\", \"loracarbef\", \"loracarbefum\", \"lorbef\", \"loribid\")" 0.6 "g" "character(0)"
|
||||
"LYM" "J01AA04" 54707177 "Lymecycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "" "c(\"biovetin\", \"chlortetracyclin\", \"ciclisin\", \"ciclolysal\", \"infaciclina\", \"limeciclina\", \"lisinbiotic\", \"lymecyclin\", \"lymecycline\", \"lymecyclinum\", \"mucomycin\", \"ntetracycline\", \"tetralisal\", \"tetralysal\", \"vebicyclysal\")" 0.6 "g" 0.6 "g" "character(0)"
|
||||
"MNA" "J01XX06" 1292 "Mandelic acid" "Other antibacterials" "Other antibacterials" "Other antibacterials" "" "c(\"acido mandelico\", \"almond acid\", \"amygdalic acid\", \"benzoglycolic acid\", \"hydroxyacetic acid\", \"kyselina mandlova\", \"mandelic acid\", \"paramandelic acid\", \"phenylglycolic acid\", \"uromaline\")" 12 "g" "character(0)"
|
||||
"MAR" 60651 "Marbofloxacin" "Quinolones" "" "c(\"marbocyl\", \"marbofloxacin\", \"marbofloxacine\", \"marbofloxacino\", \"marbofloxacinum\", \"zeniquin\")" "character(0)"
|
||||
"MEC" "J01CA11" 36273 "Mecillinam (Amdinocillin)" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"amdinocillin\", \"coactin\", \"hexacillin\", \"mecilinamo\", \"mecillinam\", \"mecillinamum\", \"micillinam\", \"penicillin hx\", \"selexidin\")" 1.2 "g" "character(0)"
|
||||
"MEL" 71306732 "Meleumycin" "Macrolides/lincosamides" "" "" ""
|
||||
"MEM" "J01DH02" 441130 "Meropenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "c(\"mem\", \"mer\", \"mero\", \"mp\", \"mrp\")" "c(\"meronem\", \"meropen\", \"meropenem\", \"meropenem anhydrous\", \"meropenem hydrate\", \"meropenem trihydrate\", \"meropenemum\", \"merrem\", \"merrem i.v.\", \"merrem iv\")" 3 "g" "41406-0"
|
||||
"MNC" "Meropenem/nacubactam" "Carbapenems" "" "" ""
|
||||
"MEV" "J01DH52" "Meropenem/vaborbactam" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "" "" ""
|
||||
"MES" 176886 "Mesulfamide" "Other antibacterials" "" "c(\"mesulfamide\", \"mesulfamido\", \"mesulfamidum\")" "character(0)"
|
||||
"MTC" "J01AA05" 54675785 "Metacycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "" "c(\"bialatan\", \"metaciclina\", \"metacycline\", \"metacyclinum\", \"methacycline\", \"methacycline base\", \"methacyclinum\", \"methylenecycline\", \"physiomycine\", \"rondomycin\")" 0.6 "g" "character(0)"
|
||||
"MTM" "J01CA14" 6713928 "Metampicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"blomopen\", \"bonopen\", \"celinmicina\", \"elatocilline\", \"fedacilina kapseln\", \"filorex\", \"italcina kapseln\", \"magnipen\", \"metabacter ampullen\", \"metambac\", \"metampicilina\", \"metampicillin\", \"metampicillin sodium\", \"metampicillina\", \"metampicilline\", \"metampicillinum\", \"methampicillin\", \"metiskia ampullen\", \"micinovo\", \"micinovo ampullen\", \"pangocilin\", \"probiotic\", \"rastomycin k\", \"relyothenate\", \"ruticina\", \"rutizina\", \"rutizina ampullen\", \"sedomycin\", \"suvipen\", \"suvipen ampullen\", \"tampilen ampullen\",
|
||||
"ITR" 3793 "Itraconazole" "Antifungals/antimycotics" "J02AC02" "Antimycotics for systemic use" "Triazole derivatives" "itra" "c(\"itraconazol\", \"itraconazole\", \"itraconazolum\", \"itraconzaole\", \"itrazole\", \"oriconazole\", \"sporanox\")" 0.2 "g" 0.2 "g" "c(\"10989-2\", \"12392-7\", \"25258-5\", \"27081-9\", \"32184-4\", \"32185-1\", \"80531-7\")"
|
||||
"JOS" 5282165 "Josamycin" "Macrolides/lincosamides" "J01FA07" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"josacine\", \"josamicina\", \"josamycin\", \"josamycine\", \"josamycinum\")" 2 "g" "character(0)"
|
||||
"KAN" 6032 "Kanamycin" "Aminoglycosides" "c(\"A07AA08\", \"J01GB04\", \"S01AA24\")" "Aminoglycoside antibacterials" "Other aminoglycosides" "c(\"hlk\", \"k\", \"kan\", \"kana\", \"km\")" "c(\"kanamicina\", \"kanamycin\", \"kanamycin a\", \"kanamycin base\", \"kanamycine\", \"kanamycinum\", \"kantrex\", \"kenamycin a\", \"klebcil\", \"liposomal kanamycin\")" 3 "g" 1 "g" "c(\"23889-9\", \"3698-8\", \"3699-6\", \"3700-2\", \"47395-9\")"
|
||||
"KAH" "Kanamycin-high" "Aminoglycosides" "c(\"\", \"k_h\", \"kahl\")" "" ""
|
||||
"KAC" "Kanamycin/cephalexin" "Aminoglycosides" "" "" ""
|
||||
"KET" 456201 "Ketoconazole" "Antifungals/antimycotics" "c(\"D01AC08\", \"G01AF11\", \"H02CA03\", \"J02AB02\")" "Antimycotics for systemic use" "Imidazole derivatives" "c(\"keto\", \"ktc\")" "c(\"extina\", \"fungarest\", \"fungoral\", \"ketocanazole\", \"ketoconazol\", \"ketoconazole\", \"ketoconazolum\", \"ketoderm\", \"nizoral\", \"xolegel\")" 0.2 "g" "c(\"10990-0\", \"12393-5\", \"25259-3\", \"60091-6\", \"60092-4\")"
|
||||
"KIT" "Kitasamycin (Leucomycin)" "Macrolides/lincosamides" "" "" ""
|
||||
"LAS" 5360807 "Lasalocid" "Other antibacterials" "" "c(\"avatec\", \"lasalocid\", \"lasalocid a\", \"lasalocide\", \"lasalocide a\", \"lasalocido\", \"lasalocidum\")" "87598-9"
|
||||
"LTM" 47499 "Latamoxef" "Cephalosporins (3rd gen.)" "J01DD06" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"mox\", \"moxa\")" "c(\"disodium moxalactam\", \"festamoxin\", \"lamoxactam\", \"latamoxef\", \"latamoxefum\", \"shiomarin\")" 4 "g" "character(0)"
|
||||
"LMU" 25185057 "Lefamulin" "Other antibacterials" "J01XX12" "" "lefamulin" "character(0)"
|
||||
"LEN" 65646 "Lenampicillin" "Beta-lactams/penicillins" "" "c(\"lenampicilina\", \"lenampicillin\", \"lenampicillin hcl\", \"lenampicilline\", \"lenampicillinum\")" "character(0)"
|
||||
"LVX" 149096 "Levofloxacin" "Quinolones" "c(\"J01MA12\", \"S01AE05\")" "Quinolone antibacterials" "Fluoroquinolones" "c(\"le\", \"lev\", \"levo\", \"lvx\")" "c(\"aeroquin\", \"cravit\", \"cravit hydrate\", \"cravit iv\", \"cravit ophthalmic\", \"elequine\", \"floxacin\", \"floxel\", \"iquix hydrate\", \"leroxacin\", \"lesacin\", \"levaquin\", \"levaquin hydrate\", \"levo floxacin\", \"levofiexacin\", \"levofloxacin\", \"levofloxacin hydrate\", \"levofloxacine\", \"levofloxacino\", \"levofloxacinum\", \"levokacin\", \"levoxacin\", \"mosardal\", \"nofaxin\", \"oftaquix\", \"quixin\", \"reskuin\", \"tavanic\", \"unibiotic\", \"venaxan\", \"volequin\")" 0.5 "g" 0.5 "g" "c(\"21368-6\", \"30532-6\", \"30533-4\")"
|
||||
"LND" 9850038 "Levonadifloxacin" "Quinolones" "J01MA24" "" "levonadifloxacin" "character(0)"
|
||||
"LSP" "Linco-spectin (lincomycin/spectinomycin)" "Other antibacterials" "" "" ""
|
||||
"LIN" 3000540 "Lincomycin" "Macrolides/lincosamides" "J01FF02" "Macrolides, lincosamides and streptogramins" "Lincosamides" "linc" "c(\"cillimycin\", \"jiemycin\", \"lincolcina\", \"lincolnensin\", \"lincomicina\", \"lincomycin\", \"lincomycin a\", \"lincomycine\", \"lincomycinum\")" 1.8 "g" 1.8 "g" "87597-1"
|
||||
"LNZ" 441401 "Linezolid" "Oxazolidinones" "J01XX08" "Other antibacterials" "Other antibacterials" "c(\"line\", \"lnz\", \"lz\", \"lzd\")" "c(\"linezlid\", \"linezoid\", \"linezolid\", \"linezolide\", \"linezolidum\", \"zivoxid\", \"zyvoxa\", \"zyvoxam\", \"zyvoxid\")" 1.2 "g" 1.2 "g" "c(\"34202-2\", \"80609-1\")"
|
||||
"LFE" "Linoprist-flopristin" "Other antibacterials" "" "" ""
|
||||
"LOM" 3948 "Lomefloxacin" "Quinolones" "c(\"J01MA07\", \"S01AE04\")" "Quinolone antibacterials" "Fluoroquinolones" "c(\"lmf\", \"lom\", \"lome\")" "c(\"lomefloxacin\", \"lomefloxacine\", \"lomefloxacino\", \"lomefloxacinum\", \"maxaquin\")" 0.4 "g" "character(0)"
|
||||
"LOR" 5284585 "Loracarbef" "Cephalosporins (2nd gen.)" "J01DC08" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"\", \"lora\")" "c(\"anhydrous loracarbef\", \"lorabid\", \"loracarbef\", \"loracarbefum\", \"lorbef\", \"loribid\")" 0.6 "g" "character(0)"
|
||||
"LYM" 54707177 "Lymecycline" "Tetracyclines" "J01AA04" "Tetracyclines" "Tetracyclines" "" "c(\"biovetin\", \"chlortetracyclin\", \"ciclisin\", \"ciclolysal\", \"infaciclina\", \"limeciclina\", \"lisinbiotic\", \"lymecyclin\", \"lymecycline\", \"lymecyclinum\", \"mucomycin\", \"ntetracycline\", \"tetralisal\", \"tetralysal\", \"vebicyclysal\")" 0.6 "g" 0.6 "g" "character(0)"
|
||||
"MNA" 1292 "Mandelic acid" "Other antibacterials" "c(\"B05CA06\", \"J01XX06\")" "Other antibacterials" "Other antibacterials" "" "c(\"acido mandelico\", \"almond acid\", \"amygdalic acid\", \"benzoglycolic acid\", \"hydroxyacetic acid\", \"kyselina mandlova\", \"mandelic acid\", \"paramandelic acid\", \"phenylglycolic acid\", \"uromaline\")" 12 "g" "character(0)"
|
||||
"MAR" 60651 "Marbofloxacin" "Quinolones" "" "c(\"marbocyl\", \"marbofloxacin\", \"marbofloxacine\", \"marbofloxacino\", \"marbofloxacinum\", \"zeniquin\")" "character(0)"
|
||||
"MEC" 36273 "Mecillinam (Amdinocillin)" "Beta-lactams/penicillins" "J01CA11" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"amdinocillin\", \"coactin\", \"hexacillin\", \"mecilinamo\", \"mecillinam\", \"mecillinamum\", \"micillinam\", \"penicillin hx\", \"selexidin\")" 1.2 "g" "character(0)"
|
||||
"MEL" 71306732 "Meleumycin" "Macrolides/lincosamides" "" "" ""
|
||||
"MEM" 441130 "Meropenem" "Carbapenems" "J01DH02" "Other beta-lactam antibacterials" "Carbapenems" "c(\"mem\", \"mer\", \"mero\", \"mp\", \"mrp\")" "c(\"meronem\", \"meropen\", \"meropenem\", \"meropenem anhydrous\", \"meropenem hydrate\", \"meropenem trihydrate\", \"meropenemum\", \"merrem\", \"merrem i.v.\", \"merrem iv\")" 3 "g" "41406-0"
|
||||
"MNC" "Meropenem/nacubactam" "Carbapenems" "" "" ""
|
||||
"MEV" "Meropenem/vaborbactam" "Carbapenems" "J01DH52" "Other beta-lactam antibacterials" "Carbapenems" "" "" 3 "g" ""
|
||||
"MES" 176886 "Mesulfamide" "Other antibacterials" "" "c(\"mesulfamide\", \"mesulfamido\", \"mesulfamidum\")" "character(0)"
|
||||
"MTC" 54675785 "Metacycline" "Tetracyclines" "J01AA05" "Tetracyclines" "Tetracyclines" "" "c(\"bialatan\", \"metaciclina\", \"metacycline\", \"metacyclinum\", \"methacycline\", \"methacycline base\", \"methacyclinum\", \"methylenecycline\", \"physiomycine\", \"rondomycin\")" 0.6 "g" "character(0)"
|
||||
"MTM" 6713928 "Metampicillin" "Beta-lactams/penicillins" "J01CA14" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"blomopen\", \"bonopen\", \"celinmicina\", \"elatocilline\", \"fedacilina kapseln\", \"filorex\", \"italcina kapseln\", \"magnipen\", \"metabacter ampullen\", \"metambac\", \"metampicilina\", \"metampicillin\", \"metampicillin sodium\", \"metampicillina\", \"metampicilline\", \"metampicillinum\", \"methampicillin\", \"metiskia ampullen\", \"micinovo\", \"micinovo ampullen\", \"pangocilin\", \"probiotic\", \"rastomycin k\", \"relyothenate\", \"ruticina\", \"rutizina\", \"rutizina ampullen\", \"sedomycin\", \"suvipen\", \"suvipen ampullen\", \"tampilen ampullen\",
|
||||
\"teonicon trofen\", \"viderpen\", \"viderpin\", \"vioplex\")" 1.5 "g" 1.5 "g" "character(0)"
|
||||
"MTH" "J01XX05" 4101 "Methenamine" "Other antibacterials" "Other antibacterials" "Other antibacterials" "" "c(\"aceto hmt\", \"aminoform\", \"aminoformaldehyde\", \"ammoform\", \"ammonioformaldehyde\", \"antihydral\", \"cystamin\", \"cystex\", \"cystogen\", \"duirexol\", \"ekagom h\", \"esametilentetramina\", \"formamine\", \"formin\", \"h.m.t.\", \"heksa k\", \"herax uts\", \"heterin\", \"hexa b\", \"hexaform\", \"hexaloids\", \"hexamethylamine\", \"hexamethylenamine\", \"hexamethyleneamine\", \"hexamethylentetramin\", \"hexamine\", \"hexamine silver\", \"hexamine superfine\", \"hexaminum\", \"hexasan\", \"hexilmethylenamine\", \"metenamina\", \"metenamine\", \"methamin\",
|
||||
"MTH" 4101 "Methenamine" "Other antibacterials" "J01XX05" "Other antibacterials" "Other antibacterials" "" "c(\"aceto hmt\", \"aminoform\", \"aminoformaldehyde\", \"ammoform\", \"ammonioformaldehyde\", \"antihydral\", \"cystamin\", \"cystex\", \"cystogen\", \"duirexol\", \"ekagom h\", \"esametilentetramina\", \"formamine\", \"formin\", \"h.m.t.\", \"heksa k\", \"herax uts\", \"heterin\", \"hexa b\", \"hexaform\", \"hexaloids\", \"hexamethylamine\", \"hexamethylenamine\", \"hexamethyleneamine\", \"hexamethylentetramin\", \"hexamine\", \"hexamine silver\", \"hexamine superfine\", \"hexaminum\", \"hexasan\", \"hexilmethylenamine\", \"metenamina\", \"metenamine\", \"methamin\",
|
||||
\"methenamin\", \"methenamine\", \"methenamine silver\", \"methenaminum\", \"metramine\", \"naphthamine\", \"nocceler h\", \"preparation af\", \"resotropin\", \"sanceler h\", \"sanceler ht\", \"silver methenamine\", \"uramin\", \"uratrine\", \"urisol\", \"uritone\", \"urodeine\", \"urotropin\", \"urotropine\", \"vesaloin\", \"vesalvine\", \"xametrin\")" 3 "g" "character(0)"
|
||||
"MET" "J01CF03" 6087 "Methicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "meti" "c(\"dimocillin\", \"metacillin\", \"methcilline\", \"methicillin\", \"methicillinum\", \"methycillin\", \"meticilina\", \"meticillin\", \"meticillina\", \"meticilline\", \"meticillinum\", \"staphcillin\")" 4 "g" "c(\"29492-6\", \"3788-7\")"
|
||||
"MTP" 68590 "Metioprim" "Other antibacterials" "" "c(\"methioprim\", \"metioprim\", \"metioprima\", \"metioprime\", \"metioprimum\")" "character(0)"
|
||||
"MXT" 3047729 "Metioxate" "Quinolones" "" "c(\"metioxate\", \"metioxato\", \"metioxatum\")" "character(0)"
|
||||
"MTR" "J01XD01" 4173 "Metronidazole" "Other antibacterials" "Other antibacterials" "Imidazole derivatives" "c(\"metr\", \"mnz\")" "c(\"acromona\", \"anagiardil\", \"arilin\", \"atrivyl\", \"danizol\", \"deflamon\", \"efloran\", \"elyzol\", \"entizol\", \"flagemona\", \"flagesol\", \"flagil\", \"flagyl\", \"flagyl er\", \"flagyl i.v.\", \"flagyl i.v. rtu\", \"flazol\", \"flegyl\", \"florazole\", \"fossyol\", \"giatricol\", \"ginefla vir\", \"gineflavir\", \"helidac\", \"mepagyl\", \"meronidal\", \"methronidazole\", \"metric\", \"metro cream\", \"metro gel\", \"metro i.v\", \"metro i.v.\", \"metro iv\", \"metrocream\", \"metrodzhil\", \"metrogel\", \"metrogyl\", \"metrolag\", \"metrolotion\", \"metrolyl\",
|
||||
"MET" 6087 "Methicillin" "Beta-lactams/penicillins" "J01CF03" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "meti" "c(\"dimocillin\", \"metacillin\", \"methcilline\", \"methicillin\", \"methicillinum\", \"methycillin\", \"meticilina\", \"meticillin\", \"meticillina\", \"meticilline\", \"meticillinum\", \"staphcillin\")" 4 "g" "c(\"29492-6\", \"3788-7\")"
|
||||
"MTP" 68590 "Metioprim" "Other antibacterials" "" "c(\"methioprim\", \"metioprim\", \"metioprima\", \"metioprime\", \"metioprimum\")" "character(0)"
|
||||
"MXT" 3047729 "Metioxate" "Quinolones" "" "c(\"metioxate\", \"metioxato\", \"metioxatum\")" "character(0)"
|
||||
"MTR" 4173 "Metronidazole" "Other antibacterials" "c(\"A01AB17\", \"D06BX01\", \"G01AF01\", \"J01XD01\", \"P01AB01\")" "Other antibacterials" "Imidazole derivatives" "c(\"metr\", \"mnz\")" "c(\"acromona\", \"anagiardil\", \"arilin\", \"atrivyl\", \"danizol\", \"deflamon\", \"efloran\", \"elyzol\", \"entizol\", \"flagemona\", \"flagesol\", \"flagil\", \"flagyl\", \"flagyl er\", \"flagyl i.v.\", \"flagyl i.v. rtu\", \"flazol\", \"flegyl\", \"florazole\", \"fossyol\", \"giatricol\", \"ginefla vir\", \"gineflavir\", \"helidac\", \"mepagyl\", \"meronidal\", \"methronidazole\", \"metric\", \"metro cream\", \"metro gel\", \"metro i.v\", \"metro i.v.\", \"metro iv\", \"metrocream\", \"metrodzhil\", \"metrogel\", \"metrogyl\", \"metrolag\", \"metrolotion\", \"metrolyl\",
|
||||
\"metromidol\", \"metronidaz\", \"metronidazol\", \"metronidazole\", \"metronidazole usp\", \"metronidazolo\", \"metronidazolum\", \"metrotop\", \"metrozine\", \"metryl\", \"mexibol\", \"mexibol 'silanes'\", \"monagyl\", \"monasin\", \"nidagel\", \"nidagyl\", \"noritate\", \"novonidazol\", \"orvagil\", \"polibiotic\", \"protostat\", \"rathimed\", \"rosased\", \"sanatrichom\", \"satric\", \"takimetol\", \"trichazol\", \"trichex\", \"tricho cordes\", \"trichobrol\", \"trichocide\", \"trichomol\", \"trichopal\", \"trichopol\", \"tricocet\", \"tricom\", \"tricowas b\", \"trikacide\",
|
||||
\"trikamon\", \"trikhopol\", \"trikojol\", \"trikozol\", \"trimeks\", \"trivazol\", \"vagilen\", \"vagimid\", \"vandazole\", \"vertisal\", \"wagitran\", \"zadstat\", \"zidoval\")" 1.5 "g" "10991-8"
|
||||
"MEZ" "J01CA10" 656511 "Mezlocillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"mez\", \"mezl\", \"mz\")" "c(\"mezlin\", \"mezlocilina\", \"mezlocillin\", \"mezlocillin acid\", \"mezlocillin sodium\", \"mezlocilline\", \"mezlocillinum\", \"multocillin\")" 6 "g" "3820-8"
|
||||
"MSU" "Mezlocillin/sulbactam" "Beta-lactams/penicillins" "" "" ""
|
||||
"MIF" "J02AX05" 477468 "Micafungin" "Antifungals/antimycotics" "Antimycotics for systemic use" "Other antimycotics for systemic use" "c(\"\", \"mica\")" "c(\"micafungin\", \"mycamine\")" 0.1 "g" "58418-5"
|
||||
"MCZ" "J02AB01" 4189 "Miconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Imidazole derivatives" "mico" "c(\"aflorix\", \"albistat\", \"andergin\", \"brentan\", \"conofite\", \"dactarin\", \"daktarin\", \"daktarin iv\", \"florid\", \"lotrimin af\", \"micantin\", \"miconasil nitrate\", \"miconazol\", \"miconazole\", \"miconazole base\", \"miconazolo\", \"miconazolum\", \"micozole\", \"minostate\", \"monista\", \"monistat\", \"monistat iv\", \"oravig\", \"vusion\", \"zimybase\", \"zimycan\")" 1 "g" "17278-3"
|
||||
"MCR" 3037206 "Micronomicin" "Aminoglycosides" "" "c(\"gentamicin c\", \"micromycin\", \"micronomicin\", \"micronomicina\", \"micronomicine\", \"micronomicinum\", \"sagamicin\", \"santemycin\")" "character(0)"
|
||||
"MID" "J01FA03" 5282169 "Midecamycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"aboren\", \"espinomycin a\", \"macropen\", \"madecacine\", \"medemycin\", \"midecamicina\", \"midecamycin\", \"midecamycin a\", \"midecamycine\", \"midecamycinum\", \"midecin\", \"momicine\", \"mydecamycin\", \"myoxam\", \"normicina\", \"rubimycin\", \"turimycin p\")" 1.2 1 "g" "character(0)"
|
||||
"MIL" 37614 "Miloxacin" "Quinolones" "" "c(\"miloxacin\", \"miloxacine\", \"miloxacino\", \"miloxacinum\")" "character(0)"
|
||||
"MNO" "J01AA08" 54675783 "Minocycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "c(\"mc\", \"mh\", \"mi\", \"min\", \"mino\", \"mn\", \"mno\")" "c(\"akamin\", \"aknemin\", \"borymycin\", \"dynacin\", \"klinomycin\", \"minociclina\", \"minocin\", \"minocline\", \"minocyclin\", \"minocycline\", \"minocyclinum\", \"minocyn\", \"minoderm\", \"minomycin\", \"sebomin\", \"solodyn\", \"vectrin\")" 0.2 "g" 0.2 "g" "c(\"34606-4\", \"3822-4\", \"49757-8\")"
|
||||
"MCM" "J01FA11" 5282188 "Miocamycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"acecamycin\", \"macroral\", \"midecamycin acetate\", \"miocamen\", \"miocamycine\", \"miokamycin\", \"myocamicin\", \"ponsinomycin\")" 1.2 "g" "character(0)"
|
||||
"MON" 23667299 "Monensin sodium" "Other antibacterials" "" "c(\"monensin sodium\", \"sodium monensin\")" "character(0)"
|
||||
"MRN" "J04AK04" 70374 "Morinamide" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "" "c(\"morfazinamide\", \"morfazinammide\", \"morfgazinamide\", \"morinamida\", \"morinamide\", \"morinamidum\", \"morphazinamid\", \"morphazinamide\", \"piazofolina\", \"piazolin\", \"piazolina\")" "character(0)"
|
||||
"MFX" "J01MA14" 152946 "Moxifloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"mox\", \"moxi\", \"mxf\")" "c(\"actira\", \"avelox\", \"avelox i.v.\", \"avelox iv\", \"avolex\", \"izilox\", \"moxeza\", \"moxifloxacin\", \"moxifloxacine\", \"vigamox\")" 0.4 "g" 0.4 "g" "c(\"43751-7\", \"45223-5\", \"80540-8\")"
|
||||
"MUP" "R01AX06" 446596 "Mupirocin" "Other antibacterials" "c(\"mup\", \"mupi\")" "c(\"bactoderm\", \"bactroban\", \"bactroban nasal\", \"bactroban ointment\", \"centany\", \"mupirocin\", \"mupirocina\", \"mupirocine\", \"mupirocinum\", \"plasimine\", \"pseudomonic acid\", \"pseudomonic acid a\", \"turixin\")" "character(0)"
|
||||
"NAC" 73386748 "Nacubactam" "Beta-lactams/penicillins" "" "nacubactam" "character(0)"
|
||||
"NAD" 4410 "Nadifloxacin" "Quinolones" "" "c(\"acuatim\", \"nadifloxacin\", \"nadifloxacine\", \"nadifloxacino\", \"nadifloxacinum\", \"nadixa\", \"nadoxin\")" "character(0)"
|
||||
"NAF" 8982 "Nafcillin" "Beta-lactams/penicillins" "" "c(\"nafcilina\", \"nafcillin\", \"nafcillin sodium\", \"nafcilline\", \"nafcillinum\", \"nallpen\", \"naphcillin\", \"unipen\")" "c(\"10993-4\", \"25232-0\")"
|
||||
"ZWK" 117587595 "Nafithromycin" "Macrolides/lincosamides" "" "nafithromycin" "character(0)"
|
||||
"NAL" "J01MB02" 4421 "Nalidixic acid" "Quinolones" "Quinolone antibacterials" "Other quinolones" "c(\"na\", \"nal\", \"nali\")" "c(\"acide nalidixico\", \"acide nalidixique\", \"acido nalidissico\", \"acido nalidixico\", \"acidum nalidixicum\", \"betaxina\", \"dixiben\", \"dixinal\", \"eucisten\", \"eucistin\", \"innoxalomn\", \"innoxalon\", \"jicsron\", \"kusnarin\", \"naldixic acid\", \"nalidic acid\", \"nalidicron\", \"nalidixan\", \"nalidixane\", \"nalidixate\", \"nalidixate sodium\", \"nalidixic\", \"nalidixic acid\", \"nalidixin\", \"nalidixinic acid\", \"nalidixinsaure\", \"nalitucsan\", \"nalurin\", \"narigix\", \"naxuril\", \"neggram\", \"negram\", \"nevigramon\", \"nicelate\", \"nogram\",
|
||||
\"trikamon\", \"trikhopol\", \"trikojol\", \"trikozol\", \"trimeks\", \"trivazol\", \"vagilen\", \"vagimid\", \"vandazole\", \"vertisal\", \"wagitran\", \"zadstat\", \"zidoval\")" 2 "g" 1.5 "g" "10991-8"
|
||||
"MEZ" 656511 "Mezlocillin" "Beta-lactams/penicillins" "J01CA10" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"mez\", \"mezl\", \"mz\")" "c(\"mezlin\", \"mezlocilina\", \"mezlocillin\", \"mezlocillin acid\", \"mezlocillin sodium\", \"mezlocilline\", \"mezlocillinum\", \"multocillin\")" 6 "g" "3820-8"
|
||||
"MSU" "Mezlocillin/sulbactam" "Beta-lactams/penicillins" "" "" ""
|
||||
"MIF" 477468 "Micafungin" "Antifungals/antimycotics" "J02AX05" "Antimycotics for systemic use" "Other antimycotics for systemic use" "c(\"\", \"mica\")" "c(\"micafungin\", \"mycamine\")" 0.1 "g" "58418-5"
|
||||
"MCZ" 4189 "Miconazole" "Antifungals/antimycotics" "c(\"A01AB09\", \"A07AC01\", \"D01AC02\", \"G01AF04\", \"J02AB01\", \"S02AA13\")" "Antimycotics for systemic use" "Imidazole derivatives" "mico" "c(\"aflorix\", \"albistat\", \"andergin\", \"brentan\", \"conofite\", \"dactarin\", \"daktarin\", \"daktarin iv\", \"florid\", \"lotrimin af\", \"micantin\", \"miconasil nitrate\", \"miconazol\", \"miconazole\", \"miconazole base\", \"miconazolo\", \"miconazolum\", \"micozole\", \"minostate\", \"monista\", \"monistat\", \"monistat iv\", \"oravig\", \"vusion\", \"zimybase\", \"zimycan\")" 0.2 "g" 1 "g" "17278-3"
|
||||
"MCR" 3037206 "Micronomicin" "Aminoglycosides" "S01AA22" "" "c(\"gentamicin c\", \"micromycin\", \"micronomicin\", \"micronomicina\", \"micronomicine\", \"micronomicinum\", \"sagamicin\", \"santemycin\")" "character(0)"
|
||||
"MID" 5282169 "Midecamycin" "Macrolides/lincosamides" "J01FA03" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"aboren\", \"espinomycin a\", \"macropen\", \"madecacine\", \"medemycin\", \"midecamicina\", \"midecamycin\", \"midecamycin a\", \"midecamycine\", \"midecamycinum\", \"midecin\", \"momicine\", \"mydecamycin\", \"myoxam\", \"normicina\", \"rubimycin\", \"turimycin p\")" 1.2 "g" 1 "g" "character(0)"
|
||||
"MIL" 37614 "Miloxacin" "Quinolones" "" "c(\"miloxacin\", \"miloxacine\", \"miloxacino\", \"miloxacinum\")" "character(0)"
|
||||
"MNO" 54675783 "Minocycline" "Tetracyclines" "c(\"A01AB23\", \"D10AF07\", \"J01AA08\")" "Tetracyclines" "Tetracyclines" "c(\"mc\", \"mh\", \"mi\", \"min\", \"mino\", \"mn\", \"mno\")" "c(\"akamin\", \"aknemin\", \"borymycin\", \"dynacin\", \"klinomycin\", \"minociclina\", \"minocin\", \"minocline\", \"minocyclin\", \"minocycline\", \"minocyclinum\", \"minocyn\", \"minoderm\", \"minomycin\", \"sebomin\", \"solodyn\", \"vectrin\")" 1 "mg" 0.2 "g" "c(\"34606-4\", \"3822-4\", \"49757-8\")"
|
||||
"MCM" 5282188 "Miocamycin" "Macrolides/lincosamides" "J01FA11" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"acecamycin\", \"macroral\", \"midecamycin acetate\", \"miocamen\", \"miocamycine\", \"miokamycin\", \"myocamicin\", \"ponsinomycin\")" 1.2 "g" "character(0)"
|
||||
"MON" 23667299 "Monensin sodium" "Other antibacterials" "" "c(\"monensin sodium\", \"sodium monensin\")" "character(0)"
|
||||
"MRN" 70374 "Morinamide" "Antimycobacterials" "J04AK04" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "" "c(\"morfazinamide\", \"morfazinammide\", \"morfgazinamide\", \"morinamida\", \"morinamide\", \"morinamidum\", \"morphazinamid\", \"morphazinamide\", \"piazofolina\", \"piazolin\", \"piazolina\")" "character(0)"
|
||||
"MFX" 152946 "Moxifloxacin" "Quinolones" "c(\"J01MA14\", \"S01AE07\")" "Quinolone antibacterials" "Fluoroquinolones" "c(\"mox\", \"moxi\", \"mxf\")" "c(\"actira\", \"avelox\", \"avelox i.v.\", \"avelox iv\", \"avolex\", \"izilox\", \"moxeza\", \"moxifloxacin\", \"moxifloxacine\", \"vigamox\")" 0.4 "g" 0.4 "g" "c(\"43751-7\", \"45223-5\", \"80540-8\")"
|
||||
"MUP" 446596 "Mupirocin" "Other antibacterials" "c(\"D06AX09\", \"R01AX06\")" "c(\"mup\", \"mupi\")" "c(\"bactoderm\", \"bactroban\", \"bactroban nasal\", \"bactroban ointment\", \"centany\", \"mupirocin\", \"mupirocina\", \"mupirocine\", \"mupirocinum\", \"plasimine\", \"pseudomonic acid\", \"pseudomonic acid a\", \"turixin\")" "character(0)"
|
||||
"NAC" 73386748 "Nacubactam" "Beta-lactams/penicillins" "" "nacubactam" "character(0)"
|
||||
"NAD" 4410 "Nadifloxacin" "Quinolones" "D10AF05" "" "c(\"acuatim\", \"nadifloxacin\", \"nadifloxacine\", \"nadifloxacino\", \"nadifloxacinum\", \"nadixa\", \"nadoxin\")" "character(0)"
|
||||
"NAF" 8982 "Nafcillin" "Beta-lactams/penicillins" "J01CF06" "" "c(\"nafcilina\", \"nafcillin\", \"nafcillin sodium\", \"nafcilline\", \"nafcillinum\", \"nallpen\", \"naphcillin\", \"unipen\")" 3 "g" "c(\"10993-4\", \"25232-0\")"
|
||||
"ZWK" 117587595 "Nafithromycin" "Macrolides/lincosamides" "" "nafithromycin" "character(0)"
|
||||
"NAL" 4421 "Nalidixic acid" "Quinolones" "J01MB02" "Quinolone antibacterials" "Other quinolones" "c(\"na\", \"nal\", \"nali\")" "c(\"acide nalidixico\", \"acide nalidixique\", \"acido nalidissico\", \"acido nalidixico\", \"acidum nalidixicum\", \"betaxina\", \"dixiben\", \"dixinal\", \"eucisten\", \"eucistin\", \"innoxalomn\", \"innoxalon\", \"jicsron\", \"kusnarin\", \"naldixic acid\", \"nalidic acid\", \"nalidicron\", \"nalidixan\", \"nalidixane\", \"nalidixate\", \"nalidixate sodium\", \"nalidixic\", \"nalidixic acid\", \"nalidixin\", \"nalidixinic acid\", \"nalidixinsaure\", \"nalitucsan\", \"nalurin\", \"narigix\", \"naxuril\", \"neggram\", \"negram\", \"nevigramon\", \"nicelate\", \"nogram\",
|
||||
\"poleon\", \"sicmylon\", \"specifen\", \"specifin\", \"unaserus\", \"uralgin\", \"uriben\", \"uriclar\", \"urisal\", \"urodixin\", \"uroman\", \"uroneg\", \"uronidix\", \"uropan\", \"wintomylon\", \"wintron\")" 4 "g" "character(0)"
|
||||
"NAR" 65452 "Narasin" "Other antibacterials" "" "c(\"monteban\", \"narasin\", \"narasin a\", \"narasine\", \"narasino\", \"narasinum\", \"narasul\")" "87570-8"
|
||||
"NEO" "J01GB05" 8378 "Neomycin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "neom" "c(\"actilin\", \"actiline\", \"antibiotique\", \"bycomycin\", \"endomixin\", \"enterfram\", \"fradiomycin\", \"fradiomycin b\", \"fradiomycinum\", \"framicetina\", \"framycetin\", \"framycetin sulfate\", \"framycetine\", \"framycetinum\", \"framygen\", \"fraquinol\", \"jernadex\", \"myacine\", \"myacyne\", \"mycerin\", \"mycifradin\", \"neobrettin\", \"neolate\", \"neomas\", \"neomcin\", \"neomicina\", \"neomin\", \"neomycin\", \"neomycin b\", \"neomycin b sulfate\", \"neomycin solution\", \"neomycin sulfate\", \"neomycin sulphate\", \"neomycinb\", \"neomycine\", \"neomycinum\",
|
||||
\"nivemycin\", \"pimavecort\", \"soframycin\", \"soframycine\", \"tuttomycin\", \"vonamycin\", \"vonamycin powder v\")" 1 "g" "c(\"10995-9\", \"25262-7\")"
|
||||
"NET" "J01GB07" 441306 "Netilmicin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "neti" "c(\"netillin\", \"netilmicin\", \"netilmicin sulfate\", \"netilmicina\", \"netilmicine\", \"netilmicinum\", \"netilyn\", \"netira\", \"vectacin\")" 0.35 "g" 0.35 "g" "c(\"25263-5\", \"3848-9\", \"3849-7\", \"3850-5\", \"47385-0\", \"59565-2\", \"59566-0\", \"59567-8\")"
|
||||
"NIC" 9507 "Nicarbazin" "Other antibacterials" "" "c(\"nicarb\", \"nicarbasin\", \"nicarbazin\", \"nicarbazine\", \"nicoxin\", \"nicrazin\", \"nicrazine\", \"nirazin\")" "character(0)"
|
||||
"NIF" 71946 "Nifuroquine" "Quinolones" "" "c(\"nifuroquina\", \"nifuroquine\", \"nifuroquinum\", \"quinaldofur\")" "character(0)"
|
||||
"NFR" "J01XE02" 9571062 "Nifurtoinol" "Other antibacterials" "Other antibacterials" "Nitrofuran derivatives" "" "c(\"levantin\", \"nifurtoinol\", \"nifurtoinolo\", \"nifurtoinolum\", \"urfadin\", \"urfadine\", \"urfadyn\")" 0.16 "g" "character(0)"
|
||||
"NTZ" 41684 "Nitazoxanide" "Other antibacterials" "" "c(\"adrovet\", \"alinia\", \"azt + nitazoxanide\", \"colufase\", \"cryptaz\", \"dexidex\", \"heliton\", \"kidonax\", \"nitaxozanid\", \"nitaxozanide\", \"nitazox\", \"nitazoxamide\", \"nitazoxanid\", \"nitazoxanida\", \"nitazoxanide\", \"nitazoxanidum\", \"omniparax\", \"pacovanton\", \"paramix\", \"taenitaz\")" "character(0)"
|
||||
"NIT" "J01XE01" 6604200 "Nitrofurantoin" "Other antibacterials" "Other antibacterials" "Nitrofuran derivatives" "c(\"f\", \"f/m\", \"fd\", \"ft\", \"ni\", \"nit\", \"nitr\")" "c(\"alfuran\", \"benkfuran\", \"berkfuran\", \"berkfurin\", \"ceduran\", \"chemiofuran\", \"cistofuran\", \"cyantin\", \"cystit\", \"dantafur\", \"fua med\", \"fuamed\", \"furabid\", \"furachel\", \"furadantin\", \"furadantin retard\", \"furadantina mc\", \"furadantine\", \"furadantine mc\", \"furadantoin\", \"furadoin\", \"furadoine\", \"furadonin\", \"furadonine\", \"furadoninum\", \"furadontin\", \"furadoxyl\", \"furalan\", \"furaloid\", \"furantoin\", \"furantoina\", \"furatoin\", \"furedan\", \"furina\", \"furobactina\", \"furodantin\", \"furophen t\", \"gerofuran\",
|
||||
"NAR" 65452 "Narasin" "Other antibacterials" "" "c(\"monteban\", \"narasin\", \"narasin a\", \"narasine\", \"narasino\", \"narasinum\", \"narasul\")" "87570-8"
|
||||
"NEO" 8378 "Neomycin" "Aminoglycosides" "c(\"A01AB08\", \"A07AA01\", \"B05CA09\", \"D06AX04\", \"J01GB05\", \"R02AB01\", \"S01AA03\", \"S02AA07\", \"S03AA01\")" "Aminoglycoside antibacterials" "Other aminoglycosides" "neom" "c(\"actilin\", \"actiline\", \"antibiotique\", \"bycomycin\", \"endomixin\", \"enterfram\", \"fradiomycin\", \"fradiomycin b\", \"fradiomycinum\", \"framicetina\", \"framycetin\", \"framycetin sulfate\", \"framycetine\", \"framycetinum\", \"framygen\", \"fraquinol\", \"jernadex\", \"myacine\", \"myacyne\", \"mycerin\", \"mycifradin\", \"neobrettin\", \"neolate\", \"neomas\", \"neomcin\", \"neomicina\", \"neomin\", \"neomycin\", \"neomycin b\", \"neomycin b sulfate\", \"neomycin solution\", \"neomycin sulfate\", \"neomycin sulphate\", \"neomycinb\", \"neomycine\", \"neomycinum\",
|
||||
\"nivemycin\", \"pimavecort\", \"soframycin\", \"soframycine\", \"tuttomycin\", \"vonamycin\", \"vonamycin powder v\")" 5 "g" "c(\"10995-9\", \"25262-7\")"
|
||||
"NET" 441306 "Netilmicin" "Aminoglycosides" "c(\"J01GB07\", \"S01AA23\")" "Aminoglycoside antibacterials" "Other aminoglycosides" "neti" "c(\"netillin\", \"netilmicin\", \"netilmicin sulfate\", \"netilmicina\", \"netilmicine\", \"netilmicinum\", \"netilyn\", \"netira\", \"vectacin\")" 0.35 "g" 0.35 "g" "c(\"25263-5\", \"3848-9\", \"3849-7\", \"3850-5\", \"47385-0\", \"59565-2\", \"59566-0\", \"59567-8\")"
|
||||
"NIC" 9507 "Nicarbazin" "Other antibacterials" "" "c(\"nicarb\", \"nicarbasin\", \"nicarbazin\", \"nicarbazine\", \"nicoxin\", \"nicrazin\", \"nicrazine\", \"nirazin\")" "character(0)"
|
||||
"NIF" 71946 "Nifuroquine" "Quinolones" "" "c(\"nifuroquina\", \"nifuroquine\", \"nifuroquinum\", \"quinaldofur\")" "character(0)"
|
||||
"NFR" 9571062 "Nifurtoinol" "Other antibacterials" "J01XE02" "Other antibacterials" "Nitrofuran derivatives" "" "c(\"levantin\", \"nifurtoinol\", \"nifurtoinolo\", \"nifurtoinolum\", \"urfadin\", \"urfadine\", \"urfadyn\")" 0.16 "g" "character(0)"
|
||||
"NTZ" 41684 "Nitazoxanide" "Other antibacterials" "P01AX11" "" "c(\"adrovet\", \"alinia\", \"azt + nitazoxanide\", \"colufase\", \"cryptaz\", \"dexidex\", \"heliton\", \"kidonax\", \"nitaxozanid\", \"nitaxozanide\", \"nitazox\", \"nitazoxamide\", \"nitazoxanid\", \"nitazoxanida\", \"nitazoxanide\", \"nitazoxanidum\", \"omniparax\", \"pacovanton\", \"paramix\", \"taenitaz\")" 1 "g" "character(0)"
|
||||
"NIT" 6604200 "Nitrofurantoin" "Other antibacterials" "J01XE01" "Other antibacterials" "Nitrofuran derivatives" "c(\"f\", \"f/m\", \"fd\", \"ft\", \"ni\", \"nit\", \"nitr\")" "c(\"alfuran\", \"benkfuran\", \"berkfuran\", \"berkfurin\", \"ceduran\", \"chemiofuran\", \"cistofuran\", \"cyantin\", \"cystit\", \"dantafur\", \"fua med\", \"fuamed\", \"furabid\", \"furachel\", \"furadantin\", \"furadantin retard\", \"furadantina mc\", \"furadantine\", \"furadantine mc\", \"furadantoin\", \"furadoin\", \"furadoine\", \"furadonin\", \"furadonine\", \"furadoninum\", \"furadontin\", \"furadoxyl\", \"furalan\", \"furaloid\", \"furantoin\", \"furantoina\", \"furatoin\", \"furedan\", \"furina\", \"furobactina\", \"furodantin\", \"furophen t\", \"gerofuran\",
|
||||
\"io>>uss>>a<<ixoo\", \"ituran\", \"ivadantin\", \"macpac\", \"macrobid\", \"macrodantin\", \"macrodantina\", \"macrofuran\", \"macrofurin\", \"nierofu\", \"nifurantin\", \"nifuretten\", \"nitoin\", \"nitrex\", \"nitrofuradantin\", \"nitrofurantion\", \"nitrofurantoin\", \"nitrofurantoin macro\", \"nitrofurantoina\", \"nitrofurantoine\", \"nitrofurantoinum\", \"novofuran\", \"orafuran\", \"parfuran\", \"phenurin\", \"piyeloseptyl\", \"siraliden\", \"trantoin\", \"uerineks\", \"urantoin\", \"urizept\", \"urodin\", \"urofuran\", \"urofurin\", \"urolisa\", \"urolong\",
|
||||
\"uvamin\", \"welfurin\", \"zoofurin\")" 0.2 "g" "3860-4"
|
||||
"NIZ" 5447130 "Nitrofurazone" "Other antibacterials" "" "c(\"acutol\", \"aldomycin\", \"alfucin\", \"amifur\", \"babrocid\", \"becafurazone\", \"biofuracina\", \"biofurea\", \"chemofuran\", \"chixin\", \"cocafurin\", \"coxistat\", \"dermofural\", \"dymazone\", \"dynazone\", \"eldezol\", \"fedacin\", \"flavazone\", \"fracine\", \"furacilin\", \"furacilinum\", \"furacillin\", \"furacin\", \"furacine\", \"furacinetten\", \"furacoccid\", \"furacort\", \"furacycline\", \"furaderm\", \"furagent\", \"furalcyn\", \"furaldon\", \"furalone\", \"furametral\", \"furaplast\", \"furaseptyl\", \"furaskin\", \"furatsilin\", \"furaziline\", \"furazin\",
|
||||
"NIZ" 5447130 "Nitrofurazone" "Other antibacterials" "" "c(\"acutol\", \"aldomycin\", \"alfucin\", \"amifur\", \"babrocid\", \"becafurazone\", \"biofuracina\", \"biofurea\", \"chemofuran\", \"chixin\", \"cocafurin\", \"coxistat\", \"dermofural\", \"dymazone\", \"dynazone\", \"eldezol\", \"fedacin\", \"flavazone\", \"fracine\", \"furacilin\", \"furacilinum\", \"furacillin\", \"furacin\", \"furacine\", \"furacinetten\", \"furacoccid\", \"furacort\", \"furacycline\", \"furaderm\", \"furagent\", \"furalcyn\", \"furaldon\", \"furalone\", \"furametral\", \"furaplast\", \"furaseptyl\", \"furaskin\", \"furatsilin\", \"furaziline\", \"furazin\",
|
||||
\"furazina\", \"furazol w\", \"furazone\", \"furazyme\", \"furesol\", \"furfurin\", \"furosem\", \"fuvacillin\", \"hemofuran\", \"ibiofural\", \"mammex\", \"mastofuran\", \"monafuracin\", \"monafuracis\", \"monofuracin\", \"nfz mix\", \"nifucin\", \"nifurid\", \"nifuzon\", \"nitrofural\", \"nitrofuralum\", \"nitrofuran\", \"nitrofurane\", \"nitrofurazan\", \"nitrofurazone\", \"nitrofurazonum\", \"nitrofurol\", \"nitrozone\", \"otofural\", \"otofuran\", \"rivafurazon\", \"sanfuran\", \"vabrocid\", \"vadrocid\", \"yatrocin\")" "character(0)"
|
||||
"NTR" "J01XX07" 19910 "Nitroxoline" "Quinolones" "Other antibacterials" "Other antibacterials" "" "c(\"galinok\", \"isinok\", \"nibiol\", \"nicene forte\", \"nitroxolin\", \"nitroxolina\", \"nitroxoline\", \"nitroxolinum\", \"notroxoline\", \"noxibiol\")" 1 "g" "character(0)"
|
||||
"NOR" "J01MA06" 4539 "Norfloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"nor\", \"norf\", \"nx\", \"nxn\")" "c(\"baccidal\", \"barazan\", \"chibroxin\", \"chibroxine\", \"chibroxol\", \"fulgram\", \"gonorcin\", \"lexinor\", \"nolicin\", \"noracin\", \"noraxin\", \"norflo\", \"norfloxacin\", \"norfloxacine\", \"norfloxacino\", \"norfloxacinum\", \"norocin\", \"noroxin\", \"noroxine\", \"norxacin\", \"sebercim\", \"uroxacin\", \"utinor\", \"zoroxin\")" 0.8 "g" "3867-9"
|
||||
"NVA" 10419027 "Norvancomycin" "Glycopeptides" "" "norvancomycin" "character(0)"
|
||||
"NOV" "QJ01XX95" 54675769 "Novobiocin" "Other antibacterials" "novo" "c(\"albamix\", \"albamycin\", \"cardelmycin\", \"cathocin\", \"cathomycin\", \"crystallinic acid\", \"inamycin\", \"novobiocin\", \"novobiocina\", \"novobiocine\", \"novobiocinum\", \"robiocina\", \"sirbiocina\", \"spheromycin\", \"stilbiocina\", \"streptonivicin\")" "17378-1"
|
||||
"NYS" "G01AA01" 6433272 "Nystatin" "Antifungals/antimycotics" "nyst" "c(\"biofanal\", \"candex lotion\", \"comycin\", \"diastatin\", \"herniocid\", \"moronal\", \"myconystatin\", \"mycostatin\", \"mycostatin pastilles\", \"mykinac\", \"mykostatyna\", \"nilstat\", \"nistatin\", \"nistatina\", \"nyamyc\", \"nyotran\", \"nyotrantrade mark\", \"nystaform\", \"nystan\", \"nystatin\", \"nystatin a\", \"nystatin g\", \"nystatin lf\", \"nystatine\", \"nystatinum\", \"nystatyna\", \"nystavescent\", \"nystex\", \"nystop\", \"stamycin\", \"terrastatin\", \"zydin e\")" "character(0)"
|
||||
"OFX" "J01MA01" 4583 "Ofloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"of\", \"ofl\", \"oflo\", \"ofx\")" "c(\"bactocin\", \"danoflox\", \"effexin\", \"exocin\", \"exocine\", \"flobacin\", \"flodemex\", \"flotavid\", \"flovid\", \"floxal\", \"floxil\", \"floxin\", \"floxin otic\", \"floxstat\", \"fugacin\", \"inoflox\", \"kinflocin\", \"kinoxacin\", \"levofloxacin hcl\", \"liflox\", \"loxinter\", \"marfloxacin\", \"medofloxine\", \"mergexin\", \"monoflocet\", \"novecin\", \"nufafloqo\", \"occidal\", \"ocuflox\", \"oflocee\", \"oflocet\", \"oflocin\", \"oflodal\", \"oflodex\", \"oflodura\", \"ofloxacin\", \"ofloxacin otic\", \"ofloxacina\", \"ofloxacine\", \"ofloxacino\", \"ofloxacinum\",
|
||||
"NTR" 19910 "Nitroxoline" "Quinolones" "J01XX07" "Other antibacterials" "Other antibacterials" "" "c(\"galinok\", \"isinok\", \"nibiol\", \"nicene forte\", \"nitroxolin\", \"nitroxolina\", \"nitroxoline\", \"nitroxolinum\", \"notroxoline\", \"noxibiol\")" 1 "g" "character(0)"
|
||||
"NOR" 4539 "Norfloxacin" "Quinolones" "c(\"J01MA06\", \"S01AE02\")" "Quinolone antibacterials" "Fluoroquinolones" "c(\"nor\", \"norf\", \"nx\", \"nxn\")" "c(\"baccidal\", \"barazan\", \"chibroxin\", \"chibroxine\", \"chibroxol\", \"fulgram\", \"gonorcin\", \"lexinor\", \"nolicin\", \"noracin\", \"noraxin\", \"norflo\", \"norfloxacin\", \"norfloxacine\", \"norfloxacino\", \"norfloxacinum\", \"norocin\", \"noroxin\", \"noroxine\", \"norxacin\", \"sebercim\", \"uroxacin\", \"utinor\", \"zoroxin\")" 0.8 "g" "3867-9"
|
||||
"NVA" 10419027 "Norvancomycin" "Glycopeptides" "" "norvancomycin" "character(0)"
|
||||
"NOV" 54675769 "Novobiocin" "Other antibacterials" "novo" "c(\"albamix\", \"albamycin\", \"cardelmycin\", \"cathocin\", \"cathomycin\", \"crystallinic acid\", \"inamycin\", \"novobiocin\", \"novobiocina\", \"novobiocine\", \"novobiocinum\", \"robiocina\", \"sirbiocina\", \"spheromycin\", \"stilbiocina\", \"streptonivicin\")" "17378-1"
|
||||
"NYS" 6433272 "Nystatin" "Antifungals/antimycotics" "c(\"A07AA02\", \"D01AA01\", \"G01AA01\")" "nyst" "c(\"biofanal\", \"candex lotion\", \"comycin\", \"diastatin\", \"herniocid\", \"moronal\", \"myconystatin\", \"mycostatin\", \"mycostatin pastilles\", \"mykinac\", \"mykostatyna\", \"nilstat\", \"nistatin\", \"nistatina\", \"nyamyc\", \"nyotran\", \"nyotrantrade mark\", \"nystaform\", \"nystan\", \"nystatin\", \"nystatin a\", \"nystatin g\", \"nystatin lf\", \"nystatine\", \"nystatinum\", \"nystatyna\", \"nystavescent\", \"nystex\", \"nystop\", \"stamycin\", \"terrastatin\", \"zydin e\")" 1.5 "MU" "character(0)"
|
||||
"OFX" 4583 "Ofloxacin" "Quinolones" "c(\"J01MA01\", \"S01AE01\", \"S02AA16\")" "Quinolone antibacterials" "Fluoroquinolones" "c(\"of\", \"ofl\", \"oflo\", \"ofx\")" "c(\"bactocin\", \"danoflox\", \"effexin\", \"exocin\", \"exocine\", \"flobacin\", \"flodemex\", \"flotavid\", \"flovid\", \"floxal\", \"floxil\", \"floxin\", \"floxin otic\", \"floxstat\", \"fugacin\", \"inoflox\", \"kinflocin\", \"kinoxacin\", \"levofloxacin hcl\", \"liflox\", \"loxinter\", \"marfloxacin\", \"medofloxine\", \"mergexin\", \"monoflocet\", \"novecin\", \"nufafloqo\", \"occidal\", \"ocuflox\", \"oflocee\", \"oflocet\", \"oflocin\", \"oflodal\", \"oflodex\", \"oflodura\", \"ofloxacin\", \"ofloxacin otic\", \"ofloxacina\", \"ofloxacine\", \"ofloxacino\", \"ofloxacinum\",
|
||||
\"ofloxin\", \"onexacin\", \"operan\", \"orocin\", \"otonil\", \"oxaldin\", \"pharflox\", \"praxin\", \"puiritol\", \"qinolon\", \"quinolon\", \"quotavil\", \"sinflo\", \"tabrin\", \"taravid\", \"tariflox\", \"tarivid\", \"telbit\", \"tructum\", \"uro tarivid\", \"viotisone\", \"visiren\", \"zanocin\")" 0.4 "g" 0.4 "g" "c(\"25264-3\", \"3877-8\")"
|
||||
"OLE" "J01FA05" 72493 "Oleandomycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"amimycin\", \"landomycin\", \"matromycin\", \"oleandomycin a\", \"romicil\")" 1 "g" "character(0)"
|
||||
"OMC" 54697325 "Omadacycline" "Tetracyclines" "" "c(\"amadacycline\", \"omadacycline\")" "character(0)"
|
||||
"OPT" 87880 "Optochin" "Other antibacterials" "" "c(\"numoquin\", \"optochin\", \"optoquine\")" "character(0)"
|
||||
"ORB" 60605 "Orbifloxacin" "Quinolones" "" "orbifloxacin" "character(0)"
|
||||
"ORI" "J01XA05" 16136912 "Oritavancin" "Glycopeptides" "Other antibacterials" "Glycopeptide antibacterials" "orit" "oritavancin" "character(0)"
|
||||
"ORS" "Ormetroprim/sulfamethoxazole" "Other antibacterials" "" "" ""
|
||||
"ORN" "J01XD03" 28061 "Ornidazole" "Other antibacterials" "Other antibacterials" "Imidazole derivatives" "" "c(\"madelen\", \"ornidal\", \"ornidazol\", \"ornidazole\", \"ornidazolum\", \"tiberal\")" 1 "g" "character(0)"
|
||||
"OXA" "J01CF04" 6196 "Oxacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "c(\"ox\", \"oxa\", \"oxac\", \"oxal\", \"oxs\")" "c(\"bactocill\", \"ossacillina\", \"oxacilina\", \"oxacillin\", \"oxacillin sodium\", \"oxacilline\", \"oxacillinum\", \"oxazocillin\", \"oxazocilline\", \"prostaphlin\", \"prostaphlyn\", \"sodium oxacillin\")" 2 "g" 2 "g" "c(\"25265-0\", \"3882-8\")"
|
||||
"OXO" "J01MB05" 4628 "Oxolinic acid" "Quinolones" "Quinolone antibacterials" "Other quinolones" "" "c(\"acide oxolinique\", \"acido ossolico\", \"acido oxolinico\", \"acidum oxolinicum\", \"aqualinic\", \"cistopax\", \"dioxacin\", \"emyrenil\", \"gramurin\", \"inoxyl\", \"nidantin\", \"oksaren\", \"orthurine\", \"ossian\", \"oxoboi\", \"oxolinic\", \"oxolinic acid\", \"pietil\", \"prodoxal\", \"prodoxol\", \"starner\", \"tiurasin\", \"ultibid\", \"urinox\", \"uritrate\", \"urotrate\", \"uroxol\", \"utibid\")" 1 "g" "character(0)"
|
||||
"OXY" "J01AA06" 54675779 "Oxytetracycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "" "c(\"adamycin\", \"berkmycen\", \"biostat\", \"biostat pa\", \"dabicycline\", \"dalimycin\", \"embryostat\", \"fanterrin\", \"galsenomycin\", \"geomycin\", \"geotilin\", \"hydroxytetracyclinum\", \"imperacin\", \"lenocycline\", \"macocyn\", \"medamycin\", \"mepatar\", \"oksisyklin\", \"ossitetraciclina\", \"oxacycline\", \"oxitetraciclina\", \"oxitetracyclin\", \"oxitetracycline\", \"oxitetracyclinum\", \"oxydon\", \"oxymycin\", \"oxymykoin\", \"oxypam\", \"oxysteclin\", \"oxyterracin\", \"oxyterracine\", \"oxyterracyne\", \"oxytetracid\", \"oxytetracyclin\", \"oxytetracycline\",
|
||||
"OLE" 72493 "Oleandomycin" "Macrolides/lincosamides" "J01FA05" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"amimycin\", \"landomycin\", \"matromycin\", \"oleandomycin a\", \"romicil\")" 1 "g" "character(0)"
|
||||
"OMC" 54697325 "Omadacycline" "Tetracyclines" "J01AA15" "" "c(\"amadacycline\", \"omadacycline\")" 0.3 "g" 0.1 "g" "character(0)"
|
||||
"OPT" 87880 "Optochin" "Other antibacterials" "" "c(\"numoquin\", \"optochin\", \"optoquine\")" "character(0)"
|
||||
"ORB" 60605 "Orbifloxacin" "Quinolones" "" "orbifloxacin" "character(0)"
|
||||
"ORI" 16136912 "Oritavancin" "Glycopeptides" "J01XA05" "Other antibacterials" "Glycopeptide antibacterials" "orit" "oritavancin" "character(0)"
|
||||
"ORS" "Ormetroprim/sulfamethoxazole" "Other antibacterials" "" "" ""
|
||||
"ORN" 28061 "Ornidazole" "Other antibacterials" "c(\"G01AF06\", \"J01XD03\", \"P01AB03\")" "Other antibacterials" "Imidazole derivatives" "" "c(\"madelen\", \"ornidal\", \"ornidazol\", \"ornidazole\", \"ornidazolum\", \"tiberal\")" 1.5 "g" 1 "g" "character(0)"
|
||||
"OXA" 6196 "Oxacillin" "Beta-lactams/penicillins" "J01CF04" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "c(\"ox\", \"oxa\", \"oxac\", \"oxal\", \"oxs\")" "c(\"bactocill\", \"ossacillina\", \"oxacilina\", \"oxacillin\", \"oxacillin sodium\", \"oxacilline\", \"oxacillinum\", \"oxazocillin\", \"oxazocilline\", \"prostaphlin\", \"prostaphlyn\", \"sodium oxacillin\")" 2 "g" 2 "g" "c(\"25265-0\", \"3882-8\")"
|
||||
"OXO" 4628 "Oxolinic acid" "Quinolones" "J01MB05" "Quinolone antibacterials" "Other quinolones" "" "c(\"acide oxolinique\", \"acido ossolico\", \"acido oxolinico\", \"acidum oxolinicum\", \"aqualinic\", \"cistopax\", \"dioxacin\", \"emyrenil\", \"gramurin\", \"inoxyl\", \"nidantin\", \"oksaren\", \"orthurine\", \"ossian\", \"oxoboi\", \"oxolinic\", \"oxolinic acid\", \"pietil\", \"prodoxal\", \"prodoxol\", \"starner\", \"tiurasin\", \"ultibid\", \"urinox\", \"uritrate\", \"urotrate\", \"uroxol\", \"utibid\")" 1 "g" "character(0)"
|
||||
"OXY" 54675779 "Oxytetracycline" "Tetracyclines" "c(\"D06AA03\", \"G01AA07\", \"J01AA06\", \"S01AA04\")" "Tetracyclines" "Tetracyclines" "" "c(\"adamycin\", \"berkmycen\", \"biostat\", \"biostat pa\", \"dabicycline\", \"dalimycin\", \"embryostat\", \"fanterrin\", \"galsenomycin\", \"geomycin\", \"geotilin\", \"hydroxytetracyclinum\", \"imperacin\", \"lenocycline\", \"macocyn\", \"medamycin\", \"mepatar\", \"oksisyklin\", \"ossitetraciclina\", \"oxacycline\", \"oxitetraciclina\", \"oxitetracyclin\", \"oxitetracycline\", \"oxitetracyclinum\", \"oxydon\", \"oxymycin\", \"oxymykoin\", \"oxypam\", \"oxysteclin\", \"oxyterracin\", \"oxyterracine\", \"oxyterracyne\", \"oxytetracid\", \"oxytetracyclin\", \"oxytetracycline\",
|
||||
\"oxytetracycline base\", \"oxytetracyclinum\", \"proteroxyna\", \"riomitsin\", \"ryomycin\", \"solkaciclina\", \"stecsolin\", \"stevacin\", \"tarocyn\", \"tarosin\", \"teravit\", \"terrafungine\", \"terramitsin\", \"terramycin\", \"terramycin im\", \"tetran\", \"unimycin\", \"ursocyclin\", \"ursocycline\", \"vendarcin\")" 1 "g" 1 "g" "c(\"17396-3\", \"25266-8\", \"87595-5\")"
|
||||
"PAS" 4649 "P-aminosalicylic acid" "Antimycobacterials" "" "c(\"aminopar\", \"aminosalicylic\", \"aminosalicylic acid\", \"aminosalyl\", \"aminox\", \"apacil\", \"deapasil\", \"entepas\", \"ferrosan\", \"gabbropas\", \"helipidyl\", \"hellipidyl\", \"neopasalate\", \"osacyl\", \"pamacyl\", \"pamisyl\", \"paramycin\", \"parasal\", \"parasalicil\", \"parasalindon\", \"pasalon\", \"pasara\", \"pascorbic\", \"pasdium\", \"paser granules\", \"paskalium\", \"pasmed\", \"pasnodia\", \"pasolac\", \"propasa\", \"rezipas\", \"teebacin\", \"wln: zr cq dvq\")" "character(0)"
|
||||
"PAN" 72015 "Panipenem" "Carbapenems" "" "c(\"panipenem\", \"panipenemum\", \"penipanem\")" "character(0)"
|
||||
"PAR" 165580 "Paromomycin" "Other antibacterials" "" "c(\"aminosidin\", \"aminosidine\", \"aminosidine i\", \"aminosidine sulfate\", \"amminosidin\", \"crestomycin\", \"estomycin\", \"gabbromicina\", \"gabbromycin\", \"gabromycin\", \"humatin\", \"humycin\", \"hydroxymycin\", \"hydroxymycin sulfate\", \"monomycin\", \"monomycin a\", \"neomycin e\", \"paramomycin\", \"paramomycin sulfate\", \"paromomicina\", \"paromomycin\", \"paromomycin i\", \"paromomycine\", \"paromomycinum\", \"paucimycin\", \"paucimycinum\", \"quintomycin c\")" "character(0)"
|
||||
"PAZ" "J01MA18" 65957 "Pazufloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "" "c(\"pazufloxacin\", \"pazufloxacine\", \"pazufloxacino\", \"pazufloxacinum\")" 1 "g" "character(0)"
|
||||
"PEF" "J01MA03" 51081 "Pefloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"pefl\")" "c(\"abactal\", \"labocton\", \"pefloxacin\", \"pefloxacine\", \"pefloxacino\", \"pefloxacinum\", \"perfloxacin\", \"silver pefloxacin\")" 0.8 "g" 0.8 "g" "3906-5"
|
||||
"PNM" "J01CE06" 10250769 "Penamecillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"hydroxymethyl\", \"penamecilina\", \"penamecillin\", \"penamecillina\", \"penamecilline\", \"penamecillinum\")" 1.05 "g" "character(0)"
|
||||
"PNO" "Penicillin/novobiocin" "Beta-lactams/penicillins" "" "" ""
|
||||
"PSU" "Penicillin/sulbactam" "Beta-lactams/penicillins" "" "" ""
|
||||
"PNM1" "J01AA10" 54686187 "Penimepicycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "" "c(\"duamine\", \"hydrocycline\", \"penetracyne\", \"penimepiciclina\", \"penimepicycline\", \"penimepicyclinum\")" "character(0)"
|
||||
"PIM" 65453 "Pentisomicin" "Aminoglycosides" "" "c(\"pentisomicin\", \"pentisomicina\", \"pentisomicine\", \"pentisomicinum\")" "character(0)"
|
||||
"PTZ" 55250256 "Pentizidone" "Other antibacterials" "" "" ""
|
||||
"PEX" 16132253 "Pexiganan" "Other antibacterials" "" "pexiganan" "character(0)"
|
||||
"PHE" "J01CE05" 272833 "Phenethicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "c(\"\", \"fene\")" "c(\"feneticilina\", \"feneticillina\", \"feneticilline\", \"k phenethicillin\", \"phenethicilin\", \"phenethicillinum\", \"pheneticillin\", \"pheneticilline\", \"pheneticillinum\", \"phenoxy pc\", \"potassium penicillin\")" 1 "g" "41471-4"
|
||||
"PHN" "J01CE02" 6869 "Phenoxymethylpenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "c(\"fepe\", \"peni v\", \"penicillin v\", \"pnv\", \"pv\")" "c(\"acipen v\", \"apocillin\", \"apopen\", \"beromycin\", \"calcipen\", \"compocillin v\", \"crystapen v\", \"distaquaine v\", \"eskacillian v\", \"eskacillin v\", \"fenacilin\", \"fenospen\", \"meropenin\", \"oracillin\", \"oratren\", \"penicillin v\", \"phenocillin\", \"phenomycilline\", \"phenopenicillin\", \"robicillin\", \"rocilin\", \"stabicillin\", \"vebecillin\", \"veetids\", \"vegacillin\")" 2 "g" "character(0)"
|
||||
"PMR" 5284447 "Pimaricin (Natamycin)" "Antifungals/antimycotics" "" "c(\"delvocid\", \"mycophyt\", \"myprozine\", \"natacyn\", \"natamicina\", \"natamycin\", \"natamycine\", \"natamycinum\", \"pimafucin\", \"pimaracin\", \"pimarizin\", \"synogil\", \"tennecetin\")" "character(0)"
|
||||
"PPA" "J01MB04" 4831 "Pipemidic acid" "Quinolones" "Quinolone antibacterials" "Other quinolones" "c(\"pipz\", \"pizu\")" "c(\"acide pipemidique\", \"acido pipemidico\", \"acidum pipemidicum\", \"deblaston\", \"dolcol\", \"pipedac\", \"pipemid\", \"pipemidic\", \"pipemidic acid\", \"pipemidicacid\", \"pipram\", \"uromidin\")" 0.8 "g" "character(0)"
|
||||
"PIP" "J01CA12" 43672 "Piperacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"pi\", \"pip\", \"pipc\", \"pipe\", \"pp\")" "c(\"isipen\", \"pentcillin\", \"peperacillin\", \"peracin\", \"piperacilina\", \"piperacillin\", \"piperacillin na\", \"piperacillin sodium\", \"piperacilline\", \"piperacillinum\", \"pipercillin\", \"pipracil\", \"pipril\")" 14 "g" "c(\"25268-4\", \"3972-7\")"
|
||||
"PIS" "Piperacillin/sulbactam" "Beta-lactams/penicillins" "" "" ""
|
||||
"TZP" "J01CR05" 461573 "Piperacillin/tazobactam" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "c(\"p/t\", \"piptaz\", \"piptazo\", \"pit\", \"pita\", \"pt\", \"ptc\", \"ptz\", \"tzp\")" "c(\"\", \"tazocel\", \"tazocillin\", \"tazocin\", \"zosyn\")" 14 "g" "character(0)"
|
||||
"PRC" 71978 "Piridicillin" "Beta-lactams/penicillins" "" "piridicillin" "character(0)"
|
||||
"PRL" 157385 "Pirlimycin" "Other antibacterials" "" "c(\"pirlimycin\", \"pirlimycina\", \"pirlimycine\", \"pirlimycinum\", \"pirsue\")" "character(0)"
|
||||
"PIR" "J01MB03" 4855 "Piromidic acid" "Quinolones" "Quinolone antibacterials" "Other quinolones" "" "c(\"acide piromidique\", \"acido piromidico\", \"acidum piromidicum\", \"actrun c\", \"bactramyl\", \"enterol\", \"gastrurol\", \"panacid\", \"pirodal\", \"piromidic acid\", \"pyrido\", \"reelon\", \"septural\", \"urisept\", \"uropir\", \"zaomeal\")" 2 "g" "character(0)"
|
||||
"PVM" "J01CA02" 33478 "Pivampicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"berocillin\", \"pivaloylampicillin\", \"pivampicilina\", \"pivampicillin\", \"pivampicilline\", \"pivampicillinum\", \"pondocillin\")" 1.05 "g" "character(0)"
|
||||
"PME" "J01CA08" 115163 "Pivmecillinam" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"amdinocillin pivoxil\", \"coactabs\", \"hydroxymethyl\", \"pivmecilinamo\", \"pivmecillinam\", \"pivmecillinam hcl\", \"pivmecillinamum\")" 0.6 "g" "character(0)"
|
||||
"PLZ" 42613186 "Plazomicin" "Aminoglycosides" "" "plazomicin" "92024-9"
|
||||
"PLB" "J01XB02" 49800004 "Polymyxin B" "Polymyxins" "Other antibacterials" "Polymyxins" "c(\"pb\", \"pol\", \"polb\", \"poly\", \"poly b\", \"polymixin\", \"polymixin b\")" "c(\"polimixina b\", \"polumyxin b\", \"polymixin b\", \"polymyxine b\")" 0.15 "g" "c(\"17473-0\", \"25269-2\")"
|
||||
"POP" "Polymyxin B/polysorbate 80" "Polymyxins" "" "" ""
|
||||
"POS" "J02AC04" 468595 "Posaconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives" "posa" "c(\"noxafil\", \"posaconazole\", \"posaconazole sp\", \"posconazole\")" 0.3 "g" 0.3 "g" "c(\"53731-6\", \"80545-7\")"
|
||||
"PRA" 9802884 "Pradofloxacin" "Quinolones" "" "pradofloxacin" "character(0)"
|
||||
"PRX" 71455 "Premafloxacin" "Quinolones" "" "premafloxacin" "character(0)"
|
||||
"PMD" "J04AK08" 456199 "Pretomanid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "" "" ""
|
||||
"PRM" 6446787 "Primycin" "Macrolides/lincosamides" "" "" ""
|
||||
"PRI" "J01FG01" 11979535 "Pristinamycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Streptogramins" "c(\"\", \"pris\")" "c(\"eskalin v\", \"mikamycin\", \"mikamycine\", \"mikamycinum\", \"ostreogrycinum\", \"pristinamycine\", \"pristinamycinum\", \"stafac\", \"stafytracine\", \"staphylomycin\", \"starfac\", \"streptogramin\", \"vernamycin\", \"virgimycin\", \"virgimycine\", \"virginiamycina\", \"virginiamycine\", \"virginiamycinum\")" 2 "g" "character(0)"
|
||||
"PRB" "J01CE09" 5903 "Procaine benzylpenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"depocillin\", \"duphapen\", \"hostacillin\", \"hydracillin\", \"jenacillin o\", \"nopcaine\", \"penicillin procaine\", \"retardillin\", \"vetspen\", \"vitablend\")" 0.6 "g" "character(0)"
|
||||
"PRP" "J01CE03" 92879 "Propicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"propicilina\", \"propicillin\", \"propicilline\", \"propicillinum\")" 0.9 "g" "character(0)"
|
||||
"PKA" 9872451 "Propikacin" "Aminoglycosides" "" "c(\"propikacin\", \"propikacina\", \"propikacine\", \"propikacinum\")" "character(0)"
|
||||
"PTH" "J04AD01" 666418 "Prothionamide" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Thiocarbamide derivatives" "prot" "c(\"ektebin\", \"peteha\", \"prothionamide\", \"prothionamidum\", \"protion\", \"protionamid\", \"protionamida\", \"protionamide\", \"protionamidum\", \"protionizina\", \"tebeform\", \"trevintix\", \"tuberex\")" 0.75 "g" "character(0)"
|
||||
"PRU" "J01MA17" 65947 "Prulifloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "" "c(\"prulifloxacin\", \"pruvel\", \"pufloxacin dioxolil\", \"quisnon\")" 0.6 "g" "character(0)"
|
||||
"PZA" "J04AK01" 1046 "Pyrazinamide" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "pyra" "c(\"aldinamid\", \"aldinamide\", \"braccopiral\", \"corsazinmid\", \"dipimide\", \"eprazin\", \"farmizina\", \"isopas\", \"lynamide\", \"novamid\", \"p ezetamid\", \"pezetamid\", \"pharozinamide\", \"piraldina\", \"pirazimida\", \"pirazinamid\", \"pirazinamida\", \"pirazinamide\", \"prazina\", \"pyrafat\", \"pyramide\", \"pyrazide\", \"pyrazinamdie\", \"pyrazinamid\", \"pyrazinamide\", \"pyrazinamidum\", \"pyrazine carboxamide\", \"pyrazineamide\", \"pyrizinamide\", \"rifafour\", \"rozide\", \"tebrazid\", \"tebrazio\", \"tisamid\", \"unipyranamide\", \"zinamide\", \"zinastat\"
|
||||
"PAS" 4649 "P-aminosalicylic acid" "Antimycobacterials" "" "c(\"aminopar\", \"aminosalicylic\", \"aminosalicylic acid\", \"aminosalyl\", \"aminox\", \"apacil\", \"deapasil\", \"entepas\", \"ferrosan\", \"gabbropas\", \"helipidyl\", \"hellipidyl\", \"neopasalate\", \"osacyl\", \"pamacyl\", \"pamisyl\", \"paramycin\", \"parasal\", \"parasalicil\", \"parasalindon\", \"pasalon\", \"pasara\", \"pascorbic\", \"pasdium\", \"paser granules\", \"paskalium\", \"pasmed\", \"pasnodia\", \"pasolac\", \"propasa\", \"rezipas\", \"teebacin\", \"wln: zr cq dvq\")" "character(0)"
|
||||
"PAN" 72015 "Panipenem" "Carbapenems" "" "c(\"panipenem\", \"panipenemum\", \"penipanem\")" "character(0)"
|
||||
"PAR" 165580 "Paromomycin" "Other antibacterials" "A07AA06" "" "c(\"aminosidin\", \"aminosidine\", \"aminosidine i\", \"aminosidine sulfate\", \"amminosidin\", \"crestomycin\", \"estomycin\", \"gabbromicina\", \"gabbromycin\", \"gabromycin\", \"humatin\", \"humycin\", \"hydroxymycin\", \"hydroxymycin sulfate\", \"monomycin\", \"monomycin a\", \"neomycin e\", \"paramomycin\", \"paramomycin sulfate\", \"paromomicina\", \"paromomycin\", \"paromomycin i\", \"paromomycine\", \"paromomycinum\", \"paucimycin\", \"paucimycinum\", \"quintomycin c\")" 3 "g" "character(0)"
|
||||
"PAZ" 65957 "Pazufloxacin" "Quinolones" "J01MA18" "Quinolone antibacterials" "Fluoroquinolones" "" "c(\"pazufloxacin\", \"pazufloxacine\", \"pazufloxacino\", \"pazufloxacinum\")" 1 "g" "character(0)"
|
||||
"PEF" 51081 "Pefloxacin" "Quinolones" "J01MA03" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"pefl\")" "c(\"abactal\", \"labocton\", \"pefloxacin\", \"pefloxacine\", \"pefloxacino\", \"pefloxacinum\", \"perfloxacin\", \"silver pefloxacin\")" 0.8 "g" 0.8 "g" "3906-5"
|
||||
"PNM" 10250769 "Penamecillin" "Beta-lactams/penicillins" "J01CE06" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"hydroxymethyl\", \"penamecilina\", \"penamecillin\", \"penamecillina\", \"penamecilline\", \"penamecillinum\")" 1.05 "g" "character(0)"
|
||||
"PNO" "Penicillin/novobiocin" "Beta-lactams/penicillins" "" "" ""
|
||||
"PSU" "Penicillin/sulbactam" "Beta-lactams/penicillins" "" "" ""
|
||||
"PNM1" 54686187 "Penimepicycline" "Tetracyclines" "J01AA10" "Tetracyclines" "Tetracyclines" "" "c(\"duamine\", \"hydrocycline\", \"penetracyne\", \"penimepiciclina\", \"penimepicycline\", \"penimepicyclinum\")" "character(0)"
|
||||
"PIM" 65453 "Pentisomicin" "Aminoglycosides" "" "c(\"pentisomicin\", \"pentisomicina\", \"pentisomicine\", \"pentisomicinum\")" "character(0)"
|
||||
"PTZ" 55250256 "Pentizidone" "Other antibacterials" "" "" ""
|
||||
"PEX" 16132253 "Pexiganan" "Other antibacterials" "" "pexiganan" "character(0)"
|
||||
"PHE" 272833 "Phenethicillin" "Beta-lactams/penicillins" "J01CE05" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "c(\"\", \"fene\")" "c(\"feneticilina\", \"feneticillina\", \"feneticilline\", \"k phenethicillin\", \"phenethicilin\", \"phenethicillinum\", \"pheneticillin\", \"pheneticilline\", \"pheneticillinum\", \"phenoxy pc\", \"potassium penicillin\")" 1 "g" "41471-4"
|
||||
"PHN" 6869 "Phenoxymethylpenicillin" "Beta-lactams/penicillins" "J01CE02" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "c(\"fepe\", \"peni v\", \"penicillin v\", \"pnv\", \"pv\")" "c(\"acipen v\", \"apocillin\", \"apopen\", \"beromycin\", \"calcipen\", \"compocillin v\", \"crystapen v\", \"distaquaine v\", \"eskacillian v\", \"eskacillin v\", \"fenacilin\", \"fenospen\", \"meropenin\", \"oracillin\", \"oratren\", \"penicillin v\", \"phenocillin\", \"phenomycilline\", \"phenopenicillin\", \"robicillin\", \"rocilin\", \"stabicillin\", \"vebecillin\", \"veetids\", \"vegacillin\")" 2 "g" "character(0)"
|
||||
"PMR" 5284447 "Pimaricin (Natamycin)" "Antifungals/antimycotics" "" "c(\"delvocid\", \"mycophyt\", \"myprozine\", \"natacyn\", \"natamicina\", \"natamycin\", \"natamycine\", \"natamycinum\", \"pimafucin\", \"pimaracin\", \"pimarizin\", \"synogil\", \"tennecetin\")" "character(0)"
|
||||
"PPA" 4831 "Pipemidic acid" "Quinolones" "J01MB04" "Quinolone antibacterials" "Other quinolones" "c(\"pipz\", \"pizu\")" "c(\"acide pipemidique\", \"acido pipemidico\", \"acidum pipemidicum\", \"deblaston\", \"dolcol\", \"pipedac\", \"pipemid\", \"pipemidic\", \"pipemidic acid\", \"pipemidicacid\", \"pipram\", \"uromidin\")" 0.8 "g" "character(0)"
|
||||
"PIP" 43672 "Piperacillin" "Beta-lactams/penicillins" "J01CA12" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"pi\", \"pip\", \"pipc\", \"pipe\", \"pp\")" "c(\"isipen\", \"pentcillin\", \"peperacillin\", \"peracin\", \"piperacilina\", \"piperacillin\", \"piperacillin na\", \"piperacillin sodium\", \"piperacilline\", \"piperacillinum\", \"pipercillin\", \"pipracil\", \"pipril\")" 14 "g" "c(\"25268-4\", \"3972-7\")"
|
||||
"PIS" "Piperacillin/sulbactam" "Beta-lactams/penicillins" "" "" ""
|
||||
"TZP" 461573 "Piperacillin/tazobactam" "Beta-lactams/penicillins" "J01CR05" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "c(\"p/t\", \"piptaz\", \"piptazo\", \"pit\", \"pita\", \"pt\", \"ptc\", \"ptz\", \"tzp\")" "c(\"\", \"tazocel\", \"tazocillin\", \"tazocin\", \"zosyn\")" 14 "g" "character(0)"
|
||||
"PRC" 71978 "Piridicillin" "Beta-lactams/penicillins" "" "piridicillin" "character(0)"
|
||||
"PRL" 157385 "Pirlimycin" "Macrolides/lincosamides" "" "c(\"pirlimycin\", \"pirlimycina\", \"pirlimycine\", \"pirlimycinum\", \"pirsue\")" "character(0)"
|
||||
"PIR" 4855 "Piromidic acid" "Quinolones" "J01MB03" "Quinolone antibacterials" "Other quinolones" "" "c(\"acide piromidique\", \"acido piromidico\", \"acidum piromidicum\", \"actrun c\", \"bactramyl\", \"enterol\", \"gastrurol\", \"panacid\", \"pirodal\", \"piromidic acid\", \"pyrido\", \"reelon\", \"septural\", \"urisept\", \"uropir\", \"zaomeal\")" 2 "g" "character(0)"
|
||||
"PVM" 33478 "Pivampicillin" "Beta-lactams/penicillins" "J01CA02" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"berocillin\", \"pivaloylampicillin\", \"pivampicilina\", \"pivampicillin\", \"pivampicilline\", \"pivampicillinum\", \"pondocillin\")" 1.05 "g" "character(0)"
|
||||
"PME" 115163 "Pivmecillinam" "Beta-lactams/penicillins" "J01CA08" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"amdinocillin pivoxil\", \"coactabs\", \"hydroxymethyl\", \"pivmecilinamo\", \"pivmecillinam\", \"pivmecillinam hcl\", \"pivmecillinamum\")" 0.6 "g" "character(0)"
|
||||
"PLZ" 42613186 "Plazomicin" "Aminoglycosides" "J01GB14" "" "plazomicin" "92024-9"
|
||||
"PLB" 49800004 "Polymyxin B" "Polymyxins" "c(\"A07AA05\", \"J01XB02\", \"S01AA18\", \"S02AA11\", \"S03AA03\")" "Other antibacterials" "Polymyxins" "c(\"pb\", \"pol\", \"polb\", \"poly\", \"poly b\", \"polymixin\", \"polymixin b\")" "c(\"polimixina b\", \"polumyxin b\", \"polymixin b\", \"polymyxine b\")" 3 "MU" 0.15 "g" "c(\"17473-0\", \"25269-2\")"
|
||||
"POP" "Polymyxin B/polysorbate 80" "Polymyxins" "" "" ""
|
||||
"POS" 468595 "Posaconazole" "Antifungals/antimycotics" "J02AC04" "Antimycotics for systemic use" "Triazole derivatives" "posa" "c(\"noxafil\", \"posaconazole\", \"posaconazole sp\", \"posconazole\")" 0.3 "g" 0.3 "g" "c(\"53731-6\", \"80545-7\")"
|
||||
"PRA" 9802884 "Pradofloxacin" "Quinolones" "" "pradofloxacin" "character(0)"
|
||||
"PRX" 71455 "Premafloxacin" "Quinolones" "" "premafloxacin" "character(0)"
|
||||
"PMD" 456199 "Pretomanid" "Antimycobacterials" "J04AK08" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "" "" ""
|
||||
"PRM" 6446787 "Primycin" "Macrolides/lincosamides" "" "" ""
|
||||
"PRI" 11979535 "Pristinamycin" "Macrolides/lincosamides" "J01FG01" "Macrolides, lincosamides and streptogramins" "Streptogramins" "c(\"\", \"pris\")" "c(\"eskalin v\", \"mikamycin\", \"mikamycine\", \"mikamycinum\", \"ostreogrycinum\", \"pristinamycine\", \"pristinamycinum\", \"stafac\", \"stafytracine\", \"staphylomycin\", \"starfac\", \"streptogramin\", \"vernamycin\", \"virgimycin\", \"virgimycine\", \"virginiamycina\", \"virginiamycine\", \"virginiamycinum\")" 2 "g" "character(0)"
|
||||
"PRB" 5903 "Procaine benzylpenicillin" "Beta-lactams/penicillins" "J01CE09" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"depocillin\", \"duphapen\", \"hostacillin\", \"hydracillin\", \"jenacillin o\", \"nopcaine\", \"penicillin procaine\", \"retardillin\", \"vetspen\", \"vitablend\")" 0.6 "g" "character(0)"
|
||||
"PRP" 92879 "Propicillin" "Beta-lactams/penicillins" "J01CE03" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"propicilina\", \"propicillin\", \"propicilline\", \"propicillinum\")" 0.9 "g" "character(0)"
|
||||
"PKA" 9872451 "Propikacin" "Aminoglycosides" "" "c(\"propikacin\", \"propikacina\", \"propikacine\", \"propikacinum\")" "character(0)"
|
||||
"PTH" 666418 "Prothionamide" "Antimycobacterials" "J04AD01" "Drugs for treatment of tuberculosis" "Thiocarbamide derivatives" "prot" "c(\"ektebin\", \"peteha\", \"prothionamide\", \"prothionamidum\", \"protion\", \"protionamid\", \"protionamida\", \"protionamide\", \"protionamidum\", \"protionizina\", \"tebeform\", \"trevintix\", \"tuberex\")" 0.75 "g" "character(0)"
|
||||
"PRU" 65947 "Prulifloxacin" "Quinolones" "J01MA17" "Quinolone antibacterials" "Fluoroquinolones" "" "c(\"prulifloxacin\", \"pruvel\", \"pufloxacin dioxolil\", \"quisnon\")" 0.6 "g" "character(0)"
|
||||
"PZA" 1046 "Pyrazinamide" "Antimycobacterials" "J04AK01" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "pyra" "c(\"aldinamid\", \"aldinamide\", \"braccopiral\", \"corsazinmid\", \"dipimide\", \"eprazin\", \"farmizina\", \"isopas\", \"lynamide\", \"novamid\", \"p ezetamid\", \"pezetamid\", \"pharozinamide\", \"piraldina\", \"pirazimida\", \"pirazinamid\", \"pirazinamida\", \"pirazinamide\", \"prazina\", \"pyrafat\", \"pyramide\", \"pyrazide\", \"pyrazinamdie\", \"pyrazinamid\", \"pyrazinamide\", \"pyrazinamidum\", \"pyrazine carboxamide\", \"pyrazineamide\", \"pyrizinamide\", \"rifafour\", \"rozide\", \"tebrazid\", \"tebrazio\", \"tisamid\", \"unipyranamide\", \"zinamide\", \"zinastat\"
|
||||
)" 1.5 "g" "c(\"11001-5\", \"25270-0\")"
|
||||
"QDA" "J01FG02" 11979418 "Quinupristin/dalfopristin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Streptogramins" "c(\"q/d\", \"qda\", \"qida\", \"quda\", \"rp\", \"syn\")" "" 1.5 "g" ""
|
||||
"RAC" 56052 "Ractopamine" "Other antibacterials" "" "c(\"ractopamina\", \"ractopamine\", \"ractopaminum\")" "character(0)"
|
||||
"RAM" 16132338 "Ramoplanin" "Glycopeptides" "" "ramoplanin" "character(0)"
|
||||
"RZM" 10993211 "Razupenem" "Carbapenems" "" "razupenem" "character(0)"
|
||||
"RTP" "A07AA11" 6918462 "Retapamulin" "Other antibacterials" "Intestinal antiinfectives" "Antibiotics" "" "c(\"altabax\", \"altargo\", \"retapamulin\")" 0.6 "g" "character(0)"
|
||||
"RBC" "J02AC05" 44631912 "Ribociclib" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives" "ribo" "c(\"kisqali\", \"ribociclib\")" 0.2 0.2 "character(0)"
|
||||
"RST" "J01GB10" 33042 "Ribostamycin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "" "c(\"dekamycin iv\", \"hetangmycin\", \"ribastamin\", \"ribostamicina\", \"ribostamycin\", \"ribostamycine\", \"ribostamycinum\", \"vistamycin\", \"xylostatin\")" 1 "g" "character(0)"
|
||||
"RID1" 16659285 "Ridinilazole" "Other antibacterials" "" "ridinilazole" "character(0)"
|
||||
"RIB" "J04AB04" 135398743 "Rifabutin" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Antibiotics" "rifb" "c(\"alfacid\", \"ansamicin\", \"ansamycin\", \"ansatipin\", \"ansatipine\", \"mycobutin\", \"rifabutin\", \"rifabutina\", \"rifabutine\", \"rifabutinum\")" 0.15 "g" "24032-5"
|
||||
"RIF" "J04AB02" 135398735 "Rifampicin" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Antibiotics" "rifa" "c(\"abrifam\", \"archidyn\", \"arficin\", \"arzide\", \"azt + rifampin\", \"benemicin\", \"benemycin\", \"dipicin\", \"doloresum\", \"eremfat\", \"famcin\", \"fenampicin\", \"rifadin\", \"rifadin i.v\", \"rifadin i.v.\", \"rifadine\", \"rifagen\", \"rifaldazin\", \"rifaldazine\", \"rifaldin\", \"rifamate\", \"rifamicin amp\", \"rifamor\", \"rifampicin\", \"rifampicin sv\", \"rifampicina\", \"rifampicine\", \"rifampicinum\", \"rifampin\", \"rifamsolin\", \"rifamycin amp\", \"rifaprodin\", \"rifcin\", \"rifobac\", \"rifoldin\", \"rifoldine\", \"riforal\", \"rimactan\", \"rimactane\",
|
||||
"QDA" 11979418 "Quinupristin/dalfopristin" "Macrolides/lincosamides" "J01FG02" "Macrolides, lincosamides and streptogramins" "Streptogramins" "c(\"q/d\", \"qda\", \"qida\", \"quda\", \"rp\", \"syn\")" "" 1.5 "g" ""
|
||||
"RAC" 56052 "Ractopamine" "Other antibacterials" "" "c(\"ractopamina\", \"ractopamine\", \"ractopaminum\")" "character(0)"
|
||||
"RAM" 16132338 "Ramoplanin" "Glycopeptides" "" "ramoplanin" "character(0)"
|
||||
"RZM" 10993211 "Razupenem" "Carbapenems" "" "razupenem" "character(0)"
|
||||
"RTP" 6918462 "Retapamulin" "Other antibacterials" "D06AX13" "Antibiotics for topical use" "Other antibiotics for topical use" "" "c(\"altabax\", \"altargo\", \"retapamulin\")" "character(0)"
|
||||
"RBC" 44631912 "Ribociclib" "Antifungals/antimycotics" "L01EF02" "Antimycotics for systemic use" "Triazole derivatives" "ribo" "c(\"kisqali\", \"ribociclib\")" "character(0)"
|
||||
"RST" 33042 "Ribostamycin" "Aminoglycosides" "J01GB10" "Aminoglycoside antibacterials" "Other aminoglycosides" "" "c(\"dekamycin iv\", \"hetangmycin\", \"ribastamin\", \"ribostamicina\", \"ribostamycin\", \"ribostamycine\", \"ribostamycinum\", \"vistamycin\", \"xylostatin\")" 1 "g" "character(0)"
|
||||
"RID1" 16659285 "Ridinilazole" "Other antibacterials" "" "ridinilazole" "character(0)"
|
||||
"RIB" 135398743 "Rifabutin" "Antimycobacterials" "J04AB04" "Drugs for treatment of tuberculosis" "Antibiotics" "rifb" "c(\"alfacid\", \"ansamicin\", \"ansamycin\", \"ansatipin\", \"ansatipine\", \"mycobutin\", \"rifabutin\", \"rifabutina\", \"rifabutine\", \"rifabutinum\")" 0.15 "g" "24032-5"
|
||||
"RIF" 135398735 "Rifampicin" "Antimycobacterials" "J04AB02" "Drugs for treatment of tuberculosis" "Antibiotics" "rifa" "c(\"abrifam\", \"archidyn\", \"arficin\", \"arzide\", \"azt + rifampin\", \"benemicin\", \"benemycin\", \"dipicin\", \"doloresum\", \"eremfat\", \"famcin\", \"fenampicin\", \"rifadin\", \"rifadin i.v\", \"rifadin i.v.\", \"rifadine\", \"rifagen\", \"rifaldazin\", \"rifaldazine\", \"rifaldin\", \"rifamate\", \"rifamicin amp\", \"rifamor\", \"rifampicin\", \"rifampicin sv\", \"rifampicina\", \"rifampicine\", \"rifampicinum\", \"rifampin\", \"rifamsolin\", \"rifamycin amp\", \"rifaprodin\", \"rifcin\", \"rifobac\", \"rifoldin\", \"rifoldine\", \"riforal\", \"rimactan\", \"rimactane\",
|
||||
\"rimactizid\", \"rimazid\", \"rimycin\", \"sinerdol\", \"tubocin\")" 0.6 "g" 0.6 "g" "character(0)"
|
||||
"RFI" "J04AM02" "Rifampicin/isoniazid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "c(\"rifinah\", \"rimactazid\")" "character(0)"
|
||||
"RPEI" "J04AM06" "Rifampicin/pyrazinamide/ethambutol/isoniazid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "" ""
|
||||
"RPI" "J04AM05" "Rifampicin/pyrazinamide/isoniazid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "" ""
|
||||
"RFM" "J04AB03" 6324616 "Rifamycin" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Antibiotics" "" "c(\"aemcolo\", \"rifacin\", \"rifamicina\", \"rifamicine sv\", \"rifamycin\", \"rifamycine\", \"rifamycinum\", \"rifocin\", \"rifocyn\", \"rifomycin\", \"rifomycin sv\", \"tuborin\")" 0.6 "g" "character(0)"
|
||||
"RFP" "J04AB05" 135403821 "Rifapentine" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Antibiotics" "rifp" "c(\"cyclopentyl rifampin\", \"priftin\", \"rifapentin\", \"rifapentina\", \"rifapentine\", \"rifapentinum\")" 0.11 "g" "character(0)"
|
||||
"RFX" "A07AA11" 6436173 "Rifaximin" "Other antibacterials" "Intestinal antiinfectives" "Antibiotics" "" "c(\"fatroximin\", \"flonorm\", \"lormyx\", \"lumenax\", \"normix\", \"redactiv\", \"rifacol\", \"rifamixin\", \"rifaxidin\", \"rifaximin\", \"rifaximina\", \"rifaximine\", \"rifaximinum\", \"rifaxin\", \"ritacol\", \"spiraxin\", \"xifaxan\", \"xifaxsan\")" 0.6 "g" "character(0)"
|
||||
"RIT" 65633 "Ritipenem" "Carbapenems" "" "ritipenem" "character(0)"
|
||||
"RIA" 163692 "Ritipenem acoxil" "Carbapenems" "" "ritipenem acoxil" "character(0)"
|
||||
"ROK" "J01FA12" 5282211 "Rokitamycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"propionylleucomycin\", \"ricamycin\", \"rokicid\", \"rokital\", \"rokitamicina\", \"rokitamycin\", \"rokitamycine\", \"rokitamycinum\")" 0.8 "g" "character(0)"
|
||||
"RLT" "J01AA09" 54682938 "Rolitetracycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "" "c(\"bristacin\", \"kinteto\", \"reverin\", \"rolitetraciclina\", \"rolitetracycline\", \"rolitetracyclinum\", \"solvocillin\", \"superciclin\", \"synotodecin\", \"synterin\", \"syntetrex\", \"syntetrin\", \"velacicline\", \"velacycline\")" 0.35 "g" "character(0)"
|
||||
"ROS" "J01MB01" 287180 "Rosoxacin" "Quinolones" "Quinolone antibacterials" "Other quinolones" "" "c(\"acrosoxacin\", \"eracine\", \"eradacil\", \"eradacin\", \"rosoxacin\", \"rosoxacine\", \"rosoxacino\", \"rosoxacinum\", \"roxadyl\", \"winuron\")" 0.3 "g" "character(0)"
|
||||
"RXT" "J01FA06" "Roxithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "roxi" "" 0.3 "g" ""
|
||||
"RFL" "J01MA10" 58258 "Rufloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "" "c(\"rufloxacin\", \"rufloxacin hcl\", \"rufloxacine\", \"rufloxacino\", \"rufloxacinum\")" 0.2 "g" "character(0)"
|
||||
"SAL" 3085092 "Salinomycin" "Other antibacterials" "" "c(\"coxistac\", \"procoxacin\", \"salinomicina\", \"salinomycin\", \"salinomycine\", \"salinomycinum\")" "87593-0"
|
||||
"SAR" 56208 "Sarafloxacin" "Quinolones" "" "c(\"difloxacine\", \"difloxacino\", \"difloxacinum\", \"saraflox\", \"sarafloxacin\", \"sarafloxacine\", \"sarafloxacino\", \"sarafloxacinum\")" "character(0)"
|
||||
"SRX" 9933415 "Sarmoxicillin" "Beta-lactams/penicillins" "" "sarmoxicillin" "character(0)"
|
||||
"SEC" 71815 "Secnidazole" "Other antibacterials" "" "c(\"flagentyl\", \"secnidal\", \"secnidazol\", \"secnidazole\", \"secnidazolum\", \"secnil\", \"sindose\", \"solosec\")" "character(0)"
|
||||
"SMF" "J04AK05" "Simvastatin/fenofibrate" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "simv" "" 86 ""
|
||||
"SIS" "J01GB08" 36119 "Sisomicin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "siso" "c(\"rickamicin\", \"salvamina\", \"siseptin sulfate\", \"sisomicin\", \"sisomicin sulfate\", \"sisomicina\", \"sisomicine\", \"sisomicinum\", \"sisomin\", \"sisomycin\", \"sissomicin\", \"sizomycin\")" 0.24 "g" "character(0)"
|
||||
"SIT" 461399 "Sitafloxacin" "Quinolones" "" "c(\"gracevit\", \"sitafloxacinisomer\")" "character(0)"
|
||||
"SDA" "J04AA02" 2724368 "Sodium aminosalicylate" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" "" "c(\"bactylan\", \"decapasil\", \"lepasen\", \"monopas\", \"nippas\", \"p.a.s. sodium\", \"pamisyl sodium\", \"parasal sodium\", \"pas sodium\", \"pasade\", \"pasnal\", \"passodico\", \"salvis\", \"sanipirol\", \"sodiopas\", \"sodium p.a.s\", \"sodium pas\", \"teebacin\", \"tubersan\")" 14 "g" 14 "g" "character(0)"
|
||||
"SOL" 25242512 "Solithromycin" "Macrolides/lincosamides" "" "" ""
|
||||
"SPX" "J01MA09" 60464 "Sparfloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"spa\", \"spar\")" "c(\"esparfloxacino\", \"sparfloxacin\", \"sparfloxacine\", \"sparfloxacinum\")" 0.2 "g" "character(0)"
|
||||
"SPT" "J01XX04" 15541 "Spectinomycin" "Other antibacterials" "Other antibacterials" "Other antibacterials" "c(\"sc\", \"spe\", \"spec\", \"spt\")" "c(\"actinospectacina\", \"adspec\", \"espectinomicina\", \"prospec\", \"specitinomycin\", \"spectam\", \"spectinomicina\", \"spectinomycin\", \"spectinomycin di hcl\", \"spectinomycine\", \"spectinomycinum\", \"stanilo\", \"togamycin\", \"trobicin\")" 3 "g" "character(0)"
|
||||
"SPI" "J01FA02" 6419898 "Spiramycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"\", \"spir\")" "c(\"espiramicin\", \"provamycin\", \"rovamycin\", \"rovamycine\", \"sequamycin\", \"spiramycine\", \"spiramycinum\")" 3 "g" "character(0)"
|
||||
"SPM" "J01RA04" "Spiramycin/metronidazole" "Other antibacterials" "Combinations of antibacterials" "Combinations of antibacterials" "" "" ""
|
||||
"STR" "J01GA02" "Streptoduocin" "Aminoglycosides" "Aminoglycoside antibacterials" "Streptomycins" "" "" 1 "g" ""
|
||||
"STR1" "J01GA01" 19649 "Streptomycin" "Aminoglycosides" "Aminoglycoside antibacterials" "Streptomycins" "c(\"s\", \"stm\", \"str\", \"stre\")" "c(\"agrept\", \"agrimycin\", \"chemform\", \"estreptomicina\", \"neodiestreptopab\", \"strepcen\", \"streptomicina\", \"streptomycin\", \"streptomycin a\", \"streptomycin spx\", \"streptomycin sulfate\", \"streptomycine\", \"streptomyzin\", \"vetstrep\")" 1 "g" "4039-4"
|
||||
"STH" "Streptomycin-high" "Aminoglycosides" "c(\"s_h\", \"sthl\", \"strepto high\", \"streptomycin high\")" "" ""
|
||||
"STI" "J04AM01" "Streptomycin/isoniazid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "" ""
|
||||
"SUL" "J01CG01" 130313 "Sulbactam" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase inhibitors" "" "c(\"betamaze\", \"sulbactam\", \"sulbactam acid\", \"sulbactam free acid\", \"sulbactamum\")" 1 "g" "character(0)"
|
||||
"SBC" "J01CA16" 20055036 "Sulbenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"kedacillina\", \"sulbenicilina\", \"sulbenicilline\", \"sulbenicillinum\")" 15 "g" "character(0)"
|
||||
"SUC" 5318 "Sulconazole" "Antifungals/antimycotics" "" "c(\"sulconazol\", \"sulconazole\", \"sulconazolum\")" "character(0)"
|
||||
"SUP" 6634 "Sulfachlorpyridazine" "Other antibacterials" "" "c(\"cluricol\", \"cosulid\", \"cosumix\", \"durasulf\", \"nefrosul\", \"nsulfanilamide\", \"prinzone vet\", \"prinzone vet.\", \"solfaclorpiridazina\", \"sonilyn\", \"sulfachlorpyridazine\", \"sulfacloropiridazina\", \"vetisulid\")" "character(0)"
|
||||
"SDI" "J01EC02" 5215 "Sulfadiazine" "Trimethoprims" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "" "c(\"adiazin\", \"adiazine\", \"cocodiazine\", \"codiazine\", \"cremodiazine\", \"cremotres\", \"debenal\", \"deltazina\", \"diazin\", \"diazolone\", \"diazovit\", \"diazyl\", \"eskadiazine\", \"honey diazine\", \"liquadiazine\", \"microsulfon\", \"neazine\", \"neotrizine\", \"nsulfanilamide\", \"palatrize\", \"piridisir\", \"pirimal\", \"pyrimal\", \"quadetts\", \"quadramoid\", \"sanodiazine\", \"sildaflo\", \"silvadene\", \"solfadiazina\", \"spofadrizine\", \"sterazine\", \"sulfacombin\", \"sulfadiazene\", \"sulfadiazin\", \"sulfadiazina\", \"sulfadiazine\", \"sulfadiazinum\",
|
||||
"RFI" "Rifampicin/isoniazid" "Antimycobacterials" "J04AM02" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "c(\"rifinah\", \"rimactazid\")" "character(0)"
|
||||
"RPEI" "Rifampicin/pyrazinamide/ethambutol/isoniazid" "Antimycobacterials" "J04AM06" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "" ""
|
||||
"RPI" "Rifampicin/pyrazinamide/isoniazid" "Antimycobacterials" "J04AM05" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "" ""
|
||||
"RFM" 6324616 "Rifamycin" "Antimycobacterials" "c(\"A07AA13\", \"D06AX15\", \"J04AB03\", \"S01AA16\", \"S02AA12\")" "Drugs for treatment of tuberculosis" "Antibiotics" "" "c(\"aemcolo\", \"rifacin\", \"rifamicina\", \"rifamicine sv\", \"rifamycin\", \"rifamycine\", \"rifamycinum\", \"rifocin\", \"rifocyn\", \"rifomycin\", \"rifomycin sv\", \"tuborin\")" 0.6 "g" "character(0)"
|
||||
"RFP" 135403821 "Rifapentine" "Antimycobacterials" "J04AB05" "Drugs for treatment of tuberculosis" "Antibiotics" "rifp" "c(\"cyclopentyl rifampin\", \"priftin\", \"rifapentin\", \"rifapentina\", \"rifapentine\", \"rifapentinum\")" 0.11 "g" "character(0)"
|
||||
"RFX" 6436173 "Rifaximin" "Other antibacterials" "c(\"A07AA11\", \"D06AX11\")" "Intestinal antiinfectives" "Antibiotics" "" "c(\"fatroximin\", \"flonorm\", \"lormyx\", \"lumenax\", \"normix\", \"redactiv\", \"rifacol\", \"rifamixin\", \"rifaxidin\", \"rifaximin\", \"rifaximina\", \"rifaximine\", \"rifaximinum\", \"rifaxin\", \"ritacol\", \"spiraxin\", \"xifaxan\", \"xifaxsan\")" 0.6 "g" "character(0)"
|
||||
"RIT" 65633 "Ritipenem" "Carbapenems" "" "ritipenem" "character(0)"
|
||||
"RIA" 163692 "Ritipenem acoxil" "Carbapenems" "" "ritipenem acoxil" "character(0)"
|
||||
"ROK" 5282211 "Rokitamycin" "Macrolides/lincosamides" "J01FA12" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"propionylleucomycin\", \"ricamycin\", \"rokicid\", \"rokital\", \"rokitamicina\", \"rokitamycin\", \"rokitamycine\", \"rokitamycinum\")" 0.8 "g" "character(0)"
|
||||
"RLT" 54682938 "Rolitetracycline" "Tetracyclines" "J01AA09" "Tetracyclines" "Tetracyclines" "" "c(\"bristacin\", \"kinteto\", \"reverin\", \"rolitetraciclina\", \"rolitetracycline\", \"rolitetracyclinum\", \"solvocillin\", \"superciclin\", \"synotodecin\", \"synterin\", \"syntetrex\", \"syntetrin\", \"velacicline\", \"velacycline\")" 0.35 "g" "character(0)"
|
||||
"ROS" 287180 "Rosoxacin" "Quinolones" "J01MB01" "Quinolone antibacterials" "Other quinolones" "" "c(\"acrosoxacin\", \"eracine\", \"eradacil\", \"eradacin\", \"rosoxacin\", \"rosoxacine\", \"rosoxacino\", \"rosoxacinum\", \"roxadyl\", \"winuron\")" 0.3 "g" "character(0)"
|
||||
"RXT" "Roxithromycin" "Macrolides/lincosamides" "J01FA06" "Macrolides, lincosamides and streptogramins" "Macrolides" "roxi" "" 0.3 "g" ""
|
||||
"RFL" 58258 "Rufloxacin" "Quinolones" "J01MA10" "Quinolone antibacterials" "Fluoroquinolones" "" "c(\"rufloxacin\", \"rufloxacin hcl\", \"rufloxacine\", \"rufloxacino\", \"rufloxacinum\")" 0.2 "g" "character(0)"
|
||||
"SAL" 3085092 "Salinomycin" "Other antibacterials" "" "c(\"coxistac\", \"procoxacin\", \"salinomicina\", \"salinomycin\", \"salinomycine\", \"salinomycinum\")" "87593-0"
|
||||
"SAR" 56208 "Sarafloxacin" "Quinolones" "" "c(\"difloxacine\", \"difloxacino\", \"difloxacinum\", \"saraflox\", \"sarafloxacin\", \"sarafloxacine\", \"sarafloxacino\", \"sarafloxacinum\")" "character(0)"
|
||||
"SRX" 9933415 "Sarmoxicillin" "Beta-lactams/penicillins" "" "sarmoxicillin" "character(0)"
|
||||
"SEC" 71815 "Secnidazole" "Other antibacterials" "P01AB07" "" "c(\"flagentyl\", \"secnidal\", \"secnidazol\", \"secnidazole\", \"secnidazolum\", \"secnil\", \"sindose\", \"solosec\")" 2 "g" "character(0)"
|
||||
"SMF" "Simvastatin/fenofibrate" "Antimycobacterials" "C10BA04" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "simv" "" ""
|
||||
"SIS" 36119 "Sisomicin" "Aminoglycosides" "J01GB08" "Aminoglycoside antibacterials" "Other aminoglycosides" "siso" "c(\"rickamicin\", \"salvamina\", \"siseptin sulfate\", \"sisomicin\", \"sisomicin sulfate\", \"sisomicina\", \"sisomicine\", \"sisomicinum\", \"sisomin\", \"sisomycin\", \"sissomicin\", \"sizomycin\")" 0.24 "g" "character(0)"
|
||||
"SIT" 461399 "Sitafloxacin" "Quinolones" "J01MA21" "" "c(\"gracevit\", \"sitafloxacinisomer\")" 0.1 "g" "character(0)"
|
||||
"SDA" 2724368 "Sodium aminosalicylate" "Antimycobacterials" "J04AA02" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" "" "c(\"bactylan\", \"decapasil\", \"lepasen\", \"monopas\", \"nippas\", \"p.a.s. sodium\", \"pamisyl sodium\", \"parasal sodium\", \"pas sodium\", \"pasade\", \"pasnal\", \"passodico\", \"salvis\", \"sanipirol\", \"sodiopas\", \"sodium p.a.s\", \"sodium pas\", \"teebacin\", \"tubersan\")" 14 "g" 14 "g" "character(0)"
|
||||
"SOL" 25242512 "Solithromycin" "Macrolides/lincosamides" "J01FA16" "" "" ""
|
||||
"SPX" 60464 "Sparfloxacin" "Quinolones" "J01MA09" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"spa\", \"spar\")" "c(\"esparfloxacino\", \"sparfloxacin\", \"sparfloxacine\", \"sparfloxacinum\")" 0.2 "g" "character(0)"
|
||||
"SPT" 15541 "Spectinomycin" "Other antibacterials" "J01XX04" "Other antibacterials" "Other antibacterials" "c(\"sc\", \"spe\", \"spec\", \"spt\")" "c(\"actinospectacina\", \"adspec\", \"espectinomicina\", \"prospec\", \"specitinomycin\", \"spectam\", \"spectinomicina\", \"spectinomycin\", \"spectinomycin di hcl\", \"spectinomycine\", \"spectinomycinum\", \"stanilo\", \"togamycin\", \"trobicin\")" 3 "g" "character(0)"
|
||||
"SPI" 6419898 "Spiramycin" "Macrolides/lincosamides" "J01FA02" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"\", \"spir\")" "c(\"espiramicin\", \"provamycin\", \"rovamycin\", \"rovamycine\", \"sequamycin\", \"spiramycine\", \"spiramycinum\")" 3 "g" "character(0)"
|
||||
"SPM" "Spiramycin/metronidazole" "Other antibacterials" "J01RA04" "Combinations of antibacterials" "Combinations of antibacterials" "" "" ""
|
||||
"STR" "Streptoduocin" "Aminoglycosides" "J01GA02" "Aminoglycoside antibacterials" "Streptomycins" "" "" 1 "g" ""
|
||||
"STR1" 19649 "Streptomycin" "Aminoglycosides" "c(\"A07AA04\", \"J01GA01\")" "Aminoglycoside antibacterials" "Streptomycins" "c(\"s\", \"stm\", \"str\", \"stre\")" "c(\"agrept\", \"agrimycin\", \"chemform\", \"estreptomicina\", \"neodiestreptopab\", \"strepcen\", \"streptomicina\", \"streptomycin\", \"streptomycin a\", \"streptomycin spx\", \"streptomycin sulfate\", \"streptomycine\", \"streptomyzin\", \"vetstrep\")" 1 "g" "4039-4"
|
||||
"STH" "Streptomycin-high" "Aminoglycosides" "c(\"sthi\", \"sthl\", \"strepto high\", \"streptomycin high\")" "" ""
|
||||
"STI" "Streptomycin/isoniazid" "Antimycobacterials" "J04AM01" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "" ""
|
||||
"SUL" 130313 "Sulbactam" "Beta-lactams/penicillins" "J01CG01" "Beta-lactam antibacterials, penicillins" "Beta-lactamase inhibitors" "" "c(\"betamaze\", \"sulbactam\", \"sulbactam acid\", \"sulbactam free acid\", \"sulbactamum\")" 1 "g" "character(0)"
|
||||
"SBC" 20055036 "Sulbenicillin" "Beta-lactams/penicillins" "J01CA16" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"kedacillina\", \"sulbenicilina\", \"sulbenicilline\", \"sulbenicillinum\")" 15 "g" "character(0)"
|
||||
"SUC" 5318 "Sulconazole" "Antifungals/antimycotics" "D01AC09" "" "c(\"sulconazol\", \"sulconazole\", \"sulconazolum\")" "character(0)"
|
||||
"SUP" 6634 "Sulfachlorpyridazine" "Other antibacterials" "" "c(\"cluricol\", \"cosulid\", \"cosumix\", \"durasulf\", \"nefrosul\", \"nsulfanilamide\", \"prinzone vet\", \"prinzone vet.\", \"solfaclorpiridazina\", \"sonilyn\", \"sulfachlorpyridazine\", \"sulfacloropiridazina\", \"vetisulid\")" "character(0)"
|
||||
"SDI" 5215 "Sulfadiazine" "Trimethoprims" "J01EC02" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "" "c(\"adiazin\", \"adiazine\", \"cocodiazine\", \"codiazine\", \"cremodiazine\", \"cremotres\", \"debenal\", \"deltazina\", \"diazin\", \"diazolone\", \"diazovit\", \"diazyl\", \"eskadiazine\", \"honey diazine\", \"liquadiazine\", \"microsulfon\", \"neazine\", \"neotrizine\", \"nsulfanilamide\", \"palatrize\", \"piridisir\", \"pirimal\", \"pyrimal\", \"quadetts\", \"quadramoid\", \"sanodiazine\", \"sildaflo\", \"silvadene\", \"solfadiazina\", \"spofadrizine\", \"sterazine\", \"sulfacombin\", \"sulfadiazene\", \"sulfadiazin\", \"sulfadiazina\", \"sulfadiazine\", \"sulfadiazinum\",
|
||||
\"sulfapirimidin\", \"sulfapyrimidin\", \"sulfapyrimidine\", \"sulfatryl\", \"sulfazine\", \"sulfolex\", \"sulfonamides duplex\", \"sulfonsol\", \"sulfose\", \"sulphadiazine\", \"sulphadiazine e\", \"terfonyl\", \"theradiazine\", \"thermazene\", \"trifonamide\", \"triple sulfa\", \"triple sulfas\", \"trisem\", \"truozine\", \"zinc sulfadiazine\")" 0.6 "g" "c(\"27216-1\", \"59742-7\", \"6907-0\")"
|
||||
"SLT" "J01EE06" 122284 "Sulfadiazine/tetroxoprim" "Trimethoprims" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "" "" ""
|
||||
"SLT1" "J01EE02" 64932 "Sulfadiazine/trimethoprim" "Trimethoprims" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "" "c(\"antastmon\", \"cotrimazine\", \"diaziprim forte\", \"ditrim\", \"ditrivet\", \"sultrisan\", \"triglobe\", \"trimin\", \"tucoprim\", \"uniprim\")" "character(0)"
|
||||
"SUD" "J01ED01" 5323 "Sulfadimethoxine" "Trimethoprims" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "" "c(\"agribon\", \"arnosulfan\", \"bactrovet\", \"deposul\", \"diasulfa\", \"diasulfyl\", \"dimetazina\", \"dinosol\", \"dorisul\", \"lasibon\", \"madribon\", \"madrigid\", \"madriqid\", \"madroxin\", \"madroxine\", \"maxulvet\", \"mecozine\", \"memcozine\", \"metoxidon\", \"neostrepal\", \"neostreptal\", \"nsulfanilamide\", \"omnibon\", \"persulfen\", \"primor\", \"radonin\", \"redifal\", \"rofenaid\", \"roscosulf\", \"scandisil\", \"solfadimetossina\", \"sudine\", \"suldixine\", \"sulfabon\", \"sulfadimethoxin\", \"sulfadimethoxine\", \"sulfadimethoxinum\", \"sulfadimetossina\",
|
||||
"SLT" 122284 "Sulfadiazine/tetroxoprim" "Trimethoprims" "J01EE06" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "" "" ""
|
||||
"SLT1" 64932 "Sulfadiazine/trimethoprim" "Trimethoprims" "J01EE02" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "" "c(\"antastmon\", \"cotrimazine\", \"diaziprim forte\", \"ditrim\", \"ditrivet\", \"sultrisan\", \"triglobe\", \"trimin\", \"tucoprim\", \"uniprim\")" "character(0)"
|
||||
"SUD" 5323 "Sulfadimethoxine" "Trimethoprims" "J01ED01" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "" "c(\"agribon\", \"arnosulfan\", \"bactrovet\", \"deposul\", \"diasulfa\", \"diasulfyl\", \"dimetazina\", \"dinosol\", \"dorisul\", \"lasibon\", \"madribon\", \"madrigid\", \"madriqid\", \"madroxin\", \"madroxine\", \"maxulvet\", \"mecozine\", \"memcozine\", \"metoxidon\", \"neostrepal\", \"neostreptal\", \"nsulfanilamide\", \"omnibon\", \"persulfen\", \"primor\", \"radonin\", \"redifal\", \"rofenaid\", \"roscosulf\", \"scandisil\", \"solfadimetossina\", \"sudine\", \"suldixine\", \"sulfabon\", \"sulfadimethoxin\", \"sulfadimethoxine\", \"sulfadimethoxinum\", \"sulfadimetossina\",
|
||||
\"sulfadimetoxin\", \"sulfadimetoxina\", \"sulfadimetoxine\", \"sulfastop\", \"sulfdimethoxine\", \"sulfoplan\", \"sulphadimethoxine\", \"sulxin\", \"sumbio\", \"symbio\", \"theracanzan\", \"ultrasulfon\")" 0.5 "g" "character(0)"
|
||||
"SDM" "J01EB03" 5327 "Sulfadimidine" "Trimethoprims" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "" "c(\"azolmetazin\", \"benzene sulfonamide\", \"calfspan\", \"calfspan tablets\", \"cremomethazine\", \"diazil\", \"diazilsulfadine\", \"dimezathine\", \"intradine\", \"kelametazine\", \"mermeth\", \"metazin\", \"neasina\", \"neazina\", \"nsulfanilamide\", \"panazin\", \"pirmazin\", \"primazin\", \"sa iii\", \"solfadimidina\", \"spanbolet\", \"sulfadimerazine\", \"sulfadimesin\", \"sulfadimesine\", \"sulfadimethyldiazine\", \"sulfadimezin\", \"sulfadimezine\", \"sulfadimezinum\", \"sulfadimidin\", \"sulfadimidina\", \"sulfadimidine\", \"sulfadimidinum\", \"sulfadine\",
|
||||
"SDM" 5327 "Sulfadimidine" "Trimethoprims" "J01EB03" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "" "c(\"azolmetazin\", \"benzene sulfonamide\", \"calfspan\", \"calfspan tablets\", \"cremomethazine\", \"diazil\", \"diazilsulfadine\", \"dimezathine\", \"intradine\", \"kelametazine\", \"mermeth\", \"metazin\", \"neasina\", \"neazina\", \"nsulfanilamide\", \"panazin\", \"pirmazin\", \"primazin\", \"sa iii\", \"solfadimidina\", \"spanbolet\", \"sulfadimerazine\", \"sulfadimesin\", \"sulfadimesine\", \"sulfadimethyldiazine\", \"sulfadimezin\", \"sulfadimezine\", \"sulfadimezinum\", \"sulfadimidin\", \"sulfadimidina\", \"sulfadimidine\", \"sulfadimidinum\", \"sulfadine\",
|
||||
\"sulfametazina\", \"sulfametazyny\", \"sulfamethazine\", \"sulfamethiazine\", \"sulfamezathine\", \"sulfamidine\", \"sulfasure sr bolus\", \"sulfodimesin\", \"sulfodimezine\", \"sulka k boluses\", \"sulka s boluses\", \"sulmet\", \"sulphadimidine\", \"sulphamethasine\", \"sulphamethazine\", \"sulphamezathine\", \"sulphamidine\", \"sulphodimezine\", \"superseptil\", \"superseptyl\", \"vertolan\")" 4 "g" "character(0)"
|
||||
"SLT2" "J01EE05" "Sulfadimidine/trimethoprim" "Trimethoprims" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "" "" ""
|
||||
"SLF" "J01EB05" 5344 "Sulfafurazole" "Trimethoprims" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "c(\"\", \"sfsz\")" "c(\"accuzole\", \"alphazole\", \"amidoxal\", \"astrazolo\", \"azo gantrisin\", \"azosulfizin\", \"bactesulf\", \"barazae\", \"chemouag\", \"cosoxazole\", \"dorsulfan\", \"dorsulfan warthausen\", \"entusil\", \"entusul\", \"eryzole\", \"gantrisin\", \"gantrisine\", \"gantrisona\", \"gantrizin\", \"gantrosan\", \"isoxamin\", \"neazolin\", \"neoxazoi\", \"neoxazol\", \"novazolo\", \"novosaxazole\", \"nsulfanilamide\", \"nsulphanilamide\", \"pancid\", \"pediazole\", \"renosulfan\", \"resoxol\", \"roxosul\", \"roxosul tablets\", \"roxoxol\", \"saxosozine\", \"sodizole\", \"solfafurazolo\",
|
||||
"SLT2" "Sulfadimidine/trimethoprim" "Trimethoprims" "J01EE05" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "" "" ""
|
||||
"SLF" 5344 "Sulfafurazole" "Trimethoprims" "c(\"J01EB05\", \"S01AB02\")" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "c(\"\", \"sfsz\")" "c(\"accuzole\", \"alphazole\", \"amidoxal\", \"astrazolo\", \"azo gantrisin\", \"azosulfizin\", \"bactesulf\", \"barazae\", \"chemouag\", \"cosoxazole\", \"dorsulfan\", \"dorsulfan warthausen\", \"entusil\", \"entusul\", \"eryzole\", \"gantrisin\", \"gantrisine\", \"gantrisona\", \"gantrizin\", \"gantrosan\", \"isoxamin\", \"neazolin\", \"neoxazoi\", \"neoxazol\", \"novazolo\", \"novosaxazole\", \"nsulfanilamide\", \"nsulphanilamide\", \"pancid\", \"pediazole\", \"renosulfan\", \"resoxol\", \"roxosul\", \"roxosul tablets\", \"roxoxol\", \"saxosozine\", \"sodizole\", \"solfafurazolo\",
|
||||
\"soxamide\", \"soxazole\", \"soxisol\", \"soxitabs\", \"soxomide\", \"stansin\", \"sulbio\", \"sulfafuraz ole\", \"sulfafurazol\", \"sulfafurazole\", \"sulfafurazolum\", \"sulfagan\", \"sulfagen\", \"sulfaisoxazole\", \"sulfalar\", \"sulfapolar\", \"sulfasol\", \"sulfasoxazole\", \"sulfasoxizole\", \"sulfazin\", \"sulfisin\", \"sulfisonazole\", \"sulfisoxasole\", \"sulfisoxazol\", \"sulfisoxazole\", \"sulfisoxazolum\", \"sulfizin\", \"sulfizol\", \"sulfizole\", \"sulfofurazole\", \"sulfoxol\", \"suloxsol\", \"sulphafuraz\", \"sulphafurazol\", \"sulphafurazole\", \"sulphafurazolum\",
|
||||
\"sulphaisoxazole\", \"sulphisoxazol\", \"sulphisoxazole\", \"sulphofurazole\", \"sulsoxin\", \"thiasin\", \"unisulf\", \"urisoxin\", \"uritrisin\", \"urogan\", \"vagilia\")" 4 "g" 4 "g" "character(0)"
|
||||
"SLF1" "J01EB01" 5343 "Sulfaisodimidine" "Trimethoprims" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "" "c(\"aristamid\", \"aristamide\", \"aristogyn\", \"domain\", \"domian\", \"elcosin\", \"elcosine\", \"elkosil\", \"elkosin\", \"elkosine\", \"erycon\", \"isosulf\", \"mefenal\", \"nsulfanilamide\", \"solfisomidina\", \"sulfadimetine\", \"sulfaisodimerazine\", \"sulfaisodimidine\", \"sulfaisodimidinum\", \"sulfaisomidine\", \"sulfamethin\", \"sulfasomidine\", \"sulfisomidina\", \"sulfisomidine\", \"sulfisomidine sodium\", \"sulfisomidinum\", \"sulphasomidine\")" 4 "g" 4 "g" "character(0)"
|
||||
"SLF2" "J01ED02" 9047 "Sulfalene" "Trimethoprims" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "" "c(\"dalysep\", \"kelfizin\", \"kelfizina\", \"kelfizine\", \"kelfizine w\", \"longum\", \"nsulfanilamide\", \"policydal\", \"polycidal\", \"solfametopirazina\", \"sulfalen\", \"sulfalene\", \"sulfaleno\", \"sulfalenum\", \"sulfamethopyrazine\", \"sulfamethoxypyrazine\", \"sulfametopyrazine\", \"sulfametoxypyridazin\", \"sulphalene\", \"sulphametopyrazine\", \"vetkelfizina\")" 0.1 "g" "character(0)"
|
||||
"SZO" "J01ED09" 187764 "Sulfamazone" "Trimethoprims" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "" "c(\"sulfamazon\", \"sulfamazona\", \"sulfamazone\", \"sulfamazonum\")" 1.5 "g" "character(0)"
|
||||
"SLF3" "J01ED07" 5325 "Sulfamerazine" "Trimethoprims" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "" "c(\"cremomerazine\", \"kelamerazine\", \"mebacid\", \"mesulfa\", \"methylpyrimal\", \"methylsulfazin\", \"methylsulfazine\", \"metilsulfadiazin\", \"metilsulfazin\", \"nsulfanilamide\", \"percoccide\", \"pyralcid\", \"pyrimal m\", \"romezin\", \"septacil\", \"septosyl\", \"solfamerazina\", \"solumedin\", \"sulfameradine\", \"sulfamerazin\", \"sulfamerazina\", \"sulfamerazine\", \"sulfamerazinum\", \"sulfamethyldiazine\", \"sulphamerazine\", \"sumedine\", \"susfamerazine\")" 3 "g" "character(0)"
|
||||
"SLT3" "J01EE07" "Sulfamerazine/trimethoprim" "Trimethoprims" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "" "" ""
|
||||
"SUM" 5327 "Sulfamethazine" "Other antibacterials" "" "c(\"azolmetazin\", \"benzene sulfonamide\", \"calfspan\", \"calfspan tablets\", \"cremomethazine\", \"diazil\", \"diazilsulfadine\", \"dimezathine\", \"intradine\", \"kelametazine\", \"mermeth\", \"metazin\", \"neasina\", \"neazina\", \"nsulfanilamide\", \"panazin\", \"pirmazin\", \"primazin\", \"sa iii\", \"solfadimidina\", \"spanbolet\", \"sulfadimerazine\", \"sulfadimesin\", \"sulfadimesine\", \"sulfadimethyldiazine\", \"sulfadimezin\", \"sulfadimezine\", \"sulfadimezinum\", \"sulfadimidin\", \"sulfadimidina\", \"sulfadimidine\", \"sulfadimidinum\", \"sulfadine\",
|
||||
"SLF1" 5343 "Sulfaisodimidine" "Trimethoprims" "J01EB01" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "" "c(\"aristamid\", \"aristamide\", \"aristogyn\", \"domain\", \"domian\", \"elcosin\", \"elcosine\", \"elkosil\", \"elkosin\", \"elkosine\", \"erycon\", \"isosulf\", \"mefenal\", \"nsulfanilamide\", \"solfisomidina\", \"sulfadimetine\", \"sulfaisodimerazine\", \"sulfaisodimidine\", \"sulfaisodimidinum\", \"sulfaisomidine\", \"sulfamethin\", \"sulfasomidine\", \"sulfisomidina\", \"sulfisomidine\", \"sulfisomidine sodium\", \"sulfisomidinum\", \"sulphasomidine\")" 4 "g" 4 "g" "character(0)"
|
||||
"SLF2" 9047 "Sulfalene" "Trimethoprims" "J01ED02" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "" "c(\"dalysep\", \"kelfizin\", \"kelfizina\", \"kelfizine\", \"kelfizine w\", \"longum\", \"nsulfanilamide\", \"policydal\", \"polycidal\", \"solfametopirazina\", \"sulfalen\", \"sulfalene\", \"sulfaleno\", \"sulfalenum\", \"sulfamethopyrazine\", \"sulfamethoxypyrazine\", \"sulfametopyrazine\", \"sulfametoxypyridazin\", \"sulphalene\", \"sulphametopyrazine\", \"vetkelfizina\")" 0.1 "g" "character(0)"
|
||||
"SZO" 187764 "Sulfamazone" "Trimethoprims" "J01ED09" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "" "c(\"sulfamazon\", \"sulfamazona\", \"sulfamazone\", \"sulfamazonum\")" 1.5 "g" "character(0)"
|
||||
"SLF3" 5325 "Sulfamerazine" "Trimethoprims" "c(\"D06BA06\", \"J01ED07\")" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "" "c(\"cremomerazine\", \"kelamerazine\", \"mebacid\", \"mesulfa\", \"methylpyrimal\", \"methylsulfazin\", \"methylsulfazine\", \"metilsulfadiazin\", \"metilsulfazin\", \"nsulfanilamide\", \"percoccide\", \"pyralcid\", \"pyrimal m\", \"romezin\", \"septacil\", \"septosyl\", \"solfamerazina\", \"solumedin\", \"sulfameradine\", \"sulfamerazin\", \"sulfamerazina\", \"sulfamerazine\", \"sulfamerazinum\", \"sulfamethyldiazine\", \"sulphamerazine\", \"sumedine\", \"susfamerazine\")" 3 "g" "character(0)"
|
||||
"SLT3" "Sulfamerazine/trimethoprim" "Trimethoprims" "J01EE07" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "" "" ""
|
||||
"SUM" 5327 "Sulfamethazine" "Other antibacterials" "" "c(\"azolmetazin\", \"benzene sulfonamide\", \"calfspan\", \"calfspan tablets\", \"cremomethazine\", \"diazil\", \"diazilsulfadine\", \"dimezathine\", \"intradine\", \"kelametazine\", \"mermeth\", \"metazin\", \"neasina\", \"neazina\", \"nsulfanilamide\", \"panazin\", \"pirmazin\", \"primazin\", \"sa iii\", \"solfadimidina\", \"spanbolet\", \"sulfadimerazine\", \"sulfadimesin\", \"sulfadimesine\", \"sulfadimethyldiazine\", \"sulfadimezin\", \"sulfadimezine\", \"sulfadimezinum\", \"sulfadimidin\", \"sulfadimidina\", \"sulfadimidine\", \"sulfadimidinum\", \"sulfadine\",
|
||||
\"sulfametazina\", \"sulfametazyny\", \"sulfamethazine\", \"sulfamethiazine\", \"sulfamezathine\", \"sulfamidine\", \"sulfasure sr bolus\", \"sulfodimesin\", \"sulfodimezine\", \"sulka k boluses\", \"sulka s boluses\", \"sulmet\", \"sulphadimidine\", \"sulphamethasine\", \"sulphamethazine\", \"sulphamezathine\", \"sulphamidine\", \"sulphodimezine\", \"superseptil\", \"superseptyl\", \"vertolan\")" "87592-2"
|
||||
"SLF4" "J01EB02" 5328 "Sulfamethizole" "Trimethoprims" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "c(\"\", \"sfmz\")" "c(\"ayerlucil\", \"lucosil\", \"methazol\", \"microsul\", \"nsulfanilamide\", \"proklar\", \"renasul\", \"salimol\", \"solfametizolo\", \"sulamethizole\", \"sulfa gram\", \"sulfamethizol\", \"sulfamethizole\", \"sulfamethizolum\", \"sulfametizol\", \"sulfapyelon\", \"sulfstat\", \"sulfurine\", \"sulphamethizole\", \"tetracid\", \"thidicur\", \"thiosulfil\", \"thiosulfil forte\", \"ultrasul\", \"urocydal\", \"urodiaton\", \"urolucosil\", \"urosulfin\")" 4 "g" "c(\"60175-7\", \"60176-5\", \"60177-3\")"
|
||||
"SMX" "J01EC01" 5329 "Sulfamethoxazole" "Trimethoprims" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "c(\"sfmx\", \"sulf\")" "c(\"azo gantanol\", \"eusaprim\", \"gamazole\", \"gantanol\", \"gantanol ds\", \"metoxal\", \"nsulfanilamide\", \"nsulphanilamide\", \"radonil\", \"septran\", \"septrin\", \"simsinomin\", \"sinomin\", \"solfametossazolo\", \"sulfamethalazole\", \"sulfamethoxazol\", \"sulfamethoxazole\", \"sulfamethoxazolum\", \"sulfamethoxizole\", \"sulfamethylisoxazole\", \"sulfametoxazol\", \"sulfisomezole\", \"sulphamethalazole\", \"sulphamethoxazol\", \"sulphamethoxazole\", \"sulphisomezole\", \"urobak\")" 2 "g" "c(\"10342-4\", \"25271-8\", \"39772-9\", \"59971-2\", \"59972-0\", \"60333-2\", \"72674-5\", \"80549-9\", \"80974-9\")"
|
||||
"SLF5" "J01ED05" 5330 "Sulfamethoxypyridazine" "Trimethoprims" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "" "c(\"altezol\", \"davosin\", \"depovernil\", \"kineks\", \"lederkyn\", \"lentac\", \"lisulfen\", \"longin\", \"medicel\", \"midicel\", \"midikel\", \"myasul\", \"nsulfanilamide\", \"opinsul\", \"paramid\", \"paramid supra\", \"petrisul\", \"piridolo\", \"quinoseptyl\", \"retamid\", \"retasulfin\", \"retasulphine\", \"slosul\", \"spofadazine\", \"sulfalex\", \"sulfapyridazine\", \"sulfdurazin\", \"sulfozona\", \"sultirene\", \"vinces\")" 0.5 "g" "character(0)"
|
||||
"SLF6" "J01ED03" 19596 "Sulfametomidine" "Trimethoprims" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "" "c(\"duroprocin\", \"methofadin\", \"methofazine\", \"nsulfanilamide\", \"solfametomidina\", \"sulfamethomidine\", \"sulfametomidin\", \"sulfametomidina\", \"sulfametomidine\", \"sulfametomidinum\")" "character(0)"
|
||||
"SLF7" "J01ED04" 5326 "Sulfametoxydiazine" "Trimethoprims" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "" "c(\"bayrena\", \"berlicid\", \"dairena\", \"durenat\", \"juvoxin\", \"kinecid\", \"kirocid\", \"longasulf\", \"methoxypyrimal\", \"nsulfanilamide\", \"solfametossidiazina\", \"sulfameter\", \"sulfamethorine\", \"sulfamethoxine\", \"sulfamethoxydiazin\", \"sulfamethoxydiazine\", \"sulfamethoxydin\", \"sulfamethoxydine\", \"sulfametin\", \"sulfametinum\", \"sulfametorin\", \"sulfametorine\", \"sulfametorinum\", \"sulfametoxidiazina\", \"sulfametoxidine\", \"sulfametoxydiazine\", \"sulfametoxydiazinum\", \"sulphameter\", \"sulphamethoxydiazine\", \"supramid\",
|
||||
"SLF4" 5328 "Sulfamethizole" "Trimethoprims" "c(\"B05CA04\", \"D06BA04\", \"J01EB02\", \"S01AB01\")" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "c(\"\", \"sfmz\")" "c(\"ayerlucil\", \"lucosil\", \"methazol\", \"microsul\", \"nsulfanilamide\", \"proklar\", \"renasul\", \"salimol\", \"solfametizolo\", \"sulamethizole\", \"sulfa gram\", \"sulfamethizol\", \"sulfamethizole\", \"sulfamethizolum\", \"sulfametizol\", \"sulfapyelon\", \"sulfstat\", \"sulfurine\", \"sulphamethizole\", \"tetracid\", \"thidicur\", \"thiosulfil\", \"thiosulfil forte\", \"ultrasul\", \"urocydal\", \"urodiaton\", \"urolucosil\", \"urosulfin\")" 4 "g" "c(\"60175-7\", \"60176-5\", \"60177-3\")"
|
||||
"SMX" 5329 "Sulfamethoxazole" "Trimethoprims" "J01EC01" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "c(\"sfmx\", \"sulf\")" "c(\"azo gantanol\", \"eusaprim\", \"gamazole\", \"gantanol\", \"gantanol ds\", \"metoxal\", \"nsulfanilamide\", \"nsulphanilamide\", \"radonil\", \"septran\", \"septrin\", \"simsinomin\", \"sinomin\", \"solfametossazolo\", \"sulfamethalazole\", \"sulfamethoxazol\", \"sulfamethoxazole\", \"sulfamethoxazolum\", \"sulfamethoxizole\", \"sulfamethylisoxazole\", \"sulfametoxazol\", \"sulfisomezole\", \"sulphamethalazole\", \"sulphamethoxazol\", \"sulphamethoxazole\", \"sulphisomezole\", \"urobak\")" 2 "g" "c(\"10342-4\", \"25271-8\", \"39772-9\", \"59971-2\", \"59972-0\", \"60333-2\", \"72674-5\", \"80549-9\", \"80974-9\")"
|
||||
"SLF5" 5330 "Sulfamethoxypyridazine" "Trimethoprims" "J01ED05" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "" "c(\"altezol\", \"davosin\", \"depovernil\", \"kineks\", \"lederkyn\", \"lentac\", \"lisulfen\", \"longin\", \"medicel\", \"midicel\", \"midikel\", \"myasul\", \"nsulfanilamide\", \"opinsul\", \"paramid\", \"paramid supra\", \"petrisul\", \"piridolo\", \"quinoseptyl\", \"retamid\", \"retasulfin\", \"retasulphine\", \"slosul\", \"spofadazine\", \"sulfalex\", \"sulfapyridazine\", \"sulfdurazin\", \"sulfozona\", \"sultirene\", \"vinces\")" 0.5 "g" "character(0)"
|
||||
"SLF6" 19596 "Sulfametomidine" "Trimethoprims" "J01ED03" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "" "c(\"duroprocin\", \"methofadin\", \"methofazine\", \"nsulfanilamide\", \"solfametomidina\", \"sulfamethomidine\", \"sulfametomidin\", \"sulfametomidina\", \"sulfametomidine\", \"sulfametomidinum\")" "character(0)"
|
||||
"SLF7" 5326 "Sulfametoxydiazine" "Trimethoprims" "J01ED04" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "" "c(\"bayrena\", \"berlicid\", \"dairena\", \"durenat\", \"juvoxin\", \"kinecid\", \"kirocid\", \"longasulf\", \"methoxypyrimal\", \"nsulfanilamide\", \"solfametossidiazina\", \"sulfameter\", \"sulfamethorine\", \"sulfamethoxine\", \"sulfamethoxydiazin\", \"sulfamethoxydiazine\", \"sulfamethoxydin\", \"sulfamethoxydine\", \"sulfametin\", \"sulfametinum\", \"sulfametorin\", \"sulfametorine\", \"sulfametorinum\", \"sulfametoxidiazina\", \"sulfametoxidine\", \"sulfametoxydiazine\", \"sulfametoxydiazinum\", \"sulphameter\", \"sulphamethoxydiazine\", \"supramid\",
|
||||
\"ultrax\")" 0.5 "g" "character(0)"
|
||||
"SLT4" "J01EE03" "Sulfametrole/trimethoprim" "Trimethoprims" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "c(\"\", \"trsm\")" "" ""
|
||||
"SLF8" "J01EC03" 12894 "Sulfamoxole" "Trimethoprims" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "" "c(\"justamil\", \"nsulfanilamide\", \"oxasulfa\", \"solfamossolo\", \"sulfadimethyloxazole\", \"sulfamoxol\", \"sulfamoxole\", \"sulfamoxolum\", \"sulfano\", \"sulfavigor\", \"sulfmidil\", \"sulfono\", \"sulfune\", \"sulfuno\", \"sulphamoxole\", \"tardamid\", \"tardamide\")" 1 "g" 1 "g" "character(0)"
|
||||
"SLT5" "J01EE04" "Sulfamoxole/trimethoprim" "Trimethoprims" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "" "" ""
|
||||
"SLF9" "J01EB06" 5333 "Sulfanilamide" "Trimethoprims" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "" "c(\"albexan\", \"albosal\", \"ambeside\", \"antistrept\", \"astreptine\", \"astrocid\", \"bacteramid\", \"bactesid\", \"collomide\", \"colsulanyde\", \"copticide\", \"deseptyl\", \"desseptyl\", \"dipron\", \"ergaseptine\", \"erysipan\", \"estreptocida\", \"exoseptoplix\", \"gerison\", \"gombardol\", \"infepan\", \"lysococcine\", \"neococcyl\", \"orgaseptine\", \"prontalbin\", \"prontosil album\", \"prontosil i\", \"prontosil white\", \"prontylin\", \"pronzin album\", \"proseptal\", \"proseptine\", \"proseptol\", \"pysococcine\", \"rubiazol a\", \"sanamid\", \"septamide album\",
|
||||
"SLT4" "Sulfametrole/trimethoprim" "Trimethoprims" "J01EE03" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "c(\"\", \"trsm\")" "" ""
|
||||
"SLF8" 12894 "Sulfamoxole" "Trimethoprims" "J01EC03" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "" "c(\"justamil\", \"nsulfanilamide\", \"oxasulfa\", \"solfamossolo\", \"sulfadimethyloxazole\", \"sulfamoxol\", \"sulfamoxole\", \"sulfamoxolum\", \"sulfano\", \"sulfavigor\", \"sulfmidil\", \"sulfono\", \"sulfune\", \"sulfuno\", \"sulphamoxole\", \"tardamid\", \"tardamide\")" 1 "g" 1 "g" "character(0)"
|
||||
"SLT5" "Sulfamoxole/trimethoprim" "Trimethoprims" "J01EE04" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "" "" ""
|
||||
"SLF9" 5333 "Sulfanilamide" "Trimethoprims" "c(\"D06BA05\", \"J01EB06\")" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "" "c(\"albexan\", \"albosal\", \"ambeside\", \"antistrept\", \"astreptine\", \"astrocid\", \"bacteramid\", \"bactesid\", \"collomide\", \"colsulanyde\", \"copticide\", \"deseptyl\", \"desseptyl\", \"dipron\", \"ergaseptine\", \"erysipan\", \"estreptocida\", \"exoseptoplix\", \"gerison\", \"gombardol\", \"infepan\", \"lysococcine\", \"neococcyl\", \"orgaseptine\", \"prontalbin\", \"prontosil album\", \"prontosil i\", \"prontosil white\", \"prontylin\", \"pronzin album\", \"proseptal\", \"proseptine\", \"proseptol\", \"pysococcine\", \"rubiazol a\", \"sanamid\", \"septamide album\",
|
||||
\"septanilam\", \"septinal\", \"septolix\", \"septoplex\", \"septoplix\", \"solfanilamide\", \"stopton album\", \"stramid\", \"strepamide\", \"strepsan\", \"streptagol\", \"streptamid\", \"streptamin\", \"streptasol\", \"streptocid\", \"streptocid album\", \"streptocide\", \"streptocide white\", \"streptocidum\", \"streptoclase\", \"streptocom\", \"streptol\", \"strepton\", \"streptopan\", \"streptosil\", \"streptozol\", \"streptozone\", \"streptrocide\", \"sulfamidyl\", \"sulfamine\", \"sulfana\", \"sulfanalone\", \"sulfanidyl\", \"sulfanil\", \"sulfanilamida\", \"sulfanilamide\",
|
||||
\"sulfanilamidum\", \"sulfanilimidic acid\", \"sulfanimide\", \"sulfocidin\", \"sulfocidine\", \"sulfonamide\", \"sulfonamide p\", \"sulfonylamide\", \"sulphanilamide\", \"sulphanilamide gr\", \"sulphonamide\", \"therapol\", \"tolder\", \"white streptocide\", \"wln: zswr dz\")" "character(0)"
|
||||
"SLF10" "J01ED06" 68933 "Sulfaperin" "Trimethoprims" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "" "c(\"anastaf\", \"archisulfa\", \"avissul\", \"chemiopen\", \"demosulfan\", \"durisan saft\", \"ipersulfidin sirup\", \"isosulfamerazine\", \"methylsulfadiazin\", \"novosul\", \"nsulfanilamide\", \"orosulfan\", \"pallidin\", \"retardon\", \"risulfasens\", \"sulfaperin\", \"sulfaperina\", \"sulfaperine\", \"sulfaperinum\", \"sulfatreis\", \"sulfopirimidine\", \"sulpenta\", \"ultrasulfon sirup\")" 0.5 "g" "character(0)"
|
||||
"SLF11" "J01ED08" 5335 "Sulfaphenazole" "Trimethoprims" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "" "c(\"depocid\", \"depotsulfonamide\", \"eftolon\", \"firmazolo\", \"inamil\", \"isarol\", \"isarol v\", \"merian\", \"microtan pirazolo\", \"nsulfanilamide\", \"orisul\", \"orisulf\", \"paidazolo\", \"phenylsulfapyrazole\", \"plisulfan\", \"raziosulfa\", \"solfafenazolo\", \"sulfabid\", \"sulfafenazol\", \"sulfafenazolo\", \"sulfaphenazol\", \"sulfaphenazole\", \"sulfaphenazolum\", \"sulfaphenazon\", \"sulfaphenylpipazol\", \"sulfaphenylpyrazol\", \"sulfaphenylpyrazole\", \"sulfonylpyrazol\", \"sulphaphenazole\", \"sulphenazole\")" 1 "g" "character(0)"
|
||||
"SLF12" "J01EB04" 5336 "Sulfapyridine" "Trimethoprims" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "" "c(\"adiplon\", \"coccoclase\", \"dagenan\", \"eubasin\", \"eubasinum\", \"haptocil\", \"piridazol\", \"plurazol\", \"pyriamid\", \"pyridazol\", \"relbapiridina\", \"septipulmon\", \"solfapiridina\", \"streptosilpyridine\", \"sulfapiridina\", \"sulfapyridin\", \"sulfapyridine\", \"sulfapyridinum\", \"sulfidin\", \"sulfidine\", \"sulphapyridin\", \"sulphapyridine\", \"thioseptal\", \"trianon\")" 1 "g" "c(\"14075-6\", \"55580-5\")"
|
||||
"SNA" 60582 "Sulfasuccinamide" "Other antibacterials" "" "c(\"ambesid\", \"derganil\", \"sulfasuccinamid\", \"sulfasuccinamida\", \"sulfasuccinamide\", \"sulfasuccinamidum\")" "character(0)"
|
||||
"SUT" "J01EB07" 5340 "Sulfathiazole" "Trimethoprims" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "" "c(\"azoquimiol\", \"azoseptale\", \"cerazol\", \"cerazole\", \"chemosept\", \"cibazol\", \"duatok\", \"dulana\", \"eleudron\", \"enterobiocine\", \"estafilol\", \"formosulfathiazole\", \"neostrepsan\", \"norsulfasol\", \"norsulfazol\", \"norsulfazole\", \"norsulfazolum\", \"nsulfanilamide\", \"planomide\", \"poliseptil\", \"sanotiazol\", \"septozol\", \"solfatiazolo\", \"streptosilthiazole\", \"sulfamul\", \"sulfathiazol\", \"sulfathiazole\", \"sulfathiazolum\", \"sulfatiazol\", \"sulfavitina\", \"sulfocerol\", \"sulphathiazole\", \"sulzol\", \"thiacoccine\", \"thiasulfol\",
|
||||
"SLF10" 68933 "Sulfaperin" "Trimethoprims" "J01ED06" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "" "c(\"anastaf\", \"archisulfa\", \"avissul\", \"chemiopen\", \"demosulfan\", \"durisan saft\", \"ipersulfidin sirup\", \"isosulfamerazine\", \"methylsulfadiazin\", \"novosul\", \"nsulfanilamide\", \"orosulfan\", \"pallidin\", \"retardon\", \"risulfasens\", \"sulfaperin\", \"sulfaperina\", \"sulfaperine\", \"sulfaperinum\", \"sulfatreis\", \"sulfopirimidine\", \"sulpenta\", \"ultrasulfon sirup\")" 0.5 "g" "character(0)"
|
||||
"SLF11" 5335 "Sulfaphenazole" "Trimethoprims" "J01ED08" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "" "c(\"depocid\", \"depotsulfonamide\", \"eftolon\", \"firmazolo\", \"inamil\", \"isarol\", \"isarol v\", \"merian\", \"microtan pirazolo\", \"nsulfanilamide\", \"orisul\", \"orisulf\", \"paidazolo\", \"phenylsulfapyrazole\", \"plisulfan\", \"raziosulfa\", \"solfafenazolo\", \"sulfabid\", \"sulfafenazol\", \"sulfafenazolo\", \"sulfaphenazol\", \"sulfaphenazole\", \"sulfaphenazolum\", \"sulfaphenazon\", \"sulfaphenylpipazol\", \"sulfaphenylpyrazol\", \"sulfaphenylpyrazole\", \"sulfonylpyrazol\", \"sulphaphenazole\", \"sulphenazole\")" 1 "g" "character(0)"
|
||||
"SLF12" 5336 "Sulfapyridine" "Trimethoprims" "J01EB04" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "" "c(\"adiplon\", \"coccoclase\", \"dagenan\", \"eubasin\", \"eubasinum\", \"haptocil\", \"piridazol\", \"plurazol\", \"pyriamid\", \"pyridazol\", \"relbapiridina\", \"septipulmon\", \"solfapiridina\", \"streptosilpyridine\", \"sulfapiridina\", \"sulfapyridin\", \"sulfapyridine\", \"sulfapyridinum\", \"sulfidin\", \"sulfidine\", \"sulphapyridin\", \"sulphapyridine\", \"thioseptal\", \"trianon\")" 1 "g" "c(\"14075-6\", \"55580-5\")"
|
||||
"SNA" 60582 "Sulfasuccinamide" "Other antibacterials" "" "c(\"ambesid\", \"derganil\", \"sulfasuccinamid\", \"sulfasuccinamida\", \"sulfasuccinamide\", \"sulfasuccinamidum\")" "character(0)"
|
||||
"SUT" 5340 "Sulfathiazole" "Trimethoprims" "c(\"D06BA02\", \"J01EB07\")" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "" "c(\"azoquimiol\", \"azoseptale\", \"cerazol\", \"cerazole\", \"chemosept\", \"cibazol\", \"duatok\", \"dulana\", \"eleudron\", \"enterobiocine\", \"estafilol\", \"formosulfathiazole\", \"neostrepsan\", \"norsulfasol\", \"norsulfazol\", \"norsulfazole\", \"norsulfazolum\", \"nsulfanilamide\", \"planomide\", \"poliseptil\", \"sanotiazol\", \"septozol\", \"solfatiazolo\", \"streptosilthiazole\", \"sulfamul\", \"sulfathiazol\", \"sulfathiazole\", \"sulfathiazolum\", \"sulfatiazol\", \"sulfavitina\", \"sulfocerol\", \"sulphathiazole\", \"sulzol\", \"thiacoccine\", \"thiasulfol\",
|
||||
\"thiazamide\", \"thiozamide\", \"wintrazole\")" "87591-4"
|
||||
"SLF13" "J01EB08" 3000579 "Sulfathiourea" "Trimethoprims" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "" "c(\"badional\", \"baldinol\", \"fontamide\", \"salvoseptyl\", \"solfatiourea\", \"solufontamide\", \"sulfanilthiourea\", \"sulfathiocarbamid\", \"sulfathiocarbamide\", \"sulfathiocarbamidum\", \"sulfathiourea\", \"sulfathiouree\", \"sulfatiourea\", \"sulphathiourea\")" 6 "g" "character(0)"
|
||||
"SOX" 5344 "Sulfisoxazole" "Other antibacterials" "" "c(\"accuzole\", \"alphazole\", \"amidoxal\", \"astrazolo\", \"azo gantrisin\", \"azosulfizin\", \"bactesulf\", \"barazae\", \"chemouag\", \"cosoxazole\", \"dorsulfan\", \"dorsulfan warthausen\", \"entusil\", \"entusul\", \"eryzole\", \"gantrisin\", \"gantrisine\", \"gantrisona\", \"gantrizin\", \"gantrosan\", \"isoxamin\", \"neazolin\", \"neoxazoi\", \"neoxazol\", \"novazolo\", \"novosaxazole\", \"nsulfanilamide\", \"nsulphanilamide\", \"pancid\", \"pediazole\", \"renosulfan\", \"resoxol\", \"roxosul\", \"roxosul tablets\", \"roxoxol\", \"saxosozine\", \"sodizole\", \"solfafurazolo\",
|
||||
"SLF13" 3000579 "Sulfathiourea" "Trimethoprims" "J01EB08" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "" "c(\"badional\", \"baldinol\", \"fontamide\", \"salvoseptyl\", \"solfatiourea\", \"solufontamide\", \"sulfanilthiourea\", \"sulfathiocarbamid\", \"sulfathiocarbamide\", \"sulfathiocarbamidum\", \"sulfathiourea\", \"sulfathiouree\", \"sulfatiourea\", \"sulphathiourea\")" 6 "g" "character(0)"
|
||||
"SOX" 5344 "Sulfisoxazole" "Other antibacterials" "" "c(\"accuzole\", \"alphazole\", \"amidoxal\", \"astrazolo\", \"azo gantrisin\", \"azosulfizin\", \"bactesulf\", \"barazae\", \"chemouag\", \"cosoxazole\", \"dorsulfan\", \"dorsulfan warthausen\", \"entusil\", \"entusul\", \"eryzole\", \"gantrisin\", \"gantrisine\", \"gantrisona\", \"gantrizin\", \"gantrosan\", \"isoxamin\", \"neazolin\", \"neoxazoi\", \"neoxazol\", \"novazolo\", \"novosaxazole\", \"nsulfanilamide\", \"nsulphanilamide\", \"pancid\", \"pediazole\", \"renosulfan\", \"resoxol\", \"roxosul\", \"roxosul tablets\", \"roxoxol\", \"saxosozine\", \"sodizole\", \"solfafurazolo\",
|
||||
\"soxamide\", \"soxazole\", \"soxisol\", \"soxitabs\", \"soxomide\", \"stansin\", \"sulbio\", \"sulfafuraz ole\", \"sulfafurazol\", \"sulfafurazole\", \"sulfafurazolum\", \"sulfagan\", \"sulfagen\", \"sulfaisoxazole\", \"sulfalar\", \"sulfapolar\", \"sulfasol\", \"sulfasoxazole\", \"sulfasoxizole\", \"sulfazin\", \"sulfisin\", \"sulfisonazole\", \"sulfisoxasole\", \"sulfisoxazol\", \"sulfisoxazole\", \"sulfisoxazolum\", \"sulfizin\", \"sulfizol\", \"sulfizole\", \"sulfofurazole\", \"sulfoxol\", \"suloxsol\", \"sulphafuraz\", \"sulphafurazol\", \"sulphafurazole\", \"sulphafurazolum\",
|
||||
\"sulphaisoxazole\", \"sulphisoxazol\", \"sulphisoxazole\", \"sulphofurazole\", \"sulsoxin\", \"thiasin\", \"unisulf\", \"urisoxin\", \"uritrisin\", \"urogan\", \"vagilia\")" "9701-4"
|
||||
"SSS" 86225 "Sulfonamide" "Other antibacterials" "c(\"\", \"sfna\")" "" ""
|
||||
"SLP" 9950244 "Sulopenem" "Other antibacterials" "" "sulopenem" "character(0)"
|
||||
"SLT6" "J01CR04" 444022 "Sultamicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "" "c(\"sultamicilina\", \"sultamicillin\", \"sultamicillinum\")" 1.5 "g" "character(0)"
|
||||
"SUR" 46700778 "Surotomycin" "Other antibacterials" "" "surotomycin" "character(0)"
|
||||
"TAL" "J01CA15" 71447 "Talampicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"talampicilina\", \"talampicillin\", \"talampicilline\", \"talampicillinum\")" 2 "g" "character(0)"
|
||||
"TLP" 163307 "Talmetoprim" "Other antibacterials" "" "talmetoprim" "character(0)"
|
||||
"TAZ" "J01CG02" 123630 "Tazobactam" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase inhibitors" "tazo" "c(\"tazobactam\", \"tazobactam acid\", \"tazobactamum\", \"tazobactum\")" "character(0)"
|
||||
"TBP" 9800194 "Tebipenem" "Carbapenems" "" "" ""
|
||||
"TZD" "J01XX11" 11234049 "Tedizolid" "Oxazolidinones" "Other antibacterials" "Other antibacterials" "tedi" "c(\"tedizolid\", \"torezolid\")" 0.2 0.2 "character(0)"
|
||||
"TEC" "J01XA02" 16131923 "Teicoplanin" "Glycopeptides" "Other antibacterials" "Glycopeptide antibacterials" "c(\"tec\", \"tei\", \"teic\", \"tp\", \"tpl\", \"tpn\")" "c(\"targocid\", \"tecoplanina\", \"tecoplanine\", \"tecoplaninum\", \"teichomycin\", \"teicoplanina\", \"teicoplanine\", \"teicoplaninum\")" 0.4 "g" "c(\"25534-9\", \"25535-6\", \"34378-0\", \"34379-8\", \"4043-6\", \"80968-1\")"
|
||||
"TCM" "Teicoplanin-macromethod" "Glycopeptides" "" "" ""
|
||||
"TLV" "J01XA03" 3081362 "Telavancin" "Glycopeptides" "Other antibacterials" "Glycopeptide antibacterials" "tela" "c(\"telavancin\", \"vibativ\")" "character(0)"
|
||||
"TLT" "J01FA15" 3002190 "Telithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"\", \"teli\")" "levviax" 0.8 "g" "character(0)"
|
||||
"TMX" "J01MA05" 60021 "Temafloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"tema\")" "c(\"omniflox\", \"temafloxacin\", \"temafloxacina\", \"temafloxacine\", \"temafloxacinum\")" 0.8 "g" "character(0)"
|
||||
"TEM" "J01CA17" 171758 "Temocillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"\", \"temo\")" "c(\"temocilina\", \"temocillin\", \"temocillina\", \"temocilline\", \"temocillinum\")" 4 "g" "character(0)"
|
||||
"TRB" "D01BA02" 1549008 "Terbinafine" "Antifungals/antimycotics" "Antifungals for systemic use" "Antifungals for systemic use" "c(\"\", \"terb\")" "c(\"corbinal\", \"lamasil\", \"lamisil\", \"lamisil at\", \"lamisil tablet\", \"terbinafina\", \"terbinafine\", \"terbinafinum\", \"terbinex\")" 0.25 "g" "character(0)"
|
||||
"TRC" 441383 "Terconazole" "Antifungals/antimycotics" "" "c(\"fungistat\", \"panlomyc\", \"terazol\", \"terconazol\", \"terconazole\", \"terconazolum\", \"tercospor\", \"triaconazole\", \"zazole\")" "character(0)"
|
||||
"TRZ" "J04AK03" 65720 "Terizidone" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "" "c(\"terivalidin\", \"terizidon\", \"terizidona\", \"terizidone\", \"terizidonum\")" "character(0)"
|
||||
"TCY" "J01AA07" 54675776 "Tetracycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "c(\"tc\", \"te\", \"tet\", \"tetr\")" "c(\"abramycin\", \"abricycline\", \"achromycin\", \"achromycin v\", \"actisite\", \"agromicina\", \"ambramicina\", \"ambramycin\", \"amycin\", \"biocycline\", \"bristaciclin\", \"bristaciclina\", \"bristacycline\", \"cefracycline\", \"centet\", \"ciclibion\", \"copharlan\", \"criseociclina\", \"cyclomycin\", \"cyclopar\", \"cytome\", \"democracin\", \"deschlorobiomycin\", \"dumocyclin\", \"enterocycline\", \"hostacyclin\", \"lexacycline\", \"limecycline\", \"liquamycin\", \"medocycline\", \"mericycline\", \"micycline\", \"neocycline\", \"oletetrin\", \"omegamycin\",
|
||||
"SSS" 86225 "Sulfonamide" "Other antibacterials" "c(\"\", \"sfna\")" "" ""
|
||||
"SLP" 9950244 "Sulopenem" "Other antibacterials" "" "sulopenem" "character(0)"
|
||||
"SLT6" 444022 "Sultamicillin" "Beta-lactams/penicillins" "J01CR04" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "" "c(\"sultamicilina\", \"sultamicillin\", \"sultamicillinum\")" 1.5 "g" "character(0)"
|
||||
"SUR" 46700778 "Surotomycin" "Other antibacterials" "" "surotomycin" "character(0)"
|
||||
"TAL" 71447 "Talampicillin" "Beta-lactams/penicillins" "J01CA15" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"talampicilina\", \"talampicillin\", \"talampicilline\", \"talampicillinum\")" 2 "g" "character(0)"
|
||||
"TLP" 163307 "Talmetoprim" "Other antibacterials" "" "talmetoprim" "character(0)"
|
||||
"TAZ" 123630 "Tazobactam" "Beta-lactams/penicillins" "J01CG02" "Beta-lactam antibacterials, penicillins" "Beta-lactamase inhibitors" "tazo" "c(\"tazobactam\", \"tazobactam acid\", \"tazobactamum\", \"tazobactum\")" "character(0)"
|
||||
"TBP" 9800194 "Tebipenem" "Carbapenems" "" "" ""
|
||||
"TZD" 11234049 "Tedizolid" "Oxazolidinones" "J01XX11" "Other antibacterials" "Other antibacterials" "tedi" "c(\"tedizolid\", \"torezolid\")" 0.2 "g" 0.2 "g" "character(0)"
|
||||
"TEC" 16131923 "Teicoplanin" "Glycopeptides" "J01XA02" "Other antibacterials" "Glycopeptide antibacterials" "c(\"tec\", \"tei\", \"teic\", \"tp\", \"tpl\", \"tpn\")" "c(\"targocid\", \"tecoplanina\", \"tecoplanine\", \"tecoplaninum\", \"teichomycin\", \"teicoplanina\", \"teicoplanine\", \"teicoplaninum\")" 0.4 "g" "c(\"25534-9\", \"25535-6\", \"34378-0\", \"34379-8\", \"4043-6\", \"80968-1\")"
|
||||
"TCM" "Teicoplanin-macromethod" "Glycopeptides" "" "" ""
|
||||
"TLV" 3081362 "Telavancin" "Glycopeptides" "J01XA03" "Other antibacterials" "Glycopeptide antibacterials" "tela" "c(\"telavancin\", \"vibativ\")" "character(0)"
|
||||
"TLT" 3002190 "Telithromycin" "Macrolides/lincosamides" "J01FA15" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"\", \"teli\")" "levviax" 0.8 "g" "character(0)"
|
||||
"TMX" 60021 "Temafloxacin" "Quinolones" "J01MA05" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"tema\")" "c(\"omniflox\", \"temafloxacin\", \"temafloxacina\", \"temafloxacine\", \"temafloxacinum\")" 0.8 "g" "character(0)"
|
||||
"TEM" 171758 "Temocillin" "Beta-lactams/penicillins" "J01CA17" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"\", \"temo\")" "c(\"temocilina\", \"temocillin\", \"temocillina\", \"temocilline\", \"temocillinum\")" 4 "g" "character(0)"
|
||||
"TRB" 1549008 "Terbinafine" "Antifungals/antimycotics" "c(\"D01AE15\", \"D01BA02\")" "Antifungals for systemic use" "Antifungals for systemic use" "c(\"\", \"terb\")" "c(\"corbinal\", \"lamasil\", \"lamisil\", \"lamisil at\", \"lamisil tablet\", \"terbinafina\", \"terbinafine\", \"terbinafinum\", \"terbinex\")" 0.25 "g" "character(0)"
|
||||
"TRC" 441383 "Terconazole" "Antifungals/antimycotics" "G01AG02" "" "c(\"fungistat\", \"panlomyc\", \"terazol\", \"terconazol\", \"terconazole\", \"terconazolum\", \"tercospor\", \"triaconazole\", \"zazole\")" "character(0)"
|
||||
"TRZ" 65720 "Terizidone" "Antimycobacterials" "J04AK03" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "" "c(\"terivalidin\", \"terizidon\", \"terizidona\", \"terizidone\", \"terizidonum\")" "character(0)"
|
||||
"TCY" 54675776 "Tetracycline" "Tetracyclines" "c(\"A01AB13\", \"D06AA04\", \"J01AA07\", \"S01AA09\", \"S02AA08\", \"S03AA02\")" "Tetracyclines" "Tetracyclines" "c(\"tc\", \"te\", \"tet\", \"tetr\")" "c(\"abramycin\", \"abricycline\", \"achromycin\", \"achromycin v\", \"actisite\", \"agromicina\", \"ambramicina\", \"ambramycin\", \"amycin\", \"biocycline\", \"bristaciclin\", \"bristaciclina\", \"bristacycline\", \"cefracycline\", \"centet\", \"ciclibion\", \"copharlan\", \"criseociclina\", \"cyclomycin\", \"cyclopar\", \"cytome\", \"democracin\", \"deschlorobiomycin\", \"dumocyclin\", \"enterocycline\", \"hostacyclin\", \"lexacycline\", \"limecycline\", \"liquamycin\", \"medocycline\", \"mericycline\", \"micycline\", \"neocycline\", \"oletetrin\", \"omegamycin\",
|
||||
\"orlycycline\", \"panmycin\", \"piracaps\", \"polycycline\", \"polyotic\", \"purocyclina\", \"resteclin\", \"robitet\", \"roviciclina\", \"sigmamycin\", \"solvocin\", \"sumycin\", \"sumycin syrup\", \"tetrabon\", \"tetrachel\", \"tetraciclina\", \"tetracycl\", \"tetracyclin\", \"tetracycline\", \"tetracycline base\", \"tetracycline i\", \"tetracycline ii\", \"tetracyclinum\", \"tetracyn\", \"tetradecin\", \"tetrafil\", \"tetramed\", \"tetrasure\", \"tetraverine\", \"tetrazyklin\", \"tetrex\", \"topicycline\", \"tsiklomistsin\", \"tsiklomitsin\", \"veracin\", \"vetacyclinum\"
|
||||
)" 1 "g" 1 "g" "c(\"25272-6\", \"4045-1\", \"87590-6\")"
|
||||
"TET" 65450 "Tetroxoprim" "Other antibacterials" "" "c(\"tetroxoprim\", \"tetroxoprima\", \"tetroxoprime\", \"tetroxoprimum\")" "character(0)"
|
||||
"THA" 9568512 "Thiacetazone" "Oxazolidinones" "" "c(\"aktivan\", \"ambathizon\", \"amithiozone\", \"amithizone\", \"amitiozon\", \"benthiozone\", \"benzothiozane\", \"benzothiozon\", \"berculon a\", \"berkazon\", \"citazone\", \"conteben\", \"diasan\", \"diazan\", \"domakol\", \"ilbion\", \"livazone\", \"mirizone neustab\", \"mivizon\", \"myvizone\", \"neotibil\", \"neustab\", \"novakol\", \"nuclon argentinian\", \"panrone\", \"parazone\", \"seroden\", \"siocarbazone\", \"tebalon\", \"tebecure\", \"tebemar\", \"tebesone i\", \"tebethion\", \"tebethione\", \"tebezon\", \"thiacetazone\", \"thiacetone\", \"thiacetozone\",
|
||||
"TET" 65450 "Tetroxoprim" "Other antibacterials" "" "c(\"tetroxoprim\", \"tetroxoprima\", \"tetroxoprime\", \"tetroxoprimum\")" "character(0)"
|
||||
"THA" 9568512 "Thiacetazone" "Oxazolidinones" "" "c(\"aktivan\", \"ambathizon\", \"amithiozone\", \"amithizone\", \"amitiozon\", \"benthiozone\", \"benzothiozane\", \"benzothiozon\", \"berculon a\", \"berkazon\", \"citazone\", \"conteben\", \"diasan\", \"diazan\", \"domakol\", \"ilbion\", \"livazone\", \"mirizone neustab\", \"mivizon\", \"myvizone\", \"neotibil\", \"neustab\", \"novakol\", \"nuclon argentinian\", \"panrone\", \"parazone\", \"seroden\", \"siocarbazone\", \"tebalon\", \"tebecure\", \"tebemar\", \"tebesone i\", \"tebethion\", \"tebethione\", \"tebezon\", \"thiacetazone\", \"thiacetone\", \"thiacetozone\",
|
||||
\"thibon\", \"thibone\", \"thioacetazon\", \"thioacetazone\", \"thioacetazonum\", \"thioazetazone\", \"thiocarbazil\", \"thiomicid\", \"thionicid\", \"thioparamizon\", \"thioparamizone\", \"thiosemicarbarzone\", \"thiosemicarbazone\", \"thiotebesin\", \"thiotebezin\", \"thiotebicina\", \"thizone\", \"tiacetazon\", \"tibicur\", \"tibion\", \"tibione\", \"tibizan\", \"tibone\", \"tioacetazon\", \"tioacetazona\", \"tioatsetazon\", \"tiobicina\", \"tiocarone\", \"tiosecolo\", \"tubercazon\", \"tubigal\")" "character(0)"
|
||||
"THI" "J01BA02" 27200 "Thiamphenicol" "Amphenicols" "Amphenicols" "Amphenicols" "" "c(\"descocin\", \"dexawin\", \"dextrosulfenidol\", \"dextrosulphenidol\", \"efnicol\", \"hyrazin\", \"igralin\", \"macphenicol\", \"masatirin\", \"neomyson\", \"racefenicol\", \"racefenicolo\", \"racefenicolum\", \"raceophenidol\", \"racephenicol\", \"rincrol\", \"thiamcol\", \"thiamphenicol\", \"thiamphenicolum\", \"thiocymetin\", \"thiomycetin\", \"thiophenicol\", \"tiamfenicol\", \"tiamfenicolo\", \"urfamicina\", \"urfamycine\", \"vicemycetin\")" 1.5 "g" 1.5 "g" "character(0)"
|
||||
"THI1" "J04AM04" "Thioacetazone/isoniazid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "" ""
|
||||
"TIA" 656958 "Tiamulin" "Other antibacterials" "" "c(\"denagard\", \"tiamulin\", \"tiamulin pamoate\", \"tiamulina\", \"tiamuline\", \"tiamulinum\")" "87589-8"
|
||||
"TIC" "J01CA13" 36921 "Ticarcillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"tc\", \"ti\", \"tic\", \"tica\")" "c(\"ticarcilina\", \"ticarcillin\", \"ticarcilline\", \"ticarcillinum\", \"ticillin\")" 15 "g" "c(\"25254-4\", \"4054-3\", \"4055-0\")"
|
||||
"TCC" "J01CR03" 6437075 "Ticarcillin/clavulanic acid" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "c(\"t/c\", \"tcc\", \"ticl\", \"tim\", \"tlc\")" "timentin" 15 "g" "character(0)"
|
||||
"TGC" "J01AA12" 54686904 "Tigecycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "c(\"tgc\", \"tig\", \"tige\")" "c(\"haizheng li xing\", \"tigeciclina\", \"tigecyclin\", \"tigecycline\", \"tigecycline hydrate\", \"tigecyclinum\", \"tigilcycline\", \"tygacil\")" 0.1 "g" "character(0)"
|
||||
"TBQ" 65592 "Tilbroquinol" "Quinolones" "" "c(\"tilbroquinol\", \"tilbroquinolum\")" "character(0)"
|
||||
"TIP" 24860548 "Tildipirosin" "Macrolides/lincosamides" "" "c(\"tildipirosin\", \"zuprevo\")" "character(0)"
|
||||
"TIL" 5282521 "Tilmicosin" "Macrolides/lincosamides" "" "c(\"micotil\", \"pulmotil\", \"tilmicosin\", \"tilmicosina\", \"tilmicosine\", \"tilmicosinum\")" "87588-0"
|
||||
"TIN" "J01XD02" 5479 "Tinidazole" "Other antibacterials" "Other antibacterials" "Imidazole derivatives" "c(\"\", \"tini\")" "c(\"amtiba\", \"bioshik\", \"ethyl sulfone\", \"fasigin\", \"fasigyn\", \"fasigyntrade mark\", \"fasygin\", \"glongyn\", \"haisigyn\", \"pletil\", \"simplotan\", \"simplotantrade mark\", \"sorquetan\", \"tindamax\", \"tindamaxtrade mark\", \"tinidazol\", \"tinidazole\", \"tinidazolum\", \"tricolam\", \"trimonase\")" 1.5 "g" "character(0)"
|
||||
"TCR" "J04AD02" 3001386 "Tiocarlide" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Thiocarbamide derivatives" "" "c(\"amixyl\", \"datanil\", \"disocarban\", \"disoxyl\", \"thiocarlide\", \"tiocarlid\", \"tiocarlida\", \"tiocarlide\", \"tiocarlidum\")" 7 "g" "character(0)"
|
||||
"TDC" 10247721 "Tiodonium chloride" "Other antibacterials" "" "c(\"cloruro de tiodonio\", \"tiodonii chloridum\", \"tiodonium chloride\")" "character(0)"
|
||||
"TXC" 65788 "Tioxacin" "Quinolones" "" "c(\"tioxacin\", \"tioxacine\", \"tioxacino\", \"tioxacinum\", \"tioxic acid\")" "character(0)"
|
||||
"TIZ" 394397 "Tizoxanide" "Other antibacterials" "" "ntzdes" "character(0)"
|
||||
"TOB" "J01GB01" 36294 "Tobramycin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "c(\"nn\", \"tm\", \"to\", \"tob\", \"tobr\")" "c(\"bethkis\", \"brulamycin\", \"deoxykanamycin b\", \"distobram\", \"gernebcin\", \"gotabiotic\", \"kitabis pak\", \"nebcin\", \"nebicin\", \"nebramycin\", \"nebramycin vi\", \"obramycin\", \"sybryx\", \"tenebrimycin\", \"tenemycin\", \"tobacin\", \"tobi podhaler\", \"tobracin\", \"tobradex\", \"tobradistin\", \"tobralex\", \"tobramaxin\", \"tobramicin\", \"tobramicina\", \"tobramitsetin\", \"tobramycetin\", \"tobramycin\", \"tobramycin base\", \"tobramycin sulfate\", \"tobramycine\", \"tobramycinum\", \"tobrased\", \"tobrasone\", \"tobrex\")" 0.24 "g" "c(\"13584-8\", \"17808-7\", \"22750-4\", \"22751-2\", \"22752-0\", \"31094-6\", \"31095-3\", \"31096-1\", \"35239-3\", \"35670-9\", \"4057-6\", \"4058-4\", \"4059-2\", \"50927-3\", \"52962-8\", \"59380-6\", \"80966-5\")"
|
||||
"TOH" "Tobramycin-high" "Aminoglycosides" "c(\"tobra high\", \"tobramycin high\", \"tohl\")" "" ""
|
||||
"TFX" 5517 "Tosufloxacin" "Quinolones" "" "tosufloxacin" "character(0)"
|
||||
"TMP" "J01EA01" 5578 "Trimethoprim" "Trimethoprims" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "c(\"t\", \"tmp\", \"tr\", \"tri\", \"trim\", \"w\")" "c(\"abaprim\", \"alprim\", \"anitrim\", \"antrima\", \"antrimox\", \"bacdan\", \"bacidal\", \"bacide\", \"bacterial\", \"bacticel\", \"bactifor\", \"bactin\", \"bactoprim\", \"bactramin\", \"bactrim\", \"bencole\", \"bethaprim\", \"biosulten\", \"briscotrim\", \"chemotrin\", \"colizole\", \"colizole ds\", \"conprim\", \"cotrimel\", \"cotrimoxizole\", \"deprim\", \"dosulfin\", \"duocide\", \"esbesul\", \"espectrin\", \"euctrim\", \"exbesul\", \"fermagex\", \"fortrim\", \"idotrim\", \"ikaprim\", \"instalac\", \"kombinax\", \"lagatrim\", \"lagatrim forte\", \"lastrim\", \"lescot\",
|
||||
"THI" 27200 "Thiamphenicol" "Amphenicols" "J01BA02" "Amphenicols" "Amphenicols" "" "c(\"descocin\", \"dexawin\", \"dextrosulfenidol\", \"dextrosulphenidol\", \"efnicol\", \"hyrazin\", \"igralin\", \"macphenicol\", \"masatirin\", \"neomyson\", \"racefenicol\", \"racefenicolo\", \"racefenicolum\", \"raceophenidol\", \"racephenicol\", \"rincrol\", \"thiamcol\", \"thiamphenicol\", \"thiamphenicolum\", \"thiocymetin\", \"thiomycetin\", \"thiophenicol\", \"tiamfenicol\", \"tiamfenicolo\", \"urfamicina\", \"urfamycine\", \"vicemycetin\")" 1.5 "g" 1.5 "g" "character(0)"
|
||||
"THI1" "Thioacetazone/isoniazid" "Antimycobacterials" "J04AM04" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "" ""
|
||||
"TIA" 656958 "Tiamulin" "Other antibacterials" "" "c(\"denagard\", \"tiamulin\", \"tiamulin pamoate\", \"tiamulina\", \"tiamuline\", \"tiamulinum\")" "87589-8"
|
||||
"TIC" 36921 "Ticarcillin" "Beta-lactams/penicillins" "J01CA13" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"tc\", \"ti\", \"tic\", \"tica\")" "c(\"ticarcilina\", \"ticarcillin\", \"ticarcilline\", \"ticarcillinum\", \"ticillin\")" 15 "g" "c(\"25254-4\", \"4054-3\", \"4055-0\")"
|
||||
"TCC" 6437075 "Ticarcillin/clavulanic acid" "Beta-lactams/penicillins" "J01CR03" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "c(\"t/c\", \"tcc\", \"ticl\", \"tim\", \"tlc\")" "timentin" 15 "g" "character(0)"
|
||||
"TGC" 54686904 "Tigecycline" "Tetracyclines" "J01AA12" "Tetracyclines" "Tetracyclines" "c(\"tgc\", \"tig\", \"tige\")" "c(\"haizheng li xing\", \"tigeciclina\", \"tigecyclin\", \"tigecycline\", \"tigecycline hydrate\", \"tigecyclinum\", \"tigilcycline\", \"tygacil\")" 0.1 "g" "character(0)"
|
||||
"TBQ" 65592 "Tilbroquinol" "Quinolones" "P01AA05" "" "c(\"tilbroquinol\", \"tilbroquinolum\")" "character(0)"
|
||||
"TIP" 24860548 "Tildipirosin" "Macrolides/lincosamides" "" "c(\"tildipirosin\", \"zuprevo\")" "character(0)"
|
||||
"TIL" 5282521 "Tilmicosin" "Macrolides/lincosamides" "" "c(\"micotil\", \"pulmotil\", \"tilmicosin\", \"tilmicosina\", \"tilmicosine\", \"tilmicosinum\")" "87588-0"
|
||||
"TIN" 5479 "Tinidazole" "Other antibacterials" "c(\"J01XD02\", \"P01AB02\")" "Other antibacterials" "Imidazole derivatives" "c(\"\", \"tini\")" "c(\"amtiba\", \"bioshik\", \"ethyl sulfone\", \"fasigin\", \"fasigyn\", \"fasigyntrade mark\", \"fasygin\", \"glongyn\", \"haisigyn\", \"pletil\", \"simplotan\", \"simplotantrade mark\", \"sorquetan\", \"tindamax\", \"tindamaxtrade mark\", \"tinidazol\", \"tinidazole\", \"tinidazolum\", \"tricolam\", \"trimonase\")" 2 "g" 1.5 "g" "character(0)"
|
||||
"TCR" 3001386 "Tiocarlide" "Antimycobacterials" "J04AD02" "Drugs for treatment of tuberculosis" "Thiocarbamide derivatives" "" "c(\"amixyl\", \"datanil\", \"disocarban\", \"disoxyl\", \"thiocarlide\", \"tiocarlid\", \"tiocarlida\", \"tiocarlide\", \"tiocarlidum\")" 7 "g" "character(0)"
|
||||
"TDC" 10247721 "Tiodonium chloride" "Other antibacterials" "" "c(\"cloruro de tiodonio\", \"tiodonii chloridum\", \"tiodonium chloride\")" "character(0)"
|
||||
"TXC" 65788 "Tioxacin" "Quinolones" "" "c(\"tioxacin\", \"tioxacine\", \"tioxacino\", \"tioxacinum\", \"tioxic acid\")" "character(0)"
|
||||
"TIZ" 394397 "Tizoxanide" "Other antibacterials" "" "ntzdes" "character(0)"
|
||||
"TOB" 36294 "Tobramycin" "Aminoglycosides" "c(\"J01GB01\", \"S01AA12\")" "Aminoglycoside antibacterials" "Other aminoglycosides" "c(\"nn\", \"tm\", \"to\", \"tob\", \"tobr\")" "c(\"bethkis\", \"brulamycin\", \"deoxykanamycin b\", \"distobram\", \"gernebcin\", \"gotabiotic\", \"kitabis pak\", \"nebcin\", \"nebicin\", \"nebramycin\", \"nebramycin vi\", \"obramycin\", \"sybryx\", \"tenebrimycin\", \"tenemycin\", \"tobacin\", \"tobi podhaler\", \"tobracin\", \"tobradex\", \"tobradistin\", \"tobralex\", \"tobramaxin\", \"tobramicin\", \"tobramicina\", \"tobramitsetin\", \"tobramycetin\", \"tobramycin\", \"tobramycin base\", \"tobramycin sulfate\", \"tobramycine\", \"tobramycinum\", \"tobrased\", \"tobrasone\", \"tobrex\")" 0.24 "g" "c(\"13584-8\", \"17808-7\", \"22750-4\", \"22751-2\", \"22752-0\", \"31094-6\", \"31095-3\", \"31096-1\", \"35239-3\", \"35670-9\", \"4057-6\", \"4058-4\", \"4059-2\", \"50927-3\", \"52962-8\", \"59380-6\", \"80966-5\")"
|
||||
"TOH" "Tobramycin-high" "Aminoglycosides" "c(\"tobra high\", \"tobramycin high\", \"tohl\")" "" ""
|
||||
"TFX" 5517 "Tosufloxacin" "Quinolones" "J01MA22" "" "tosufloxacin" 0.45 "g" "character(0)"
|
||||
"TMP" 5578 "Trimethoprim" "Trimethoprims" "J01EA01" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "c(\"t\", \"tmp\", \"tr\", \"tri\", \"trim\", \"w\")" "c(\"abaprim\", \"alprim\", \"anitrim\", \"antrima\", \"antrimox\", \"bacdan\", \"bacidal\", \"bacide\", \"bacterial\", \"bacticel\", \"bactifor\", \"bactin\", \"bactoprim\", \"bactramin\", \"bactrim\", \"bencole\", \"bethaprim\", \"biosulten\", \"briscotrim\", \"chemotrin\", \"colizole\", \"colizole ds\", \"conprim\", \"cotrimel\", \"cotrimoxizole\", \"deprim\", \"dosulfin\", \"duocide\", \"esbesul\", \"espectrin\", \"euctrim\", \"exbesul\", \"fermagex\", \"fortrim\", \"idotrim\", \"ikaprim\", \"instalac\", \"kombinax\", \"lagatrim\", \"lagatrim forte\", \"lastrim\", \"lescot\",
|
||||
\"methoprim\", \"metoprim\", \"monoprim\", \"monotrim\", \"monotrimin\", \"novotrimel\", \"omstat\", \"oraprim\", \"pancidim\", \"polytrim\", \"priloprim\", \"primosept\", \"primsol\", \"proloprim\", \"protrin\", \"purbal\", \"resprim\", \"resprim forte\", \"roubac\", \"roubal\", \"salvatrim\", \"septrin ds\", \"septrin forte\", \"septrin s\", \"setprin\", \"sinotrim\", \"stopan\", \"streptoplus\", \"sugaprim\", \"sulfamar\", \"sulfamethoprim\", \"sulfoxaprim\", \"sulthrim\", \"sultrex\", \"syraprim\", \"tiempe\", \"tmp smx\", \"toprim\", \"trimanyl\", \"trimethioprim\", \"trimethopim\",
|
||||
\"trimethoprim\", \"trimethoprime\", \"trimethoprimum\", \"trimethopriom\", \"trimetoprim\", \"trimetoprima\", \"trimexazole\", \"trimexol\", \"trimezol\", \"trimogal\", \"trimono\", \"trimopan\", \"trimpex\", \"triprim\", \"trisul\", \"trisulcom\", \"trisulfam\", \"trisural\", \"uretrim\", \"urobactrim\", \"utetrin\", \"velaten\", \"wellcoprim\", \"wellcoprin\", \"xeroprim\", \"zamboprim\")" 0.4 "g" 0.4 "g" "c(\"11005-6\", \"17747-7\", \"25273-4\", \"32342-8\", \"4079-0\", \"4080-8\", \"4081-6\", \"55584-7\", \"80552-3\", \"80973-1\")"
|
||||
"SXT" "J01EE01" 358641 "Trimethoprim/sulfamethoxazole" "Trimethoprims" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "c(\"cot\", \"cotrim\", \"sxt\", \"t/s\", \"trsu\", \"trsx\", \"ts\")" "c(\"bactrim\", \"bactrimel\", \"belcomycine\", \"colimycin\", \"colimycin sulphate\", \"colisticin\", \"colistimethate\", \"colistimethate sodium\", \"colistin sulfate\", \"colistin sulphate\", \"colomycin\", \"coly-mycin\", \"cotrimazole\", \"cotrimoxazole\", \"polymyxin e\", \"polymyxin e. sulfate\", \"promixin\", \"septra\", \"totazina\")" "character(0)"
|
||||
"TRL" "J01FA08" 202225 "Troleandomycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"acetyloleandomycin\", \"aovine\", \"cyclamycin\", \"evramicina\", \"matromicina\", \"matromycin t\", \"oleandocetine\", \"t.a.o.\", \"treolmicina\", \"tribiocillina\", \"triocetin\", \"triolan\", \"troleandomicina\", \"troleandomycin\", \"troleandomycine\", \"troleandomycinum\", \"viamicina\", \"wytrion\")" 1 "g" "character(0)"
|
||||
"TRO" 55886 "Trospectomycin" "Other antibacterials" "" "c(\"trospectinomycin\", \"trospectomicina\", \"trospectomycin\", \"trospectomycine\", \"trospectomycinum\")" "character(0)"
|
||||
"TVA" "J01MA13" 62959 "Trovafloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"trov\")" "c(\"trovafloxacin\", \"trovan\")" 0.2 "g" 0.2 "g" "character(0)"
|
||||
"TUL" 9832301 "Tulathromycin" "Macrolides/lincosamides" "" "c(\"draxxin\", \"tulathrmycin a\", \"tulathromycin\", \"tulathromycin a\")" "character(0)"
|
||||
"TYL" 5280440 "Tylosin" "Macrolides/lincosamides" "" "c(\"fradizine\", \"tilosina\", \"tylocine\", \"tylosin\", \"tylosin a\", \"tylosine\", \"tylosinum\")" "87587-2"
|
||||
"TYL1" "A07AA11" 6441094 "Tylvalosin" "Other antibacterials" "Intestinal antiinfectives" "Antibiotics" "" "" 0.6 "g" ""
|
||||
"PRU1" 124225 "Ulifloxacin (Prulifloxacin)" "Other antibacterials" "" "ulifloxacin" "character(0)"
|
||||
"VAN" "J01XA01" 14969 "Vancomycin" "Glycopeptides" "Other antibacterials" "Glycopeptide antibacterials" "c(\"va\", \"van\", \"vanc\")" "c(\"vancocin\", \"vancocin hcl\", \"vancoled\", \"vancomicina\", \"vancomycin\", \"vancomycin hcl\", \"vancomycine\", \"vancomycinum\", \"vancor\", \"viomycin derivative\")" 2 "g" "c(\"13586-3\", \"13587-1\", \"20578-1\", \"31012-8\", \"39092-2\", \"39796-8\", \"39797-6\", \"4089-9\", \"4090-7\", \"4091-5\", \"4092-3\", \"50938-0\", \"59381-4\")"
|
||||
"VAM" "Vancomycin-macromethod" "Glycopeptides" "" "" ""
|
||||
"VIO" 135398671 "Viomycin" "Antimycobacterials" "" "c(\"celiomycin\", \"florimycin\", \"floromycin\", \"viomicina\", \"viomycin\", \"viomycine\", \"viomycinum\")" "character(0)"
|
||||
"VIR" 11979535 "Virginiamycine" "Other antibacterials" "" "c(\"eskalin v\", \"mikamycin\", \"mikamycine\", \"mikamycinum\", \"ostreogrycinum\", \"pristinamycine\", \"pristinamycinum\", \"stafac\", \"stafytracine\", \"staphylomycin\", \"starfac\", \"streptogramin\", \"vernamycin\", \"virgimycin\", \"virgimycine\", \"virginiamycina\", \"virginiamycine\", \"virginiamycinum\")" "character(0)"
|
||||
"VOR" "J02AC03" 71616 "Voriconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives" "c(\"vori\", \"vrc\")" "c(\"pfizer\", \"vfend i.v.\", \"voriconazol\", \"voriconazole\", \"voriconazolum\", \"vorikonazole\")" 0.4 "g" 0.4 "g" "c(\"38370-3\", \"53902-3\", \"73676-9\", \"80553-1\", \"80651-3\")"
|
||||
"XBR" "J01XX02" 72144 "Xibornol" "Other antibacterials" "Other antibacterials" "Other antibacterials" "" "c(\"bactacine\", \"bracen\", \"nanbacine\", \"xibornol\", \"xibornolo\", \"xibornolum\")" "character(0)"
|
||||
"ZID" 77846445 "Zidebactam" "Other antibacterials" "" "zidebactam" "character(0)"
|
||||
"SXT" 358641 "Trimethoprim/sulfamethoxazole" "Trimethoprims" "J01EE01" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "c(\"cot\", \"cotrim\", \"sxt\", \"t/s\", \"trsu\", \"trsx\", \"ts\")" "c(\"bactrim\", \"bactrimel\", \"belcomycine\", \"colimycin\", \"colimycin sulphate\", \"colisticin\", \"colistimethate\", \"colistimethate sodium\", \"colistin sulfate\", \"colistin sulphate\", \"colomycin\", \"coly-mycin\", \"cotrimazole\", \"cotrimoxazole\", \"polymyxin e\", \"polymyxin e. sulfate\", \"promixin\", \"septra\", \"totazina\")" "character(0)"
|
||||
"TRL" 202225 "Troleandomycin" "Macrolides/lincosamides" "J01FA08" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"acetyloleandomycin\", \"aovine\", \"cyclamycin\", \"evramicina\", \"matromicina\", \"matromycin t\", \"oleandocetine\", \"t.a.o.\", \"treolmicina\", \"tribiocillina\", \"triocetin\", \"triolan\", \"troleandomicina\", \"troleandomycin\", \"troleandomycine\", \"troleandomycinum\", \"viamicina\", \"wytrion\")" 1 "g" "character(0)"
|
||||
"TRO" 55886 "Trospectomycin" "Other antibacterials" "" "c(\"trospectinomycin\", \"trospectomicina\", \"trospectomycin\", \"trospectomycine\", \"trospectomycinum\")" "character(0)"
|
||||
"TVA" 62959 "Trovafloxacin" "Quinolones" "J01MA13" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"trov\")" "c(\"trovafloxacin\", \"trovan\")" 0.2 "g" 0.2 "g" "character(0)"
|
||||
"TUL" 9832301 "Tulathromycin" "Macrolides/lincosamides" "" "c(\"draxxin\", \"tulathrmycin a\", \"tulathromycin\", \"tulathromycin a\")" "character(0)"
|
||||
"TYL" 5280440 "Tylosin" "Macrolides/lincosamides" "" "c(\"fradizine\", \"tilosina\", \"tylocine\", \"tylosin\", \"tylosin a\", \"tylosine\", \"tylosinum\")" "87587-2"
|
||||
"TYL1" 6441094 "Tylvalosin" "Macrolides/lincosamides" "" "" ""
|
||||
"PRU1" 124225 "Ulifloxacin (Prulifloxacin)" "Other antibacterials" "" "ulifloxacin" "character(0)"
|
||||
"VAN" 14969 "Vancomycin" "Glycopeptides" "c(\"A07AA09\", \"J01XA01\", \"S01AA28\")" "Other antibacterials" "Glycopeptide antibacterials" "c(\"va\", \"van\", \"vanc\")" "c(\"vancocin\", \"vancocin hcl\", \"vancoled\", \"vancomicina\", \"vancomycin\", \"vancomycin hcl\", \"vancomycine\", \"vancomycinum\", \"vancor\", \"viomycin derivative\")" 2 "g" 2 "g" "c(\"13586-3\", \"13587-1\", \"20578-1\", \"31012-8\", \"39092-2\", \"39796-8\", \"39797-6\", \"4089-9\", \"4090-7\", \"4091-5\", \"4092-3\", \"50938-0\", \"59381-4\")"
|
||||
"VAM" "Vancomycin-macromethod" "Glycopeptides" "" "" ""
|
||||
"VIO" 135398671 "Viomycin" "Antimycobacterials" "" "c(\"celiomycin\", \"florimycin\", \"floromycin\", \"viomicina\", \"viomycin\", \"viomycine\", \"viomycinum\")" "character(0)"
|
||||
"VIR" 11979535 "Virginiamycine" "Other antibacterials" "" "c(\"eskalin v\", \"mikamycin\", \"mikamycine\", \"mikamycinum\", \"ostreogrycinum\", \"pristinamycine\", \"pristinamycinum\", \"stafac\", \"stafytracine\", \"staphylomycin\", \"starfac\", \"streptogramin\", \"vernamycin\", \"virgimycin\", \"virgimycine\", \"virginiamycina\", \"virginiamycine\", \"virginiamycinum\")" "character(0)"
|
||||
"VOR" 71616 "Voriconazole" "Antifungals/antimycotics" "J02AC03" "Antimycotics for systemic use" "Triazole derivatives" "c(\"vori\", \"vrc\")" "c(\"pfizer\", \"vfend i.v.\", \"voriconazol\", \"voriconazole\", \"voriconazolum\", \"vorikonazole\")" 0.4 "g" 0.4 "g" "c(\"38370-3\", \"53902-3\", \"73676-9\", \"80553-1\", \"80651-3\")"
|
||||
"XBR" 72144 "Xibornol" "Other antibacterials" "J01XX02" "Other antibacterials" "Other antibacterials" "" "c(\"bactacine\", \"bracen\", \"nanbacine\", \"xibornol\", \"xibornolo\", \"xibornolum\")" "character(0)"
|
||||
"ZID" 77846445 "Zidebactam" "Other antibacterials" "" "zidebactam" "character(0)"
|
||||
|
||||
Binary file not shown.
+121
-3
@@ -7,7 +7,7 @@
|
||||
# The like.is.one_of column must be 'like' or 'is' or 'one_of' ('like' will read the 'this_value' column as regular expression)
|
||||
# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group are noted on the 'B.cepacia' sheet of the EUCAST Clinical Breakpoint v.10.0 Excel file of 2020 (v_10.0_Breakpoint_Tables.xlsx).
|
||||
# >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 10 LINES SKIPPED <<<<<
|
||||
# -------------------------------------------------------------------------------------------------------------------------------
|
||||
# -------------------------------------------------------------------------------------------------------------------------------
|
||||
if_mo_property like.is.one_of this_value and_these_antibiotics have_these_values then_change_these_antibiotics to_value reference.rule reference.rule_group reference.version note
|
||||
order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 10
|
||||
order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 10
|
||||
@@ -303,7 +303,7 @@ fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) am
|
||||
fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Enterobacter cloacae aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Escherichia hermannii aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Hafnia alvei aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX, polymyxins R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Hafnia alvei aminopenicillins, AMC, SAM, CXM, CZO, CEP, LEX, CFR, FOX, polymyxins R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Klebsiella aerogenes aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Klebsiella oxytoca aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
fullname like ^Klebsiella( pneumoniae| quasipneumoniae| variicola)? aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
@@ -367,7 +367,7 @@ genus_species one_of Escherichia coli, Proteus mirabilis AMP R PIP R Expert Rule
|
||||
genus_species one_of Escherichia coli, Proteus mirabilis AMP S PIP S Expert Rules on Enterobacterales Expert Rules 3.2
|
||||
fullname like ^(Klebsiella(?! aerogenes)|Raoultella) PIP R Expert Rules on Enterobacterales Expert Rules 3.2
|
||||
fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter freundii|Serratia|Morganella morganii|Hafnia alvei|Providencia) CXM S CXM, cephalosporins_2nd R Expert Rules on Enterobacterales Expert Rules 3.2
|
||||
genus one_of Arsenophonus, Biostraticola, Brenneria, Buchnera, Budvicia, Buttiauxella, Cedecea, Citrobacter, Cosenzaea, Cronobacter, Dickeya, Edwardsiella, Enterobacillus, Enterobacter, Erwinia, Escherichia, Ewingella, Franconibacter, Gibbsiella, Hafnia, Izhakiella, Klebsiella, Kluyvera, Kosakonia, Leclercia, Lelliottia, Leminorella, Lonsdalea, Mangrovibacter, Metakosakonia, Mixta, Moellerella, Morganella, Obesumbacterium, Pantoea, Pectobacterium, Phaseolibacter, Photorhabdus, Phytobacter, Plesiomonas, Pluralibacter, Pragia, Proteus, Providencia, Pseudescherichia, Pseudocitrobacter, Rahnella, Raoultella, Rosenbergiella, Rouxiella, Saccharobacter, Samsonia, Serratia, Shigella, Shimwellia, Siccibacter, Sodalis, Tatumella, Thorsellia, Trabulsiella, Wigglesworthia, Xenorhabdus, Yersinia, Yokenella CIP R fluoroquinolones R Expert Rules on Enterobacterales Expert Rules 3.2 This is Enterobacterales except Salmonella spp.
|
||||
genus one_of Arsenophonus, Biostraticola, Brenneria, Buchnera, Budvicia, Buttiauxella, Cedecea, Citrobacter, Cosenzaea, Cronobacter, Dickeya, Edwardsiella, Enterobacillus, Enterobacter, Erwinia, Escherichia, Ewingella, Franconibacter, Gibbsiella, Hafnia, Izhakiella, Klebsiella, Kluyvera, Kosakonia, Leclercia, Lelliottia, Leminorella, Lonsdalea, Mangrovibacter, Mixta, Moellerella, Morganella, Obesumbacterium, Pantoea, Pectobacterium, Phaseolibacter, Photorhabdus, Phytobacter, Plesiomonas, Pluralibacter, Pragia, Proteus, Providencia, Pseudescherichia, Pseudocitrobacter, Rahnella, Raoultella, Rosenbergiella, Rouxiella, Saccharobacter, Samsonia, Serratia, Shigella, Shimwellia, Siccibacter, Sodalis, Tatumella, Thorsellia, Trabulsiella, Wigglesworthia, Xenorhabdus, Yersinia, Yokenella CIP R fluoroquinolones R Expert Rules on Enterobacterales Expert Rules 3.2 This is Enterobacterales except Salmonella spp.
|
||||
fullname like ^(Serratia|Providencia|Morganella morganii) TGC R Expert Rules on Enterobacterales Expert Rules 3.2
|
||||
genus is Salmonella cephalosporins_2nd R Expert Rules on Salmonella Expert Rules 3.2
|
||||
genus is Salmonella aminoglycosides R Expert Rules on Salmonella Expert Rules 3.2
|
||||
@@ -415,3 +415,121 @@ fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacte
|
||||
fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CTX I CTX, CRO, CAZ Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.2 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CRO I CTX, CRO, CAZ Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.2 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CAZ I CTX, CRO, CAZ Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.2 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
order is Enterobacterales PEN, glycopeptides_except_lipo, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
genus_species is Enterobacter cloacae aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
genus_species is Escherichia hermannii aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
genus_species is Hafnia alvei aminopenicillins, AMC, polymyxins R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
genus_species is Klebsiella aerogenes aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
genus_species is Klebsiella oxytoca aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
fullname like ^Klebsiella( pneumoniae| quasipneumoniae| variicola)? aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
genus_species is Leclercia adecarboxylata FOS R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
genus_species is Morganella morganii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
genus_species is Plesiomonas shigelloides aminopenicillins, AMC, SAM R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
genus_species is Proteus mirabilis DOX, MNO, TCY, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
genus_species is Proteus penneri aminopenicillins, CZO, CEP, LEX, CFR, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
genus_species is Proteus vulgaris aminopenicillins, CZO, CEP, LEX, CFR, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
genus_species is Providencia rettgeri aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
genus_species is Providencia stuartii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
genus is Raoultella aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
genus_species is Serratia marcescens aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX, CXM, DOX, TCY, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
genus_species is Yersinia enterocolitica aminopenicillins, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
genus_species is Yersinia pseudotuberculosis polymyxins R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
genus_species is Aeromonas hydrophila aminopenicillins, SAM R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
genus_species is Aeromonas veronii aminopenicillins, SAM, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
genus_species is Aeromonas dhakensis aminopenicillins, SAM, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
genus_species is Aeromonas caviae aminopenicillins, SAM R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
|
||||
genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, cephalosporins_1st, cephalosporins_2nd, glycopeptides_except_lipo, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3
|
||||
fullname like ^Acinetobacter (baumannii|pittii|nosocomialis) aminopenicillins, AMC, CRO, CTX, ATM, ETP, TMP, FOS, DOX, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus is Acinetobacter DOX, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus_species is Achromobacter xylosoxidans aminopenicillins, CRO, CTX, ETP, ATM R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
|
||||
fullname like ^Burkholderia (ambifaria|anthina|arboris|cepacia|cenocepacia|contaminans|diffusa|dolosa|lata|latens|metallica|multivorans|paludis|pseudomultivorans|pyrrocinia|pseudomultivorans|seminalis|stabilis|stagnalis|territorii|ubonensis|vietnamiensis) aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CRO, CTX, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus_species is Elizabethkingia anophelis aminopenicillins, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus_species is Brucella anthropi aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, SAM, CTX, CRO, ETP, CHL, KAN, NEO, TMP, DOX, MNO, TCY, TGC R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus_species is Stenotrophomonas maltophilia aminopenicillins, AMC, SAM, TIC, PIP, TZP, CRO, CTX, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus is Chryseobacterium aminopenicillins, AMC, SAM, TIC, TCC, CRO, CTX, CAZ, ATM, ETP, IPM, MEM, aminoglycosides, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus_species is Haemophilus influenzae FUS, streptogramins, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.3
|
||||
genus_species is Moraxella catarrhalis TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.3
|
||||
genus is Neisseria TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.3
|
||||
genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.3
|
||||
fullname like ^Campylobacter (jejuni|coli) FUS, streptogramins, TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.3
|
||||
gramstain is Gram-positive ATM, TEM, polymyxins, NAL R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
|
||||
genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
|
||||
genus_species is Staphylococcus cohnii CAZ, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
|
||||
genus_species is Staphylococcus xylosus CAZ, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
|
||||
genus_species is Staphylococcus capitis CAZ, FOS R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
|
||||
genus_species is Staphylococcus aureus CAZ R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
|
||||
genus_species is Staphylococcus coagulase-negative CAZ R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
|
||||
genus is Streptococcus FUS, CAZ, aminoglycosides R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
|
||||
genus_species is Enterococcus faecalis FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 These last ones are all true sulfonamides
|
||||
genus_species is Enterococcus faecalis TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations
|
||||
genus_species is Enterococcus faecalis TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations
|
||||
genus_species is Enterococcus faecalis TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations
|
||||
fullname like ^Enterococcus (gallinarum|casseliflavus) FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 These last ones are all true sulfonamides
|
||||
fullname like ^Enterococcus (gallinarum|casseliflavus) TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations
|
||||
fullname like ^Enterococcus (gallinarum|casseliflavus) TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations
|
||||
fullname like ^Enterococcus (gallinarum|casseliflavus) TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations
|
||||
genus_species is Enterococcus faecium FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 These last ones are all true sulfonamides
|
||||
genus_species is Enterococcus faecium TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations
|
||||
genus_species is Enterococcus faecium TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations
|
||||
genus_species is Enterococcus faecium TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations
|
||||
genus is Corynebacterium FOS R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
|
||||
genus_species is Listeria monocytogenes CAZ, cephalosporins_except_CAZ R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
|
||||
genus one_of Leuconostoc, Pediococcus VAN, TEC R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
|
||||
genus is Lactobacillus VAN, TEC R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
|
||||
fullname like ^Clostridium (ramosum|innocuum) VAN R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
|
||||
genus_species one_of Escherichia coli, Proteus mirabilis AMP R PIP R Expert Rules on Enterobacterales Expert Rules 3.3
|
||||
genus_species one_of Escherichia coli, Proteus mirabilis AMP S PIP S Expert Rules on Enterobacterales Expert Rules 3.3
|
||||
fullname like ^(Klebsiella(?! aerogenes)|Raoultella) PIP R Expert Rules on Enterobacterales Expert Rules 3.3
|
||||
fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter freundii|Serratia|Morganella morganii|Hafnia alvei|Providencia) CXM S CXM, cephalosporins_2nd R Expert Rules on Enterobacterales Expert Rules 3.3
|
||||
genus one_of Arsenophonus, Biostraticola, Brenneria, Buchnera, Budvicia, Buttiauxella, Cedecea, Citrobacter, Cosenzaea, Cronobacter, Dickeya, Edwardsiella, Enterobacillus, Enterobacter, Erwinia, Escherichia, Ewingella, Franconibacter, Gibbsiella, Hafnia, Izhakiella, Klebsiella, Kluyvera, Kosakonia, Leclercia, Lelliottia, Leminorella, Lonsdalea, Mangrovibacter, Mixta, Moellerella, Morganella, Obesumbacterium, Pantoea, Pectobacterium, Phaseolibacter, Photorhabdus, Phytobacter, Plesiomonas, Pluralibacter, Pragia, Proteus, Providencia, Pseudescherichia, Pseudocitrobacter, Rahnella, Raoultella, Rosenbergiella, Rouxiella, Saccharobacter, Samsonia, Serratia, Shigella, Shimwellia, Siccibacter, Sodalis, Tatumella, Thorsellia, Trabulsiella, Wigglesworthia, Xenorhabdus, Yersinia, Yokenella CIP R fluoroquinolones R Expert Rules on Enterobacterales Expert Rules 3.3 This is Enterobacterales except Salmonella spp.
|
||||
fullname like ^(Serratia|Providencia|Morganella morganii) TGC R Expert Rules on Enterobacterales Expert Rules 3.3
|
||||
genus is Salmonella cephalosporins_2nd R Expert Rules on Salmonella Expert Rules 3.3
|
||||
genus is Salmonella aminoglycosides R Expert Rules on Salmonella Expert Rules 3.3
|
||||
genus is Salmonella PEF R CIP R Expert Rules on Salmonella Expert Rules 3.3
|
||||
genus_species is Staphylococcus aureus FOX1 R betalactams R Expert Rules on Staphylococcus Expert Rules 3.3
|
||||
genus_species is Staphylococcus aureus FOX1 S betalactams S Expert Rules on Staphylococcus Expert Rules 3.3
|
||||
genus_species one_of Staphylococcus aureus, Staphylococcus lugdunensis PEN R AMP, AMX, AZL, BAM, CRB, CRN, EPC, HET, MEC, MEZ, MTM, PIP, PME, PVM, SBC, TAL, TEM, TIC R Expert Rules on Staphylococcus Expert Rules 3.3 all penicillins without beta-lactamse inhibitor
|
||||
genus is Staphylococcus ERY, CLI S macrolides, lincosamides S Expert Rules on Staphylococcus Expert Rules 3.3
|
||||
genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Expert Rules on Staphylococcus Expert Rules 3.3
|
||||
genus is Staphylococcus LVX R fluoroquinolones R Expert Rules on Staphylococcus Expert Rules 3.3
|
||||
genus is Staphylococcus MFX R fluoroquinolones R Expert Rules on Staphylococcus Expert Rules 3.3
|
||||
genus is Staphylococcus TCY S DOX, MNO, TGC S Expert Rules on Staphylococcus Expert Rules 3.3
|
||||
genus is Staphylococcus TCY R DOX, MNO R Expert Rules on Staphylococcus Expert Rules 3.3
|
||||
genus is Staphylococcus VAN S lipoglycopeptides S Expert Rules on Staphylococcus Expert Rules 3.3
|
||||
genus is Staphylococcus LNZ S TZD S Expert Rules on Staphylococcus Expert Rules 3.3
|
||||
fullname like ^Enterococcus (faecalis|faecium) AMP R ureidopenicillins, IPM R Expert Rules on Enterococcus Expert Rules 3.3
|
||||
fullname like ^Enterococcus (faecalis|faecium) AMX R ureidopenicillins, IPM R Expert Rules on Enterococcus Expert Rules 3.3
|
||||
genus is Enterococcus NOR S CIP, LVX S Expert Rules on Enterococcus Expert Rules 3.3
|
||||
genus is Enterococcus VAN S lipoglycopeptides S Expert Rules on Enterococcus Expert Rules 3.3
|
||||
genus_species is Enterococcus faecium CLI R Expert Rules on Enterococcus Expert Rules 3.3
|
||||
genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN S aminopenicillins, cephalosporins, carbapenems S Expert Rules on Streptococcus A, B, C and G Expert Rules 3.3
|
||||
genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR S LVX, MFX S Expert Rules on Streptococcus A, B, C and G Expert Rules 3.3
|
||||
genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR R LVX, MFX R Expert Rules on Streptococcus A, B, C and G Expert Rules 3.3
|
||||
genus_species is Streptococcus pneumoniae OXA S PHN, PEN, aminopenicillins, cephalosporins_except_CAZ, carbapenems S Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
|
||||
genus_species is Streptococcus pneumoniae NOR S LVX, MFX S Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
|
||||
genus_species is Streptococcus pneumoniae NOR R LVX, MFX R Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
|
||||
genus_species is Streptococcus pneumoniae LVX R fluoroquinolones R Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
|
||||
genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
|
||||
genus_species is Streptococcus pneumoniae TCY S DOX, MNO S Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
|
||||
genus_species is Streptococcus pneumoniae TCY R DOX, MNO R Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
|
||||
genus_species is Streptococcus pneumoniae VAN S lipoglycopeptides S Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
|
||||
fullname like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ PEN S aminopenicillins, CTX, CRO S Expert Rules on Viridans Group Streptococci Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae PEN S betalactams S Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae NAL S fluoroquinolones S Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae NAL R CIP, LVX, MFX R Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae TCY S DOX, MNO S Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae TCY R DOX, MNO R Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
genus_species is Moraxella catarrhalis NAL S fluoroquinolones S Expert Rules on Moraxella catarrhalis Expert Rules 3.3
|
||||
genus_species is Moraxella catarrhalis NAL R fluoroquinolones R Expert Rules on Moraxella catarrhalis Expert Rules 3.3
|
||||
genus is Campylobacter ERY S CLR, AZM S Expert Rules on Campylobacter Expert Rules 3.3
|
||||
genus_species is Campylobacter ERY R CLR, AZM R Expert Rules on Campylobacter Expert Rules 3.3
|
||||
fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CTX S CTX, CRO, CAZ Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.3 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CRO S CTX, CRO, CAZ Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.3 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CAZ S CTX, CRO, CAZ Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.3 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CTX I CTX, CRO, CAZ Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.3 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CRO I CTX, CRO, CAZ Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.3 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CAZ I CTX, CRO, CAZ Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.3 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
|
||||
|
Can't render this file because it contains an unexpected character in line 6 and column 96.
|
@@ -0,0 +1,13 @@
|
||||
ex2 <- example_isolates
|
||||
for (extra_id in seq_len(50)) {
|
||||
ex2 <- ex2 %>%
|
||||
bind_rows(example_isolates %>% mutate(patient_id = paste0(patient_id, extra_id)))
|
||||
}
|
||||
# randomly clear antibibiograms of 2%
|
||||
clr <- sort(sample(x = seq_len(nrow(ex2)),
|
||||
size = nrow(ex2) * 0.02))
|
||||
for (row in which(is.rsi(ex2))) {
|
||||
ex2[clr, row] <- NA_rsi_
|
||||
}
|
||||
|
||||
|
||||
Binary file not shown.
Binary file not shown.
@@ -0,0 +1,28 @@
|
||||
library(dplyr)
|
||||
example_isolates %>%
|
||||
select(mo, where(is.rsi)) %>%
|
||||
tidyr::pivot_longer(cols = where(is.rsi)) %>%
|
||||
# remove intrisic R
|
||||
filter(!paste(mo, name) %in% AMR:::INTRINSIC_R) %>%
|
||||
mutate(name = as.ab(name),
|
||||
value = ifelse(value == "R", 1, 0),
|
||||
class = ab_group(name)) %>%
|
||||
group_by(mo, class) %>%
|
||||
summarise(n = n(),
|
||||
res = mean(value, na.rm = TRUE)) %>%
|
||||
filter(n > 30, !is.na(res))
|
||||
|
||||
|
||||
|
||||
df <- example_isolates
|
||||
search_mo <- "B_ESCHR_COLI"
|
||||
intrinsic_res <- INTRINSIC_R[INTRINSIC_R %like% search_mo]
|
||||
intrinsic_res <- gsub(".* (.*)", "\\1", intrinsic_res)
|
||||
|
||||
x <- df %>%
|
||||
select(mo, where(is.rsi)) %>%
|
||||
filter(mo == search_mo) %>%
|
||||
# at least 30 results available
|
||||
select(function(x) sum(!is.na(x)) >= 30) %>%
|
||||
# remove intrisic R
|
||||
select(!matches(paste(intrinsic_res, collapse = "|")))
|
||||
Binary file not shown.
@@ -1 +1 @@
|
||||
9c58b2d894dbad7593cd44b78d04cd78
|
||||
43d5b2e1df4e0d12d6ad0c7a4591199c
|
||||
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
+622
-622
File diff suppressed because it is too large
Load Diff
Binary file not shown.
Binary file not shown.
@@ -1 +1 @@
|
||||
8338ff5f079f4519fa3c44f8c5bace64
|
||||
ee4434541c7b6529b391d2684748e28b
|
||||
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
+417
-179
File diff suppressed because it is too large
Load Diff
Binary file not shown.
Binary file not shown.
Binary file not shown.
+70753
-70019
File diff suppressed because it is too large
Load Diff
+1
-1
@@ -1 +1 @@
|
||||
82bd6236cf159569f6f5c99f48f92d86
|
||||
638a06636d8b547c2cb9d1ec243ecb7e
|
||||
|
||||
+19
-1
@@ -118,7 +118,7 @@ read_EUCAST <- function(sheet, file, guideline_name) {
|
||||
seq(from = 41, to = 49, by = 1),
|
||||
seq(from = 81, to = 89, by = 1))
|
||||
has_superscript <- function(x) {
|
||||
# because due to floating point error 0.1252 is not in:
|
||||
# because due to floating point error, 0.1252 is not in:
|
||||
# seq(from = 0.1251, to = 0.1259, by = 0.0001)
|
||||
sapply(x, function(x) any(near(x, MICs_with_trailing_superscript)))
|
||||
}
|
||||
@@ -242,3 +242,21 @@ for (i in 2:length(sheets_to_analyse)) {
|
||||
guideline_name = guideline_name))
|
||||
, error = function(e) message(e$message))
|
||||
}
|
||||
|
||||
# 2021-07-12 fix for Morganellaceae (check other lines too next time)
|
||||
morg <- rsi_translation %>%
|
||||
as_tibble() %>%
|
||||
filter(ab == "IPM",
|
||||
guideline == "EUCAST 2021",
|
||||
mo == as.mo("Enterobacterales")) %>%
|
||||
mutate(mo = as.mo("Morganellaceae"))
|
||||
morg[which(morg$method == "MIC"), "breakpoint_S"] <- 0.001
|
||||
morg[which(morg$method == "MIC"), "breakpoint_R"] <- 4
|
||||
morg[which(morg$method == "DISK"), "breakpoint_S"] <- 50
|
||||
morg[which(morg$method == "DISK"), "breakpoint_R"] <- 19
|
||||
|
||||
rsi_translation <- rsi_translation %>%
|
||||
bind_rows(morg) %>%
|
||||
bind_rows(morg %>%
|
||||
mutate(guideline = "EUCAST 2020")) %>%
|
||||
arrange(desc(guideline), ab, mo, method)
|
||||
|
||||
@@ -546,8 +546,8 @@ antibiotics[which(antibiotics$ab == "FEP"), "abbreviations"][[1]] <- list(c(anti
|
||||
antibiotics[which(antibiotics$ab == "CTC"), "abbreviations"][[1]] <- list(c("xctl"))
|
||||
antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]], "xct"))
|
||||
# High level Gentamcin and Streptomycin
|
||||
antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]] <- list(c("gehl", "gentamicin high", "genta high"))
|
||||
antibiotics[which(antibiotics$ab == "STH"), "abbreviations"][[1]] <- list(c("sthl", "streptomycin high", "strepto high"))
|
||||
antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]] <- list(c("gehl", "gentamicin high", "genta high", "gehi"))
|
||||
antibiotics[which(antibiotics$ab == "STH"), "abbreviations"][[1]] <- list(c("sthl", "streptomycin high", "strepto high", "sthi"))
|
||||
# add imi and "imipenem/cilastatine" to imipenem
|
||||
antibiotics[which(antibiotics$ab == "IPM"), "abbreviations"][[1]] <- list(c("imip", "imi", "imp"))
|
||||
antibiotics[which(antibiotics$ab == "IPM"), "synonyms"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "IPM"), "synonyms"][[1]], "imipenem/cilastatin")))
|
||||
@@ -646,28 +646,104 @@ antibiotics <- antibiotics %>%
|
||||
oral_ddd = NA_real_))
|
||||
|
||||
|
||||
# update DDDs from WHOCC website
|
||||
ddd_oral <- double(length = nrow(antibiotics))
|
||||
ddd_iv <- double(length = nrow(antibiotics))
|
||||
|
||||
# update ATC codes from WHOCC website -------------------------------------
|
||||
|
||||
# last time checked: 2021-08-16
|
||||
|
||||
updated_atc <- as.list(antibiotics$atc)
|
||||
|
||||
get_atcs <- function(ab_name, url = "https://www.whocc.no/atc_ddd_index/") {
|
||||
|
||||
ab_name <- gsub("/", " and ", tolower(ab_name), fixed = TRUE)
|
||||
|
||||
# we will do a search on their website, which means:
|
||||
|
||||
# go to the url
|
||||
atc_tbl <- read_html(url) %>%
|
||||
# get all forms
|
||||
html_form() %>%
|
||||
# get the second form (the first form is a global website form)
|
||||
.[[2]] %>%
|
||||
# set the name input box to our search parameter
|
||||
html_form_set(name = ab_name) %>%
|
||||
# hit Submit
|
||||
html_form_submit() %>%
|
||||
# read the resulting page
|
||||
read_html() %>%
|
||||
# retrieve the table on it
|
||||
html_node("table") %>%
|
||||
# transform it to an R data set
|
||||
html_table(header = FALSE)
|
||||
# and get the ATCs (first column) of only exact hits
|
||||
unique(as.character(atc_tbl[which(tolower(atc_tbl[, 2, drop = TRUE]) == ab_name), 1, drop = TRUE]))
|
||||
}
|
||||
|
||||
# this takes around 4 minutes (some are skipped and go faster)
|
||||
for (i in seq_len(nrow(antibiotics))) {
|
||||
message(percentage(i / nrow(antibiotics), digits = 1),
|
||||
" - Downloading ", antibiotics$name[i],
|
||||
appendLF = FALSE)
|
||||
atcs <- get_atcs(antibiotics$name[i])
|
||||
if (length(atcs) > 0) {
|
||||
updated_atc[[i]] <- atcs
|
||||
message(" (", length(atcs), " results)")
|
||||
# let the WHO server rest for a second - they might have a limitation on the queries per second
|
||||
Sys.sleep(1)
|
||||
} else {
|
||||
message(" (skipping)")
|
||||
}
|
||||
}
|
||||
|
||||
antibiotics$atc <- updated_atc
|
||||
|
||||
# update DDDs from WHOCC website ------------------------------------------
|
||||
|
||||
# last time checked: 2021-08-19
|
||||
ddd_oral <- rep(NA_real_, nrow(antibiotics))
|
||||
ddd_oral_units <- rep(NA_character_, nrow(antibiotics))
|
||||
ddd_iv <- rep(NA_real_, nrow(antibiotics))
|
||||
ddd_iv_units <- rep(NA_character_, nrow(antibiotics))
|
||||
progress <- progress_ticker(nrow(antibiotics))
|
||||
for (i in seq_len(nrow(antibiotics))) {
|
||||
on.exit(close(progress))
|
||||
progress$tick()
|
||||
if (!is.na(antibiotics$atc[i])) {
|
||||
ddd_oral[i] <- atc_online_ddd(antibiotics$atc[i], administration = "O")
|
||||
ddd_iv[i] <- atc_online_ddd(antibiotics$atc[i], administration = "P") # parenteral
|
||||
Sys.sleep(1)
|
||||
atcs <- antibiotics$atc[[i]]
|
||||
if (!all(is.na(atcs))) {
|
||||
for (j in seq_len(length(atcs))) {
|
||||
# oral
|
||||
if (is.na(ddd_oral[i])) {
|
||||
ddd_oral[i] <- atc_online_ddd(atcs[j], administration = "O")
|
||||
if (!is.na(ddd_oral[i])) {
|
||||
ddd_oral_units[i] <- atc_online_ddd_units(atcs[j], administration = "O")
|
||||
}
|
||||
}
|
||||
# parenteral
|
||||
if (is.na(ddd_iv[i])) {
|
||||
ddd_iv[i] <- atc_online_ddd(atcs[j], administration = "P")
|
||||
if (!is.na(ddd_iv[i])) {
|
||||
ddd_iv_units[i] <- atc_online_ddd_units(atcs[j], administration = "P")
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
if (!is.na(ddd_oral[i]) | !is.na(ddd_iv[i])) {
|
||||
# let the WHO server rest for 0.25 second - they might have a limitation on the queries per second
|
||||
Sys.sleep(0.25)
|
||||
}
|
||||
}
|
||||
ddd_oral[ddd_oral == 0] <- NA_real_
|
||||
ddd_iv[ddd_iv == 0] <- NA_real_
|
||||
|
||||
antibiotics$oral_ddd <- ddd_oral
|
||||
antibiotics$oral_units <- ddd_oral_units
|
||||
antibiotics$iv_ddd <- ddd_iv
|
||||
antibiotics$iv_units <- ddd_iv_units
|
||||
|
||||
# Wrap up -----------------------------------------------------------------
|
||||
|
||||
# set as data.frame again
|
||||
antibiotics <- as.data.frame(antibiotics, stringsAsFactors = FALSE)
|
||||
class(antibiotics$ab) <- c("ab", "character")
|
||||
antibiotics <- antibiotics %>% dplyr::arrange(name)
|
||||
antibiotics <- dplyr::arrange(antibiotics, name)
|
||||
|
||||
# make all abbreviations and synonyms lower case, unique and alphabetically sorted ----
|
||||
for (i in 1:nrow(antibiotics)) {
|
||||
@@ -683,5 +759,5 @@ for (i in 1:nrow(antibiotics)) {
|
||||
|
||||
# REFER TO data-raw/loinc.R FOR ADDING LOINC CODES
|
||||
|
||||
usethis::use_data(antibiotics, overwrite = TRUE, version = 2)
|
||||
usethis::use_data(antibiotics, overwrite = TRUE, version = 2, compress = "xz")
|
||||
rm(antibiotics)
|
||||
|
||||
@@ -32,7 +32,7 @@ for (i in seq_len(nrow(antibiotics))) {
|
||||
}
|
||||
|
||||
int_resis <- eucast_rules(int_resis,
|
||||
eucast_rules_df = subset(AMR:::eucast_rules_file,
|
||||
eucast_rules_df = subset(AMR:::EUCAST_RULES_DF,
|
||||
is.na(have_these_values) & reference.version == 3.2),
|
||||
info = FALSE)
|
||||
|
||||
|
||||
@@ -23,8 +23,9 @@
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
# Register at List of Prokaryotic names with Standing in Nomenclature (LPSN)
|
||||
# then got to https://lpsn.dsmz.de/downloads and download the latest CSV file.
|
||||
# Go to https://lpsn.dsmz.de/downloads (register first) and download the latest CSV file.
|
||||
|
||||
file_location <- "data-raw/taxonomy.csv"
|
||||
|
||||
library(tidyverse)
|
||||
library(AMR)
|
||||
@@ -112,7 +113,7 @@ abbreviate_mo <- function(x, minlength = 5, prefix = "", ...) {
|
||||
|
||||
# Read data ---------------------------------------------------------------
|
||||
|
||||
taxonomy <- read_csv("~/Downloads/taxonomy.csv")
|
||||
taxonomy <- read_csv(file_location)
|
||||
|
||||
# Create synonyms ---------------------------------------------------------
|
||||
|
||||
@@ -130,8 +131,7 @@ new_synonyms <- taxonomy %>%
|
||||
filter(fullname != fullname_new) %>%
|
||||
# this part joins this table to itself to correct for entries that had >1 renames,
|
||||
# such as:
|
||||
# Bacteroides tectum -> Bacteroides tectus
|
||||
# Bacteroides tectus -> Bacteroides pyogenes
|
||||
# Bacteroides tectum -> Bacteroides tectus -> Bacteroides pyogenes
|
||||
left_join(., .,
|
||||
by = c("fullname_new" = "fullname"),
|
||||
suffix = c("", ".2")) %>%
|
||||
@@ -178,8 +178,7 @@ genera_without_mo_code <- updated_microorganisms %>%
|
||||
pull(genus) %>%
|
||||
unique()
|
||||
|
||||
genera_without_mo_code_abbr <- genera_without_mo_code %>%
|
||||
abbreviate_mo(5, prefix = "B_")
|
||||
genera_without_mo_code_abbr <- genera_without_mo_code %>% abbreviate_mo(5, prefix = "B_")
|
||||
genera_without_mo_code_abbr[genera_without_mo_code_abbr %in% microorganisms$mo] <- abbreviate_mo(genera_without_mo_code[genera_without_mo_code_abbr %in% microorganisms$mo], 6, prefix = "B_")
|
||||
genera_without_mo_code_abbr[genera_without_mo_code_abbr %in% microorganisms$mo] <- abbreviate_mo(genera_without_mo_code[genera_without_mo_code_abbr %in% microorganisms$mo], 7, prefix = "B_")
|
||||
# all unique??
|
||||
@@ -361,6 +360,22 @@ MOs <- MOs %>%
|
||||
MOs <- MOs %>%
|
||||
df_remove_nonASCII()
|
||||
|
||||
# Add LPSN record IDs -----------------------------------------------------
|
||||
|
||||
records_ids <- taxonomy %>%
|
||||
mutate(across(1:3, function(x) { x[is.na(x)] <- ""; x}),
|
||||
fullname = trimws(paste(genus_name, sp_epithet, subsp_epithet))) %>%
|
||||
transmute(fullname, species_id = as.numeric(record_no)) %>%
|
||||
arrange(fullname, species_id) %>%
|
||||
distinct(fullname, .keep_all = TRUE)
|
||||
message("Adding ", sum(records_ids$fullname %in% microorganisms$fullname), " LPSN record IDs")
|
||||
MOs <- MOs %>%
|
||||
select(-species_id) %>%
|
||||
left_join(records_ids, by = "fullname") %>%
|
||||
relocate(species_id, .after = ref) %>%
|
||||
mutate(source = case_when(!is.na(species_id) ~ "LPSN",
|
||||
source %unlike% "manual" ~ "CoL",
|
||||
TRUE ~ source))
|
||||
|
||||
# Merge synonyms ----------------------------------------------------------
|
||||
|
||||
@@ -377,41 +392,6 @@ MOs.old <- microorganisms.old %>%
|
||||
# clean up
|
||||
df_remove_nonASCII()
|
||||
|
||||
# Keep old codes for translation ------------------------------------------
|
||||
|
||||
# add removed microbial IDs to the internal translation table so old package versions keep working
|
||||
# MOs.translation <- microorganisms %>%
|
||||
# filter(!mo %in% MOs$mo) %>%
|
||||
# select(mo, fullname) %>%
|
||||
# left_join(new_synonyms) %>%
|
||||
# left_join(MOs %>% transmute(fullname_new = fullname, mo2 = as.character(mo))) %>%
|
||||
# select(mo_old = mo, mo_new = mo2) %>%
|
||||
# distinct()
|
||||
# MOs.translation <- AMR:::microorganisms.translation %>%
|
||||
# left_join(MOs.translation %>% select(mo_new_update = mo_new, mo_new = mo_old)) %>%
|
||||
# mutate(mo_new = as.character(ifelse(!is.na(mo_new_update), mo_new_update, mo_new))) %>%
|
||||
# select(-mo_new_update) %>%
|
||||
# bind_rows(
|
||||
# # old IDs used in microorganisms.codes must put in here as well
|
||||
# microorganisms.codes %>%
|
||||
# filter(!mo %in% MOs$mo) %>%
|
||||
# transmute(mo_old = mo, fullname = mo_name(mo)) %>%
|
||||
# left_join(MOs.old %>%
|
||||
# select(fullname, fullname_new)) %>%
|
||||
# left_join(MOs %>%
|
||||
# select(mo_new = mo, fullname_new = fullname)) %>%
|
||||
# transmute(mo_old = as.character(mo_old), mo_new)) %>%
|
||||
# arrange(mo_old) %>%
|
||||
# filter(mo_old != mo_new,
|
||||
# !mo_old %in% MOs$mo) %>%
|
||||
# left_join(., .,
|
||||
# by = c("mo_new" = "mo_old"),
|
||||
# suffix = c("", ".2")) %>%
|
||||
# mutate(mo_new = ifelse(!is.na(mo_new.2), mo_new.2, mo_new)) %>%
|
||||
# distinct(mo_old, mo_new) %>%
|
||||
# # clean up
|
||||
# df_remove_nonASCII()
|
||||
|
||||
message("microorganisms new: ", sum(!MOs$fullname %in% c(microorganisms$fullname, MOs.old$fullname)))
|
||||
message("microorganisms renamed: ", sum(!MOs.old$fullname %in% microorganisms.old$fullname))
|
||||
|
||||
@@ -420,33 +400,49 @@ message("microorganisms renamed: ", sum(!MOs.old$fullname %in% microorganisms.ol
|
||||
|
||||
# class <mo>
|
||||
class(MOs$mo) <- c("mo", "character")
|
||||
class(MOs.translation$mo_new) <- c("mo", "character")
|
||||
|
||||
microorganisms <- MOs
|
||||
microorganisms.old <- MOs.old
|
||||
# microorganisms.translation <- MOs.translation
|
||||
|
||||
# --- Moraxella catarrhalis was named Branhamella catarrhalis (Catlin, 1970), but this is unaccepted in clinical microbiology
|
||||
# we keep them both
|
||||
microorganisms <- microorganisms %>%
|
||||
bind_rows(microorganisms %>%
|
||||
filter(fullname == "Branhamella catarrhalis") %>%
|
||||
mutate(mo = "B_MRXLL_CTRR",
|
||||
fullname = "Moraxella catarrhalis",
|
||||
genus = "Moraxella",
|
||||
ref = "Henriksen et al., 1968",
|
||||
species_id = "a374f6f0868e05f9c0f5077b60ee0a6c",
|
||||
snomed = as.list(24226003))) %>%
|
||||
arrange(fullname) %>%
|
||||
df_remove_nonASCII()
|
||||
microorganisms.old <- microorganisms.old %>%
|
||||
filter(fullname != "Moraxella catarrhalis")
|
||||
# ---
|
||||
|
||||
# (this would be a great moment to run data-raw/snomed.R as well)
|
||||
|
||||
# on the server, do:
|
||||
usethis::use_data(microorganisms, overwrite = TRUE, version = 2, compress = "xz")
|
||||
usethis::use_data(microorganisms.old, overwrite = TRUE, version = 2)
|
||||
# saveRDS(microorganisms.translation, file = "data-raw/microorganisms.translation.rds", version = 2)
|
||||
usethis::use_data(microorganisms.old, overwrite = TRUE, version = 2, compress = "xz")
|
||||
rm(microorganisms)
|
||||
rm(microorganisms.old)
|
||||
rm(microorganisms.translation)
|
||||
# to save microorganisms.translation internally to the package
|
||||
devtools::load_all(".")
|
||||
source("data-raw/_internals.R")
|
||||
|
||||
# DON'T FORGET TO UPDATE R/globals.R!
|
||||
|
||||
# load new data sets
|
||||
devtools::load_all(".")
|
||||
|
||||
# reset previously changed mo codes
|
||||
rsi_translation$mo <- as.mo(rsi_translation$mo, language = NULL)
|
||||
usethis::use_data(rsi_translation, overwrite = TRUE, version = 2)
|
||||
usethis::use_data(rsi_translation, overwrite = TRUE, version = 2, compress = "xz")
|
||||
rm(rsi_translation)
|
||||
|
||||
microorganisms.codes$mo <- as.mo(microorganisms.codes$mo, language = NULL)
|
||||
usethis::use_data(microorganisms.codes, overwrite = TRUE, version = 2)
|
||||
# new NAs introduced?
|
||||
any(is.na(microorganisms.codes$mo))
|
||||
usethis::use_data(microorganisms.codes, overwrite = TRUE, version = 2, compress = "xz")
|
||||
rm(microorganisms.codes)
|
||||
|
||||
example_isolates$mo <- as.mo(example_isolates$mo, language = NULL)
|
||||
|
||||
@@ -78,4 +78,4 @@ writeLines(contents, "R/aa_helper_pm_functions.R")
|
||||
|
||||
# after this, comment out:
|
||||
# pm_left_join() since we use a faster version
|
||||
# pm_group_split() since we don't use it and it relies on R 3.5.0 for the use of ...length(), which is hard to support with C++ code
|
||||
# pm_group_split() since we don't use it and it relies on R 3.5.0 for the use of ...length(), which is hard to support without C++ code
|
||||
|
||||
+1
-1
@@ -1 +1 @@
|
||||
1a7fe52f8185c9bb2c470712863d1887
|
||||
67a83b234f25a303c7944222bea47d73
|
||||
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
@@ -754,6 +754,8 @@
|
||||
"EUCAST 2021" "MIC" "Staphylococcus saccharolyticus" "Imipenem/relebactam" "Anaerobes, Grampositive" 2 2 FALSE
|
||||
"EUCAST 2021" "MIC" "Viridans Group Streptococcus (VGS)" "Imipenem/relebactam" "Viridans group streptococci" 2 2 FALSE
|
||||
"EUCAST 2021" "MIC" "(unknown name)" "Imipenem/relebactam" "PK PD breakpoints" 2 2 FALSE
|
||||
"EUCAST 2021" "DISK" "Morganellaceae" "Imipenem" "Enterobacterales" "10ug" 50 19 FALSE
|
||||
"EUCAST 2021" "MIC" "Morganellaceae" "Imipenem" "Enterobacterales" 0.001 4 FALSE
|
||||
"EUCAST 2021" "DISK" "Enterobacterales" "Imipenem" "Enterobacterales" "10ug" 22 19 FALSE
|
||||
"EUCAST 2021" "MIC" "Enterobacterales" "Imipenem" "Enterobacterales" 2 4 FALSE
|
||||
"EUCAST 2021" "DISK" "Acinetobacter" "Imipenem" "Acinetobacter" "10ug" 24 21 FALSE
|
||||
@@ -2542,6 +2544,8 @@
|
||||
"EUCAST 2020" "MIC" "Staphylococcus saccharolyticus" "Imipenem/relebactam" "Anaerobes, Grampositive" 2 2 FALSE
|
||||
"EUCAST 2020" "MIC" "Viridans Group Streptococcus (VGS)" "Imipenem/relebactam" "Viridans group streptococci" 2 2 FALSE
|
||||
"EUCAST 2020" "MIC" "(unknown name)" "Imipenem/relebactam" "PK PD breakpoints" 2 2 FALSE
|
||||
"EUCAST 2020" "DISK" "Morganellaceae" "Imipenem" "Enterobacterales" "10ug" 50 19 FALSE
|
||||
"EUCAST 2020" "MIC" "Morganellaceae" "Imipenem" "Enterobacterales" 0.001 4 FALSE
|
||||
"EUCAST 2020" "DISK" "Enterobacterales" "Imipenem" "Enterobacterales" "10ug" 22 17 FALSE
|
||||
"EUCAST 2020" "MIC" "Enterobacterales" "Imipenem" "Enterobacterales" 2 4 FALSE
|
||||
"EUCAST 2020" "DISK" "Acinetobacter" "Imipenem" "Acinetobacter" "10ug" 24 21 FALSE
|
||||
|
||||
+6
-1
@@ -40,6 +40,7 @@ vctr <- unique(unlist(strsplit(c(microorganisms$fullname, microorganisms.old$ful
|
||||
vctr <- tolower(vctr[vctr %like% "^[a-z]+$"])
|
||||
|
||||
# remove all parts of the name that are no valid values in genera, species or subspecies
|
||||
# this takes ~20 seconds
|
||||
snomed <- snomed %>%
|
||||
mutate(fullname = vapply(FUN.VALUE = character(1),
|
||||
# split on space and/or comma
|
||||
@@ -53,6 +54,8 @@ snomed_keep <- snomed %>%
|
||||
group_by(fullname_lower = fullname) %>%
|
||||
summarise(snomed = list(snomed))
|
||||
|
||||
message(nrow(snomed_keep), " MO's will get a SNOMED code.")
|
||||
|
||||
# save to microorganisms data set
|
||||
microorganisms <- microorganisms %>%
|
||||
# remove old snomed
|
||||
@@ -64,6 +67,8 @@ microorganisms <- microorganisms %>%
|
||||
# remove dummy var
|
||||
select(-fullname_lower) %>%
|
||||
AMR:::dataset_UTF8_to_ASCII()
|
||||
usethis::use_data(microorganisms, overwrite = TRUE, compress = "xz")
|
||||
|
||||
# don't forget to update the version number in SNOMED_VERSION in ./R/globals.R!
|
||||
|
||||
# usethis::use_data(microorganisms, overwrite = TRUE, version = 2, compress = "xz")
|
||||
|
||||
|
||||
Binary file not shown.
+269
-266
@@ -1,266 +1,269 @@
|
||||
pattern regular_expr case_sensitive affect_ab_name affect_mo_name de nl es it fr pt
|
||||
Coagulase-negative Staphylococcus TRUE TRUE FALSE TRUE Koagulase-negative Staphylococcus Coagulase-negatieve Staphylococcus Staphylococcus coagulasa negativo Staphylococcus negativo coagulasi Staphylococcus à coagulase négative Staphylococcus coagulase negativo
|
||||
Coagulase-positive Staphylococcus TRUE TRUE FALSE TRUE Koagulase-positive Staphylococcus Coagulase-positieve Staphylococcus Staphylococcus coagulasa positivo Staphylococcus positivo coagulasi Staphylococcus à coagulase positif Staphylococcus coagulase positivo
|
||||
Beta-haemolytic Streptococcus TRUE TRUE FALSE TRUE Beta-hämolytischer Streptococcus Beta-hemolytische Streptococcus Streptococcus Beta-hemolítico Streptococcus Beta-emolitico Streptococcus Bêta-hémolytique Streptococcus Beta-hemolítico
|
||||
unknown Gram-negatives TRUE TRUE FALSE TRUE unbekannte Gramnegativen onbekende Gram-negatieven Gram negativos desconocidos Gram negativi sconosciuti Gram négatifs inconnus Gram negativos desconhecidos
|
||||
unknown Gram-positives TRUE TRUE FALSE TRUE unbekannte Grampositiven onbekende Gram-positieven Gram positivos desconocidos Gram positivi sconosciuti Gram positifs inconnus Gram positivos desconhecidos
|
||||
unknown fungus TRUE TRUE FALSE TRUE unbekannter Pilze onbekende schimmel hongo desconocido fungo sconosciuto champignon inconnu fungo desconhecido
|
||||
unknown yeast TRUE TRUE FALSE TRUE unbekannte Hefe onbekende gist levadura desconocida lievito sconosciuto levure inconnue levedura desconhecida
|
||||
unknown name TRUE TRUE FALSE TRUE unbekannte Name onbekende naam nombre desconocido nome sconosciuto nom inconnu nome desconhecido
|
||||
unknown kingdom TRUE TRUE FALSE TRUE unbekanntes Reich onbekend koninkrijk reino desconocido regno sconosciuto règme inconnu reino desconhecido
|
||||
unknown phylum TRUE TRUE FALSE TRUE unbekannter Stamm onbekend fylum filo desconocido phylum sconosciuto embranchement inconnu filo desconhecido
|
||||
unknown class TRUE TRUE FALSE TRUE unbekannte Klasse onbekende klasse clase desconocida classe sconosciuta classe inconnue classe desconhecida
|
||||
unknown order TRUE TRUE FALSE TRUE unbekannte Ordnung onbekende orde orden desconocido ordine sconosciuto ordre inconnu ordem desconhecido
|
||||
unknown family TRUE TRUE FALSE TRUE unbekannte Familie onbekende familie familia desconocida famiglia sconosciuta famille inconnue família desconhecida
|
||||
unknown genus TRUE TRUE FALSE TRUE unbekannte Gattung onbekend geslacht género desconocido genere sconosciuto genre inconnu gênero desconhecido
|
||||
unknown species TRUE TRUE FALSE TRUE unbekannte Art onbekende soort especie desconocida specie sconosciute espèce inconnue espécies desconhecida
|
||||
unknown subspecies TRUE TRUE FALSE TRUE unbekannte Unterart onbekende ondersoort subespecie desconocida sottospecie sconosciute sous-espèce inconnue subespécies desconhecida
|
||||
unknown rank TRUE TRUE FALSE TRUE unbekannter Rang onbekende rang rango desconocido grado sconosciuto rang inconnu classificação desconhecido
|
||||
CoNS FALSE TRUE FALSE TRUE KNS CNS SCN
|
||||
CoPS FALSE TRUE FALSE TRUE KPS CPS SCP
|
||||
Gram-negative TRUE TRUE FALSE FALSE Gramnegativ Gram-negatief Gram negativo Gram negativo Gram négatif Gram negativo
|
||||
Gram-positive TRUE TRUE FALSE FALSE Grampositiv Gram-positief Gram positivo Gram positivo Gram positif Gram positivo
|
||||
^Bacteria$ TRUE TRUE FALSE FALSE Bakterien Bacteriën Bacterias Batteri Bactéries Bactérias
|
||||
^Fungi$ TRUE TRUE FALSE FALSE Pilze Schimmels Hongos Funghi Champignons Fungos
|
||||
^Yeasts$ TRUE TRUE FALSE FALSE Hefen Gisten Levaduras Lieviti Levures Leveduras
|
||||
^Protozoa$ TRUE TRUE FALSE FALSE Protozoen Protozoën Protozoarios Protozoi Protozoaires Protozoários
|
||||
biogroup TRUE TRUE FALSE FALSE Biogruppe biogroep biogrupo biogruppo biogroupe biogrupo
|
||||
biotype TRUE TRUE FALSE FALSE Biotyp biotipo biotipo biótipo
|
||||
vegetative TRUE TRUE FALSE FALSE vegetativ vegetatief vegetativo vegetativo végétatif vegetativo
|
||||
([([ ]*?)group TRUE TRUE FALSE FALSE \\1Gruppe \\1groep \\1grupo \\1gruppo \\1groupe \\1grupo
|
||||
([([ ]*?)Group TRUE TRUE FALSE FALSE \\1Gruppe \\1Groep \\1Grupo \\1Gruppo \\1Groupe \\1Grupo
|
||||
no .*growth TRUE FALSE FALSE FALSE keine? .*wachstum geen .*groei no .*crecimientonon sem .*crescimento pas .*croissance sem .*crescimento
|
||||
no|not TRUE FALSE FALSE FALSE keine? geen|niet no|sin sem non sem
|
||||
Susceptible TRUE FALSE FALSE FALSE Empfindlich Gevoelig Susceptible
|
||||
Intermediate TRUE FALSE FALSE FALSE Mittlere Intermediair Intermedio
|
||||
Incr. exposure TRUE FALSE FALSE FALSE Empfindlich, erh Belastung 'Incr. exposure' 'Incr. exposure'
|
||||
Resistant TRUE FALSE FALSE FALSE Resistent Resistent Resistente
|
||||
antibiotic TRUE TRUE FALSE FALSE Antibiotikum antibioticum antibiótico
|
||||
Antibiotic TRUE TRUE FALSE FALSE Antibiotikum Antibioticum Antibiótico
|
||||
Drug TRUE TRUE FALSE FALSE Medikament Middel Fármaco
|
||||
drug TRUE TRUE FALSE FALSE Medikament middel fármaco
|
||||
Frequency FALSE TRUE FALSE FALSE Zahl Aantal
|
||||
Minimum Inhibitory Concentration (mg/L) FALSE FALSE FALSE FALSE Minimale Hemm-Konzentration (mg/L) Minimale inhiberende concentratie (mg/L)
|
||||
Disk diffusion diameter (mm) FALSE FALSE FALSE FALSE Durchmesser der Scheibenzone (mm) Diameter diskzone (mm)
|
||||
Antimicrobial Interpretation FALSE FALSE FALSE FALSE Antimikrobielle Auswertung Antimicrobiële interpretatie
|
||||
4-aminosalicylic acid FALSE TRUE TRUE FALSE 4-Aminosalicylsäure 4-aminosalicylzuur Ácido 4-aminosalicílico
|
||||
Adefovir dipivoxil FALSE TRUE TRUE FALSE Adefovir Dipivoxil Adefovir Adefovir dipivoxil
|
||||
Aldesulfone sodium FALSE TRUE TRUE FALSE Aldesulfon-Natrium Aldesulfon Aldesulfona sódica
|
||||
Amikacin FALSE TRUE TRUE FALSE Amikacin Amikacine Amikacina
|
||||
Amoxicillin FALSE TRUE TRUE FALSE Amoxicillin Amoxicilline Amoxicilina
|
||||
Amoxicillin/beta-lactamase inhibitor FALSE TRUE TRUE FALSE Amoxicillin/Beta-Lactamase-Hemmer Amoxicilline/enzymremmer amoxicilina/inhib. de la beta-lactamasa
|
||||
Amphotericin B FALSE TRUE TRUE FALSE Amphotericin B Amfotericine B Anfotericina B
|
||||
Ampicillin FALSE TRUE TRUE FALSE Ampicillin Ampicilline Ampicilina
|
||||
Ampicillin/beta-lactamase inhibitor FALSE TRUE TRUE FALSE Ampicillin/Beta-Laktamase-Hemmer Ampicilline/enzymremmer Ampicilina/inhib. de la betalactamasa
|
||||
Anidulafungin FALSE TRUE TRUE FALSE Anidulafungin Anidulafungine Anidulafungina
|
||||
Azidocillin FALSE TRUE TRUE FALSE Azidocillin Azidocilline Azidocilina
|
||||
Azithromycin FALSE TRUE TRUE FALSE Azithromycin Azitromycine Azitromicina
|
||||
Azlocillin FALSE TRUE TRUE FALSE Azlocillin Azlocilline Azlocilina
|
||||
Bacampicillin FALSE TRUE TRUE FALSE Bacampicillin Bacampicilline Bacampicilina
|
||||
Bacitracin FALSE TRUE TRUE FALSE Bacitracin Bacitracine Bacitracina
|
||||
Benzathine benzylpenicillin FALSE TRUE TRUE FALSE Benzathin-Benzylpenicillin Benzylpenicillinebenzathine Bencilpenicilina benzatínica
|
||||
Benzathine phenoxymethylpenicillin FALSE TRUE TRUE FALSE Benzathin-Phenoxymethylpenicillin Fenoxymethylpenicillinebenzathine Fenoximetilpenicilina benzatínica
|
||||
Benzylpenicillin FALSE TRUE TRUE FALSE Benzylpenicillin Benzylpenicilline Bencilpenicilina
|
||||
Calcium aminosalicylate FALSE TRUE TRUE FALSE Kalzium-Aminosalicylat Aminosalicylzuur Aminosalicilato de calcio
|
||||
Capreomycin FALSE TRUE TRUE FALSE Capreomycin Capreomycine Capreomicina
|
||||
Carbenicillin FALSE TRUE TRUE FALSE Carbenicillin Carbenicilline Carbenicilina
|
||||
Carindacillin FALSE TRUE TRUE FALSE Carindacillin Carindacilline Carindacilina
|
||||
Caspofungin FALSE TRUE TRUE FALSE Caspofungin Caspofungine Caspofungina
|
||||
Ce(f|ph)acetrile TRUE TRUE TRUE FALSE Cefacetril Cefacetril Cefacetrilo
|
||||
Ce(f|ph)alotin TRUE TRUE TRUE FALSE Cefalotin Cefalotine Cefalotina
|
||||
Ce(f|ph)amandole TRUE TRUE TRUE FALSE Cefamandol Cefamandol Cefamandole
|
||||
Ce(f|ph)apirin TRUE TRUE TRUE FALSE Cefapirin Cefapirine Cefapirina
|
||||
Ce(f|ph)azedone TRUE TRUE TRUE FALSE Cefazedon Cefazedon Cefazedona
|
||||
Ce(f|ph)azolin TRUE TRUE TRUE FALSE Cefazolin Cefazoline Cefazolina
|
||||
Ce(f|ph)alothin TRUE TRUE TRUE FALSE Cefalothin Cefalotine Cefalotina
|
||||
Ce(f|ph)alexin TRUE TRUE TRUE FALSE Cefalexin Cefalexine Cefalexina
|
||||
Ce(f|ph)epime TRUE TRUE TRUE FALSE Cefepim Cefepim Cefepime
|
||||
Ce(f|ph)ixime TRUE TRUE TRUE FALSE Cefixim Cefixim Cefixima
|
||||
Ce(f|ph)menoxime TRUE TRUE TRUE FALSE Cefmenoxim Cefmenoxim Cefmenoxima
|
||||
Ce(f|ph)metazole TRUE TRUE TRUE FALSE Cefmetazol Cefmetazol Cefmetazol
|
||||
Ce(f|ph)odizime TRUE TRUE TRUE FALSE Cefodizim Cefodizim Cefodizima
|
||||
Ce(f|ph)onicid TRUE TRUE TRUE FALSE Cefonicid Cefonicide Cefonicid
|
||||
Ce(f|ph)operazone TRUE TRUE TRUE FALSE Cefoperazon Cefoperazon Cefoperazona
|
||||
Ce(f|ph)operazone/beta-lactamase inhibitor TRUE TRUE TRUE FALSE Cefoperazon/Beta-Lactamase-Hemmer Cefoperazon/enzymremmer Cefoperazona/inhib. de la betalactamasa
|
||||
Ce(f|ph)otaxime TRUE TRUE TRUE FALSE Cefotaxim Cefotaxim Cefotaxima
|
||||
Ce(f|ph)oxitin TRUE TRUE TRUE FALSE Cefoxitin Cefoxitine Cefoxitina
|
||||
Ce(f|ph)pirome TRUE TRUE TRUE FALSE Cefpirom Cefpirom Cefpirome
|
||||
Ce(f|ph)podoxime TRUE TRUE TRUE FALSE Cefpodoxim Cefpodoxim Cefpodoxima
|
||||
Ce(f|ph)radine TRUE TRUE TRUE FALSE Cefradin Cefradine Cefradina
|
||||
Ce(f|ph)sulodin TRUE TRUE TRUE FALSE Cefsulodin Cefsulodine Cefsulodina
|
||||
Ce(f|ph)tazidime TRUE TRUE TRUE FALSE Ceftazidim Ceftazidim Ceftazidima
|
||||
Ce(f|ph)tezole TRUE TRUE TRUE FALSE Ceftezol Ceftezol Ceftezol
|
||||
Ce(f|ph)tizoxime TRUE TRUE TRUE FALSE Ceftizoxim Ceftizoxim Ceftizoxima
|
||||
Ce(f|ph)triaxone TRUE TRUE TRUE FALSE Ceftriaxon Ceftriaxon Ceftriaxona
|
||||
Ce(f|ph)uroxime TRUE TRUE TRUE FALSE Cefuroxim Cefuroxim Cefuroxima
|
||||
Ce(f|ph)uroxime/metronidazole TRUE TRUE TRUE FALSE Cefuroxim/Metronidazol Cefuroxim/andere antibacteriele middelen Cefuroxima/metronidazol
|
||||
Chloramphenicol FALSE TRUE TRUE FALSE Chloramphenicol Chlooramfenicol Cloranfenicol
|
||||
Chlortetracycline FALSE TRUE TRUE FALSE Chlortetracyclin Chloortetracycline Clortetraciclina
|
||||
Cinoxacin FALSE TRUE TRUE FALSE Cinoxacin Cinoxacine Cinoxacina
|
||||
Ciprofloxacin FALSE TRUE TRUE FALSE Ciprofloxacin Ciprofloxacine Ciprofloxacina
|
||||
Clarithromycin FALSE TRUE TRUE FALSE Clarithromycin Claritromycine Claritromicina
|
||||
Clavulanic acid FALSE TRUE TRUE FALSE Clavulansäure Clavulaanzuur Ácido clavulánico
|
||||
clavulanic acid FALSE TRUE TRUE FALSE Clavulansäure clavulaanzuur ácido clavulánico
|
||||
Clindamycin FALSE TRUE TRUE FALSE Clindamycin Clindamycine Clindamicina
|
||||
Clometocillin FALSE TRUE TRUE FALSE Clometocillin Clometocilline Clometocilina
|
||||
Clotrimazole FALSE TRUE TRUE FALSE Clotrimazol Clotrimazol Clotrimazol
|
||||
Cloxacillin FALSE TRUE TRUE FALSE Cloxacillin Cloxacilline Cloxacilina
|
||||
Colistin FALSE TRUE TRUE FALSE Colistin Colistine Colistina
|
||||
Dapsone FALSE TRUE TRUE FALSE Dapson Dapson Dapsona
|
||||
Daptomycin FALSE TRUE TRUE FALSE Daptomycin Daptomycine Daptomicina
|
||||
Dibekacin FALSE TRUE TRUE FALSE Dibekacin Dibekacine Dibekacina
|
||||
Dicloxacillin FALSE TRUE TRUE FALSE Dicloxacillin Dicloxacilline Dicloxacilina
|
||||
Dirithromycin FALSE TRUE TRUE FALSE Dirithromycin Diritromycine Diritromicina
|
||||
Econazole FALSE TRUE TRUE FALSE Econazol Econazol Econazol
|
||||
Enoxacin FALSE TRUE TRUE FALSE Enoxacin Enoxacine Enoxacina
|
||||
Epicillin FALSE TRUE TRUE FALSE Epicillin Epicilline Epicilina
|
||||
Erythromycin FALSE TRUE TRUE FALSE Erythromycin Erytromycine Eritromicina
|
||||
Ethambutol/isoniazid FALSE TRUE TRUE FALSE Ethambutol/Isoniazid Ethambutol/isoniazide Etambutol/isoniazida
|
||||
Fleroxacin FALSE TRUE TRUE FALSE Fleroxacin Fleroxacine Fleroxacina
|
||||
Flucloxacillin FALSE TRUE TRUE FALSE Flucloxacillin Flucloxacilline Flucloxacilina
|
||||
Fluconazole FALSE TRUE TRUE FALSE Fluconazol Fluconazol Fluconazol
|
||||
Flucytosine FALSE TRUE TRUE FALSE Flucytosin Fluorocytosine Flucitosina
|
||||
Flurithromycin FALSE TRUE TRUE FALSE Flurithromycin Fluritromycine Fluritromicina
|
||||
Fosfomycin FALSE TRUE TRUE FALSE Fosfomycin Fosfomycine Fosfomicina
|
||||
Fusidic acid FALSE TRUE TRUE FALSE Fusidinsäure Fusidinezuur Ácido fusídico
|
||||
Gatifloxacin FALSE TRUE TRUE FALSE Gatifloxacin Gatifloxacine Gatifloxacina
|
||||
Gemifloxacin FALSE TRUE TRUE FALSE Gemifloxacin Gemifloxacine Gemifloxacina
|
||||
Gentamicin FALSE TRUE TRUE FALSE Gentamicin Gentamicine Gentamicina
|
||||
Grepafloxacin FALSE TRUE TRUE FALSE Grepafloxacin Grepafloxacine Grepafloxacina
|
||||
Hachimycin FALSE TRUE TRUE FALSE Hachimycin Hachimycine Hachimycin
|
||||
Hetacillin FALSE TRUE TRUE FALSE Hetacillin Hetacilline Hetacilina
|
||||
Imipenem/cilastatin FALSE TRUE TRUE FALSE Imipenem/Cilastatin Imipenem/enzymremmer Imipenem/cilastatina
|
||||
Inosine pranobex FALSE TRUE TRUE FALSE Inosin-Pranobex Inosiplex Inosina pranobex
|
||||
Isepamicin FALSE TRUE TRUE FALSE Isepamicin Isepamicine Isepamicina
|
||||
Isoconazole FALSE TRUE TRUE FALSE Isoconazol Isoconazol Isoconazol
|
||||
Isoniazid FALSE TRUE TRUE FALSE Isoniazid Isoniazide Isoniazida
|
||||
Itraconazole FALSE TRUE TRUE FALSE Itraconazol Itraconazol Itraconazol
|
||||
Josamycin FALSE TRUE TRUE FALSE Josamycin Josamycine Josamicina
|
||||
Kanamycin FALSE TRUE TRUE FALSE Kanamycin Kanamycine Kanamicina
|
||||
Ketoconazole FALSE TRUE TRUE FALSE Ketoconazol Ketoconazol Ketoconazol
|
||||
Levofloxacin FALSE TRUE TRUE FALSE Levofloxacin Levofloxacine Levofloxacina
|
||||
Lincomycin FALSE TRUE TRUE FALSE Lincomycin Lincomycine Lincomicina
|
||||
Lomefloxacin FALSE TRUE TRUE FALSE Lomefloxacin Lomefloxacine Lomefloxacina
|
||||
Lysozyme FALSE TRUE TRUE FALSE Lysozym Lysozym Lisozima
|
||||
Mandelic acid FALSE TRUE TRUE FALSE Mandelsäure Amandelzuur Ácido mandélico
|
||||
Metampicillin FALSE TRUE TRUE FALSE Metampicillin Metampicilline Metampicilina
|
||||
Meticillin FALSE TRUE TRUE FALSE Meticillin Meticilline Meticilina
|
||||
Metisazone FALSE TRUE TRUE FALSE Metisazon Metisazon Metisazona
|
||||
Metronidazole FALSE TRUE TRUE FALSE Metronidazol Metronidazol Metronidazol
|
||||
Mezlocillin FALSE TRUE TRUE FALSE Mezlocillin Mezlocilline Mezlocilina
|
||||
Micafungin FALSE TRUE TRUE FALSE Micafungin Micafungine Micafungina
|
||||
Miconazole FALSE TRUE TRUE FALSE Miconazol Miconazol Miconazol
|
||||
Midecamycin FALSE TRUE TRUE FALSE Midecamycin Midecamycine Midecamicina
|
||||
Miocamycin FALSE TRUE TRUE FALSE Miocamycin Miocamycine Miocamycin
|
||||
Moxifloxacin FALSE TRUE TRUE FALSE Moxifloxacin Moxifloxacine Moxifloxacina
|
||||
Mupirocin FALSE TRUE TRUE FALSE Mupirocin Mupirocine Mupirocina
|
||||
Nalidixic acid FALSE TRUE TRUE FALSE Nalidixinsäure Nalidixinezuur Ácido nalidíxico
|
||||
Neomycin FALSE TRUE TRUE FALSE Neomycin Neomycine Neomicina
|
||||
Netilmicin FALSE TRUE TRUE FALSE Netilmicin Netilmicine Netilmicina
|
||||
Nitrofurantoin FALSE TRUE TRUE FALSE Nitrofurantoin Nitrofurantoine Nitrofurantoína
|
||||
Norfloxacin FALSE TRUE TRUE FALSE Norfloxacin Norfloxacine Norfloxacina
|
||||
Novobiocin FALSE TRUE TRUE FALSE Novobiocin Novobiocine Novobiocina
|
||||
Nystatin FALSE TRUE TRUE FALSE Nystatin Nystatine Nistatina
|
||||
Ofloxacin FALSE TRUE TRUE FALSE Ofloxacin Ofloxacine Ofloxacina
|
||||
Oleandomycin FALSE TRUE TRUE FALSE Oleandomycin Oleandomycine Oleandomicina
|
||||
Ornidazole FALSE TRUE TRUE FALSE Ornidazol Ornidazol Ornidazol
|
||||
Oxacillin FALSE TRUE TRUE FALSE Oxacillin Oxacilline Oxacilina
|
||||
Oxolinic acid FALSE TRUE TRUE FALSE Oxolinsäure Oxolinezuur Ácido oxolínico
|
||||
Oxytetracycline FALSE TRUE TRUE FALSE Oxytetracyclin Oxytetracycline Oxitetraciclina
|
||||
Pazufloxacin FALSE TRUE TRUE FALSE Pazufloxacin Pazufloxacine Pazufloxacina
|
||||
Pefloxacin FALSE TRUE TRUE FALSE Pefloxacin Pefloxacine Pefloxacina
|
||||
Penamecillin FALSE TRUE TRUE FALSE Penamecillin Penamecilline Penamecilina
|
||||
Penicillin FALSE TRUE TRUE FALSE Penicillin Penicilline Penicilina
|
||||
Pheneticillin FALSE TRUE TRUE FALSE Pheneticillin Feneticilline Feneticilina
|
||||
Phenoxymethylpenicillin FALSE TRUE TRUE FALSE Phenoxymethylpenicillin Fenoxymethylpenicilline Fenoximetilpenicilina
|
||||
Pipemidic acid FALSE TRUE TRUE FALSE Pipemidinsäure Pipemidinezuur Ácido pipemídico
|
||||
Piperacillin FALSE TRUE TRUE FALSE Piperacillin Piperacilline Piperacilina
|
||||
Piperacillin/beta-lactamase inhibitor FALSE TRUE TRUE FALSE Piperacillin/Beta-Lactamase-Hemmer Piperacilline/enzymremmer Piperacilina/inhib. de la betalactamasa
|
||||
Piromidic acid FALSE TRUE TRUE FALSE Piromidinsäure Piromidinezuur Ácido piromídico
|
||||
Pivampicillin FALSE TRUE TRUE FALSE Pivampicillin Pivampicilline Pivampicilina
|
||||
Polymyxin B FALSE TRUE TRUE FALSE Polymyxin B Polymyxine B Polimixina B
|
||||
Posaconazole FALSE TRUE TRUE FALSE Posaconazol Posaconazol Posaconazol
|
||||
Pristinamycin FALSE TRUE TRUE FALSE Pristinamycin Pristinamycine Pristinamicina
|
||||
Procaine benzylpenicillin FALSE TRUE TRUE FALSE Procain-Benzylpenicillin Benzylpenicillineprocaine Bencilpenicilina procaína
|
||||
Propicillin FALSE TRUE TRUE FALSE Propicillin Propicilline Propicilina
|
||||
Prulifloxacin FALSE TRUE TRUE FALSE Prulifloxacin Prulifloxacine Prulifloxacina
|
||||
Quinupristin/dalfopristin FALSE TRUE TRUE FALSE Quinupristin/Dalfopristin Quinupristine/dalfopristine Quinupristina/dalfopristina
|
||||
Ribostamycin FALSE TRUE TRUE FALSE Ribostamycin Ribostamycine Ribostamicina
|
||||
Rifabutin FALSE TRUE TRUE FALSE Rifabutin Rifabutine Rifabutina
|
||||
Rifampicin FALSE TRUE TRUE FALSE Rifampicin Rifampicine Rifampicina
|
||||
Rifampicin/pyrazinamide/ethambutol/isoniazid FALSE TRUE TRUE FALSE Rifampicin/Pyrazinamid/Ethambutol/Isoniazid Rifampicine/pyrazinamide/ethambutol/isoniazide Rifampicina/pirazinamida/etambutol/isoniazida
|
||||
Rifampicin/pyrazinamide/isoniazid FALSE TRUE TRUE FALSE Rifampicin/Pyrazinamid/Isoniazid Rifampicine/pyrazinamide/isoniazide Rifampicina/pirazinamida/isoniazida
|
||||
Rifampicin/isoniazid FALSE TRUE TRUE FALSE Rifampicin/Isoniazid Rifampicine/isoniazide Rifampicina/isoniazida
|
||||
Rifamycin FALSE TRUE TRUE FALSE Rifamycin Rifamycine Rifamicina
|
||||
Rifaximin FALSE TRUE TRUE FALSE Rifaximin Rifaximine Rifaximina
|
||||
Rokitamycin FALSE TRUE TRUE FALSE Rokitamycin Rokitamycine Rokitamicina
|
||||
Rosoxacin FALSE TRUE TRUE FALSE Rosoxacin Rosoxacine Rosoxacina
|
||||
Roxithromycin FALSE TRUE TRUE FALSE Roxithromycin Roxitromycine Roxitromicina
|
||||
Rufloxacin FALSE TRUE TRUE FALSE Rufloxacin Rufloxacine Rufloxacina
|
||||
Sisomicin FALSE TRUE TRUE FALSE Sisomicin Sisomicine Sisomicina
|
||||
Sodium aminosalicylate FALSE TRUE TRUE FALSE Natrium-Aminosalicylat Aminosalicylzuur Aminosalicilato de sodio
|
||||
Sparfloxacin FALSE TRUE TRUE FALSE Sparfloxacin Sparfloxacine Esparfloxacina
|
||||
Spectinomycin FALSE TRUE TRUE FALSE Spectinomycin Spectinomycine Espectinomicina
|
||||
Spiramycin FALSE TRUE TRUE FALSE Spiramycin Spiramycine Espiramicina
|
||||
Spiramycin/metronidazole FALSE TRUE TRUE FALSE Spiramycin/Metronidazol Spiramycine/metronidazol Espiramicina/metronidazol
|
||||
Staphylococcus immunoglobulin FALSE TRUE TRUE FALSE Staphylococcus-Immunoglobulin Stafylokokkenimmunoglobuline Inmunoglobulina estafilocócica
|
||||
Streptoduocin FALSE TRUE TRUE FALSE Streptoduocin Streptoduocine Estreptoduocina
|
||||
Streptomycin FALSE TRUE TRUE FALSE Streptomycin Streptomycine Estreptomicina
|
||||
Streptomycin/isoniazid FALSE TRUE TRUE FALSE Streptomycin/Isoniazid Streptomycine/isoniazide Estreptomicina/isoniazida
|
||||
Sulbenicillin FALSE TRUE TRUE FALSE Sulbenicillin Sulbenicilline Sulbenicilina
|
||||
Sulfadiazine/tetroxoprim FALSE TRUE TRUE FALSE Sulfadiazin/Tetroxoprim Sulfadiazine/tetroxoprim Sulfadiazina/tetroxoprima
|
||||
Sulfadiazine/trimethoprim FALSE TRUE TRUE FALSE Sulfadiazin/Trimethoprim Sulfadiazine/trimethoprim Sulfadiazina/trimetoprima
|
||||
Sulfadimidine/trimethoprim FALSE TRUE TRUE FALSE Sulfadimidin/Trimethoprim Sulfadimidine/trimethoprim Sulfadimidina/trimetoprima
|
||||
Sulfafurazole FALSE TRUE TRUE FALSE Sulfafurazol Sulfafurazol Sulfafurazol
|
||||
Sulfaisodimidine FALSE TRUE TRUE FALSE Sulfaisodimidin Sulfisomidine Sulfaisodimidina
|
||||
Sulfalene FALSE TRUE TRUE FALSE Sulfalene Sulfaleen Sulfaleno
|
||||
Sulfamazone FALSE TRUE TRUE FALSE Sulfamazon Sulfamazon Sulfamazona
|
||||
Sulfamerazine/trimethoprim FALSE TRUE TRUE FALSE Sulfamerazin/Trimethoprim Sulfamerazine/trimethoprim Sulfamerazina/trimetoprima
|
||||
Sulfamethizole FALSE TRUE TRUE FALSE Sulfamethizol Sulfamethizol Sulfametozol
|
||||
Sulfamethoxazole FALSE TRUE TRUE FALSE Sulfamethoxazol Sulfamethoxazol Sulfametoxazol
|
||||
Sulfamethoxazole/trimethoprim FALSE TRUE TRUE FALSE Sulfamethoxazol/Trimethoprim Sulfamethoxazol/trimethoprim Sulfametoxazol/trimetoprima
|
||||
Sulfametoxydiazine FALSE TRUE TRUE FALSE Sulfametoxydiazin Sulfamethoxydiazine Sulfametoxidiazina
|
||||
Sulfametrole/trimethoprim FALSE TRUE TRUE FALSE Sulfametrole/Trimethoprim Sulfametrol/trimethoprim Sulfametrole/trimethoprim
|
||||
Sulfamoxole FALSE TRUE TRUE FALSE Sulfamoxol Sulfamoxol Sulfamoxole
|
||||
Sulfamoxole/trimethoprim FALSE TRUE TRUE FALSE Sulfamoxol/Trimethoprim Sulfamoxol/trimethoprim Sulfamoxol/trimetoprima
|
||||
Sulfaperin FALSE TRUE TRUE FALSE Sulfaperin Sulfaperine Sulfaproxeno
|
||||
Sulfaphenazole FALSE TRUE TRUE FALSE Sulfaphenazol Sulfafenazol Sulfafenazol
|
||||
Sulfathiazole FALSE TRUE TRUE FALSE Sulfathiazol Sulfathiazol Sulfatiazol
|
||||
Sulfathiourea FALSE TRUE TRUE FALSE Sulfathioharnstoff Sulfathioureum Sulfathiourea
|
||||
Sultamicillin FALSE TRUE TRUE FALSE Sultamicillin Sultamicilline Sultamicilina
|
||||
Talampicillin FALSE TRUE TRUE FALSE Talampicillin Talampicilline Talampicilina
|
||||
Teicoplanin FALSE TRUE TRUE FALSE Teicoplanin Teicoplanine Teicoplanina
|
||||
Telithromycin FALSE TRUE TRUE FALSE Telithromycin Telitromycine Telitromicina
|
||||
Temafloxacin FALSE TRUE TRUE FALSE Temafloxacin Temafloxacine Temafloxacina
|
||||
Temocillin FALSE TRUE TRUE FALSE Temocillin Temocilline Temocilina
|
||||
Tenofovir disoproxil FALSE TRUE TRUE FALSE Tenofovir Disoproxil Tenofovir Tenofovir disoproxil
|
||||
Terizidone FALSE TRUE TRUE FALSE Terizidon Terizidon Terizidona
|
||||
Thiamphenicol FALSE TRUE TRUE FALSE Thiamphenicol Thiamfenicol Tiamfenicol
|
||||
Thioacetazone/isoniazid FALSE TRUE TRUE FALSE Thioacetazon/Isoniazid Thioacetazon/isoniazide Tioacetazona/isoniazida
|
||||
Ticarcillin FALSE TRUE TRUE FALSE Ticarcillin Ticarcilline Ticarcilina
|
||||
Ticarcillin/beta-lactamase inhibitor FALSE TRUE TRUE FALSE Ticarcillin/Beta-Lactamase-Hemmer Ticarcilline/enzymremmer Ticarcilina/inhib. de la betalactamasa
|
||||
Ticarcillin/clavulanic acid FALSE TRUE TRUE FALSE Ticarcillin/Clavulansäure Ticarcilline/clavulaanzuur Ticarcilina/ácido clavulánico
|
||||
Tinidazole FALSE TRUE TRUE FALSE Tinidazol Tinidazol Tinidazol
|
||||
Tobramycin FALSE TRUE TRUE FALSE Tobramycin Tobramycine Tobramicina
|
||||
Trimethoprim/sulfamethoxazole FALSE TRUE TRUE FALSE Trimethoprim/Sulfamethoxazol Cotrimoxazol Trimetoprima/sulfametoxazol
|
||||
Troleandomycin FALSE TRUE TRUE FALSE Troleandomycin Troleandomycine Troleandomicina
|
||||
Trovafloxacin FALSE TRUE TRUE FALSE Trovafloxacin Trovafloxacine Trovafloxacina
|
||||
Vancomycin FALSE TRUE TRUE FALSE Vancomycin Vancomycine Vancomicina
|
||||
Voriconazole FALSE TRUE TRUE FALSE Voriconazol Voriconazol Voriconazol
|
||||
Aminoglycosides FALSE TRUE TRUE FALSE Aminoglykoside Aminoglycosiden Aminoglucósidos
|
||||
Amphenicols FALSE TRUE TRUE FALSE Amphenicole Amfenicolen Anfenicoles
|
||||
Antifungals/antimycotics FALSE TRUE TRUE FALSE Antimykotika/Antimykotika Antifungica/antimycotica Antifúngicos/antimicóticos
|
||||
Antimycobacterials FALSE TRUE TRUE FALSE Antimykobakterielle Mittel Antimycobacteriele middelen Antimicrobianos
|
||||
Beta-lactams/penicillins FALSE TRUE TRUE FALSE Beta-Lactame/Penicilline Beta-lactams/penicillines Beta-lactámicos/penicilinas
|
||||
Cephalosporins (1st gen.) FALSE TRUE TRUE FALSE Cephalosporine (1. Gen.) Cefalosporines (1e gen.) Cefalosporinas (1er gen.)
|
||||
Cephalosporins (2nd gen.) FALSE TRUE TRUE FALSE Cephalosporine (2. Gen.) Cefalosporines (2e gen.) Cefalosporinas (2do gen.)
|
||||
Cephalosporins (3rd gen.) FALSE TRUE TRUE FALSE Cephalosporine (3. Gen.) Cefalosporines (3e gen.) Cefalosporinas (3er gen.)
|
||||
Cephalosporins (4th gen.) FALSE TRUE TRUE FALSE Cephalosporine (4. Gen.) Cefalosporines (4e gen.) Cefalosporinas (4º gen.)
|
||||
Cephalosporins (5th gen.) FALSE TRUE TRUE FALSE Cephalosporine (5. Gen.) Cefalosporines (5e gen.) Cefalosporinas (5º gen.)
|
||||
Cephalosporins (unclassified gen.) FALSE TRUE TRUE FALSE Cephalosporine (unklassifiziert) Cefalosporines (ongeclassificeerd) Cefalosporinas (no clasificado)
|
||||
Cephalosporins FALSE TRUE TRUE FALSE Cephalosporine Cefalosporines Cefalosporinas
|
||||
Glycopeptides FALSE TRUE TRUE FALSE Glykopeptide Glycopeptiden Glicopéptidos
|
||||
Macrolides/lincosamides FALSE TRUE TRUE FALSE Makrolide/Linkosamide Macroliden/lincosamiden Macrólidos/lincosamidas
|
||||
Other antibacterials FALSE TRUE TRUE FALSE Andere Antibiotika Overige antibiotica Otros antibacterianos
|
||||
Polymyxins FALSE TRUE TRUE FALSE Polymyxine Polymyxines Polimixinas
|
||||
Quinolones FALSE TRUE TRUE FALSE Quinolone Quinolonen Quinolonas
|
||||
pattern regular_expr case_sensitive affect_ab_name affect_mo_name de nl es it fr pt da
|
||||
Coagulase-negative Staphylococcus TRUE TRUE FALSE TRUE Koagulase-negative Staphylococcus Coagulase-negatieve Staphylococcus Staphylococcus coagulasa negativo Staphylococcus negativo coagulasi Staphylococcus à coagulase négative Staphylococcus coagulase negativo Koagulase-negative stafylokokker
|
||||
Coagulase-positive Staphylococcus TRUE TRUE FALSE TRUE Koagulase-positive Staphylococcus Coagulase-positieve Staphylococcus Staphylococcus coagulasa positivo Staphylococcus positivo coagulasi Staphylococcus à coagulase positif Staphylococcus coagulase positivo Koagulase-positive stafylokokker
|
||||
Beta-haemolytic Streptococcus TRUE TRUE FALSE TRUE Beta-hämolytischer Streptococcus Beta-hemolytische Streptococcus Streptococcus Beta-hemolítico Streptococcus Beta-emolitico Streptococcus Bêta-hémolytique Streptococcus Beta-hemolítico Beta-haemolytiske streptokokker
|
||||
unknown Gram-negatives TRUE TRUE FALSE TRUE unbekannte Gramnegativen onbekende Gram-negatieven Gram negativos desconocidos Gram negativi sconosciuti Gram négatifs inconnus Gram negativos desconhecidos ukendte Gram-negative
|
||||
unknown Gram-positives TRUE TRUE FALSE TRUE unbekannte Grampositiven onbekende Gram-positieven Gram positivos desconocidos Gram positivi sconosciuti Gram positifs inconnus Gram positivos desconhecidos ukendte Gram-positive
|
||||
unknown fungus TRUE TRUE FALSE TRUE unbekannter Pilze onbekende schimmel hongo desconocido fungo sconosciuto champignon inconnu fungo desconhecido ukendt svamp
|
||||
unknown yeast TRUE TRUE FALSE TRUE unbekannte Hefe onbekende gist levadura desconocida lievito sconosciuto levure inconnue levedura desconhecida ukendt gær
|
||||
unknown name TRUE TRUE FALSE TRUE unbekannte Name onbekende naam nombre desconocido nome sconosciuto nom inconnu nome desconhecido ukendt navn
|
||||
unknown kingdom TRUE TRUE FALSE TRUE unbekanntes Reich onbekend koninkrijk reino desconocido regno sconosciuto règme inconnu reino desconhecido ukendt kongerige
|
||||
unknown phylum TRUE TRUE FALSE TRUE unbekannter Stamm onbekend fylum filo desconocido phylum sconosciuto embranchement inconnu filo desconhecido ukendt stamme
|
||||
unknown class TRUE TRUE FALSE TRUE unbekannte Klasse onbekende klasse clase desconocida classe sconosciuta classe inconnue classe desconhecida ukendt klasse
|
||||
unknown order TRUE TRUE FALSE TRUE unbekannte Ordnung onbekende orde orden desconocido ordine sconosciuto ordre inconnu ordem desconhecido ukendt orden
|
||||
unknown family TRUE TRUE FALSE TRUE unbekannte Familie onbekende familie familia desconocida famiglia sconosciuta famille inconnue família desconhecida ukendt familie
|
||||
unknown genus TRUE TRUE FALSE TRUE unbekannte Gattung onbekend geslacht género desconocido genere sconosciuto genre inconnu gênero desconhecido ukendt slægt
|
||||
unknown species TRUE TRUE FALSE TRUE unbekannte Art onbekende soort especie desconocida specie sconosciute espèce inconnue espécies desconhecida ukendt art
|
||||
unknown subspecies TRUE TRUE FALSE TRUE unbekannte Unterart onbekende ondersoort subespecie desconocida sottospecie sconosciute sous-espèce inconnue subespécies desconhecida ukendt underart
|
||||
unknown rank TRUE TRUE FALSE TRUE unbekannter Rang onbekende rang rango desconocido grado sconosciuto rang inconnu classificação desconhecido ukendt rang
|
||||
group TRUE TRUE FALSE TRUE Gruppe groep grupo gruppo groupe grupo gruppe
|
||||
CoNS FALSE TRUE FALSE TRUE KNS CNS SCN
|
||||
CoPS FALSE TRUE FALSE TRUE KPS CPS SCP
|
||||
Gram-negative TRUE TRUE FALSE FALSE Gramnegativ Gram-negatief Gram negativo Gram negativo Gram négatif Gram negativo Gram-negativ
|
||||
Gram-positive TRUE TRUE FALSE FALSE Grampositiv Gram-positief Gram positivo Gram positivo Gram positif Gram positivo Gram-positiv
|
||||
^Bacteria$ TRUE TRUE FALSE FALSE Bakterien Bacteriën Bacterias Batteri Bactéries Bactérias Bakterier
|
||||
^Fungi$ TRUE TRUE FALSE FALSE Pilze Schimmels Hongos Funghi Champignons Fungos Støbeforme
|
||||
^Yeasts$ TRUE TRUE FALSE FALSE Hefen Gisten Levaduras Lieviti Levures Leveduras Gær
|
||||
^Protozoa$ TRUE TRUE FALSE FALSE Protozoen Protozoën Protozoarios Protozoi Protozoaires Protozoários Protozoer
|
||||
biogroup TRUE TRUE FALSE FALSE Biogruppe biogroep biogrupo biogruppo biogroupe biogrupo biogruppe
|
||||
biotype TRUE TRUE FALSE FALSE Biotyp biotipo biotipo biótipo
|
||||
vegetative TRUE TRUE FALSE FALSE vegetativ vegetatief vegetativo vegetativo végétatif vegetativo
|
||||
([([ ]*?)group TRUE TRUE FALSE FALSE \\1Gruppe \\1groep \\1grupo \\1gruppo \\1groupe \\1grupo
|
||||
([([ ]*?)Group TRUE TRUE FALSE FALSE \\1Gruppe \\1Groep \\1Grupo \\1Gruppo \\1Groupe \\1Grupo
|
||||
no .*growth TRUE FALSE FALSE FALSE keine? .*wachstum geen .*groei no .*crecimientonon sem .*crescimento pas .*croissance sem .*crescimento
|
||||
no|not TRUE FALSE FALSE FALSE keine? geen|niet no|sin sem non sem
|
||||
Intermediate TRUE FALSE FALSE FALSE Mittlere Intermediair Intermedio
|
||||
Susceptible, incr. exp. FALSE TRUE FALSE FALSE Empfindlich, erh Belastung Gevoelig, hoge dosis
|
||||
susceptible, incr. exp. FALSE TRUE FALSE FALSE empfindlich, erh Belastung gevoelig, hoge dosis
|
||||
Susceptible TRUE FALSE FALSE FALSE Empfindlich Gevoelig Susceptible
|
||||
Incr. exposure TRUE FALSE FALSE FALSE Empfindlich, erh Belastung 'Incr. exposure' 'Incr. exposure'
|
||||
Resistant TRUE FALSE FALSE FALSE Resistent Resistent Resistente
|
||||
antibiotic TRUE TRUE FALSE FALSE Antibiotikum antibioticum antibiótico antibiotico antibiotique antibiótico antibiotikum
|
||||
Antibiotic TRUE TRUE FALSE FALSE Antibiotikum Antibioticum Antibiótico Antibiotico Antibiotique Antibiótico Antibiotikum
|
||||
Drug TRUE TRUE FALSE FALSE Medikament Middel Fármaco Droga Médicament Droga Lægemiddel
|
||||
drug TRUE TRUE FALSE FALSE Medikament middel fármaco droga médicament droga lægemiddel
|
||||
Frequency FALSE TRUE FALSE FALSE Zahl Aantal Frecuencia Frequenza Fréquence Frequência Frekvens
|
||||
Minimum Inhibitory Concentration (mg/L) FALSE FALSE FALSE FALSE Minimale Hemm-Konzentration (mg/L) Minimale inhiberende concentratie (mg/L) Concentración mínima inhibitoria (mg/L) Concentrazione minima inibitoria (mg/L) Concentration minimale inhibitrice (mg/L) Concentração Inibitória Mínima (mg/L) Mindste hæmmende koncentration (mg/L)
|
||||
Disk diffusion diameter (mm) FALSE FALSE FALSE FALSE Durchmesser der Scheibenzone (mm) Diameter diskzone (mm) Diámetro de difusión en disco (mm) Diametro di diffusione del disco (mm) Diamètre de diffusion en disque (mm) Diâmetro de difusão do disco (mm) Diskdiffusionsdiameter (mm)
|
||||
Antimicrobial Interpretation FALSE FALSE FALSE FALSE Antimikrobielle Auswertung Antimicrobiële interpretatie Interpretación antimicrobiana Interpretazione antimicrobica Interprétation antimicrobienne Interpretação Antimicrobiana Antimikrobiel fortolkning
|
||||
4-aminosalicylic acid FALSE TRUE TRUE FALSE 4-Aminosalicylsäure 4-aminosalicylzuur Ácido 4-aminosalicílico Acido 4-aminosalicilico Acide 4-aminosalicylique Ácido 4-aminosalicílico 4-aminosalicylsyre
|
||||
Adefovir dipivoxil FALSE TRUE TRUE FALSE Adefovir Dipivoxil Adefovir Adefovir dipivoxil Adefovir dipivoxil Adéfovir dipivoxil Adefovir dipivoxil Adefovir dipivoxil
|
||||
Aldesulfone sodium FALSE TRUE TRUE FALSE Aldesulfon-Natrium Aldesulfon Aldesulfona sódica Aldesulfone sodio Aldésulfone sodique Aldesulfona de sódio Aldesulfon-natrium
|
||||
Amikacin FALSE TRUE TRUE FALSE Amikacin Amikacine Amikacina Amikacin Amikacine Amikacin Amikacin
|
||||
Amoxicillin FALSE TRUE TRUE FALSE Amoxicillin Amoxicilline Amoxicilina Amoxicillina Amoxicilline Amoxicilina Amoxicillin
|
||||
Amoxicillin/beta-lactamase inhibitor FALSE TRUE TRUE FALSE Amoxicillin/Beta-Lactamase-Hemmer Amoxicilline/enzymremmer Amoxicilina/inhib. de la beta-lactamasa Amoxicillina/inib. d. beta-lattamasi Amoxicilline/inhib. de bêta-lactamase Amoxicilina/inibid. da beta-lactamase Amoxicillin/beta-lactamasehæmmer
|
||||
Amphotericin B FALSE TRUE TRUE FALSE Amphotericin B Amfotericine B Anfotericina B Amfotericina B Amphotéricine B Anfotericina B Amfotericin B
|
||||
Ampicillin FALSE TRUE TRUE FALSE Ampicillin Ampicilline Ampicilina Ampicillina Ampicilline Ampicilina Ampicillin
|
||||
Ampicillin/beta-lactamase inhibitor FALSE TRUE TRUE FALSE Ampicillin/Beta-Laktamase-Hemmer Ampicilline/enzymremmer Ampicilina/inhib. de la beta-lactamasa Ampicillina/inib. d. beta-lattamasi Ampicilline/inhib. de bêta-lactamase Ampicilina/inibid. da beta-lactamase Ampicillin/beta-lactamasehæmmer
|
||||
Anidulafungin FALSE TRUE TRUE FALSE Anidulafungin Anidulafungine Anidulafungina Anidulafungin Anidulafungine Anidulafungin Anidulafungin
|
||||
Azidocillin FALSE TRUE TRUE FALSE Azidocillin Azidocilline Azidocilina Azidocillina Azidocilline Azidocillin Azidocillin
|
||||
Azithromycin FALSE TRUE TRUE FALSE Azithromycin Azitromycine Azitromicina Azitromicina Azithromycine Azitromicina Azithromycin
|
||||
Azlocillin FALSE TRUE TRUE FALSE Azlocillin Azlocilline Azlocilina Azlocillina Azlocilline Azlocillin Azlocillin
|
||||
Bacampicillin FALSE TRUE TRUE FALSE Bacampicillin Bacampicilline Bacampicilina Bacampicillina Bacampicilline Bacampicilina Bacampicillin
|
||||
Bacitracin FALSE TRUE TRUE FALSE Bacitracin Bacitracine Bacitracina Bacitracina Bacitracine Bacitracin Bacitracin
|
||||
Benzathine benzylpenicillin FALSE TRUE TRUE FALSE Benzathin-Benzylpenicillin Benzylpenicillinebenzathine Bencilpenicilina benzatínica Benzatina benzilpenicillina Benzathine benzylpénicilline Benzatina benzatina benzilpenicilina Benzathinbenzylpenicillin
|
||||
Benzathine phenoxymethylpenicillin FALSE TRUE TRUE FALSE Benzathin-Phenoxymethylpenicillin Fenoxymethylpenicillinebenzathine Fenoximetilpenicilina benzatínica Benzatina fenossimetilpenicillina Phénoxyméthylpénicilline benzathine Benzatina fenoximetilpenicilina Benzathinfenoxymethylpenicillin
|
||||
Benzylpenicillin FALSE TRUE TRUE FALSE Benzylpenicillin Benzylpenicilline Bencilpenicilina Benzilpenicillina Benzylpénicilline Benzilpenicilina Benzylpenicillin
|
||||
Calcium aminosalicylate FALSE TRUE TRUE FALSE Kalzium-Aminosalicylat Aminosalicylzuur Aminosalicilato de calcio Calcio aminosalicilato Aminosalicylate de calcium Aminosalicilato de cálcio Calciumaminosalicylat
|
||||
Capreomycin FALSE TRUE TRUE FALSE Capreomycin Capreomycine Capreomicina Capreomicina Capréomycine Capreomicina Capreomycin
|
||||
Carbenicillin FALSE TRUE TRUE FALSE Carbenicillin Carbenicilline Carbenicilina Carbenicillina Carbénicilline Carbenicilina Carbenicillin
|
||||
Carindacillin FALSE TRUE TRUE FALSE Carindacillin Carindacilline Carindacilina Carindacillina Carindacilline Carindacillin Carindacillin
|
||||
Caspofungin FALSE TRUE TRUE FALSE Caspofungin Caspofungine Caspofungina Caspofungin Caspofungine Caspofungin Caspofungin
|
||||
Ce(f|ph)acetrile TRUE TRUE TRUE FALSE Cefacetril Cefacetril Cefacetrilo Cefacetrile Céphacétrile Cephacetrile Cephacetril
|
||||
Ce(f|ph)alotin TRUE TRUE TRUE FALSE Cefalotin Cefalotine Cefalotina Cefalotina Céphalotine Cefalotina Cephalotin
|
||||
Ce(f|ph)amandole TRUE TRUE TRUE FALSE Cefamandol Cefamandol Cefamandole Cephamandole Céphamandole Cephamandole Cephamandol
|
||||
Ce(f|ph)apirin TRUE TRUE TRUE FALSE Cefapirin Cefapirine Cefapirina Cefapirina Céphapirine Cephapirin Cephapirin
|
||||
Ce(f|ph)azedone TRUE TRUE TRUE FALSE Cefazedon Cefazedon Cefazedona Cefazedone Céphazédone Cephazedone Cephazedon
|
||||
Ce(f|ph)azolin TRUE TRUE TRUE FALSE Cefazolin Cefazoline Cefazolina Cephazolin Céphazoline Cephazolin Cephazolin
|
||||
Ce(f|ph)alothin TRUE TRUE TRUE FALSE Cefalothin Cefalotine Cefalotina Cefalotina Céphalothine Cephalothin Cephalothin
|
||||
Ce(f|ph)alexin TRUE TRUE TRUE FALSE Cefalexin Cefalexine Cefalexina Cephalexin Céphalexine Cephalexin Cephalexin
|
||||
Ce(f|ph)epime TRUE TRUE TRUE FALSE Cefepim Cefepim Cefepime Cephepime Céphépime Cephepime Cephepime
|
||||
Ce(f|ph)ixime TRUE TRUE TRUE FALSE Cefixim Cefixim Cefixima Cephixime Céphixime Cephixime Cephixim
|
||||
Ce(f|ph)menoxime TRUE TRUE TRUE FALSE Cefmenoxim Cefmenoxim Cefmenoxima Cephmenoxime Céphénoxime Cephmenoxime Cephmenoxim
|
||||
Ce(f|ph)metazole TRUE TRUE TRUE FALSE Cefmetazol Cefmetazol Cefmetazol Cephmetazole Céphmétazole Cefmetazole Cephmetazol
|
||||
Ce(f|ph)odizime TRUE TRUE TRUE FALSE Cefodizim Cefodizim Cefodixima Cephodizime Céphodizime Cephodizime Cephodizim
|
||||
Ce(f|ph)onicid TRUE TRUE TRUE FALSE Cefonicid Cefonicide Cefonicida Cephonicid Céphonicide Cefonicid Cephonicid
|
||||
Ce(f|ph)operazone TRUE TRUE TRUE FALSE Cefoperazon Cefoperazon Cefoperazona Cephoperazone Céphopérazone Cephoperazone Cephoperazon
|
||||
Ce(f|ph)operazone/beta-lactamase inhibitor TRUE TRUE TRUE FALSE Cefoperazon/Beta-Lactamase-Hemmer Cefoperazon/enzymremmer Cefoperazona/inhib. de betalactamasas Cephoperazone/inib. d. beta-lattamasi Céphopérazone/inhib. de bêta-lactamase Cephoperazona/inibid. da beta-lactamase Cephoperazon/beta-lactamasehæmmer
|
||||
Ce(f|ph)otaxime TRUE TRUE TRUE FALSE Cefotaxim Cefotaxim Cefotaxima Cephotaxime Céphotaxime Cephotaxime Cephotaxim
|
||||
Ce(f|ph)oxitin TRUE TRUE TRUE FALSE Cefoxitin Cefoxitine Cefoxitina Cefossitina Céphoxitine Cephoxitin Cephoxitin
|
||||
Ce(f|ph)pirome TRUE TRUE TRUE FALSE Cefpirom Cefpirom Cephpirome Cephpirome Céphpirome Cefpirome Cephpirom
|
||||
Ce(f|ph)podoxime TRUE TRUE TRUE FALSE Cefpodoxim Cefpodoxim Cefpodoxima Cephpodoxime Céphpodoxime Cephpodoxime Cephpodoxim
|
||||
Ce(f|ph)radine TRUE TRUE TRUE FALSE Cefradin Cefradine Cefradina Cefradina Céphradine Cephradine Cephradin
|
||||
Ce(f|ph)sulodin TRUE TRUE TRUE FALSE Cefsulodin Cefsulodine Cefsulodina Cephsulodin Céphsulodine Cephsulodin Cephsulodin
|
||||
Ce(f|ph)tazidime TRUE TRUE TRUE FALSE Ceftazidim Ceftazidim Ceftazidima Ceftazidima Céphtazidime Ceftazidima Cephtazidim
|
||||
Ce(f|ph)tezole TRUE TRUE TRUE FALSE Ceftezol Ceftezol Ceftezol Cephtezole Céphtézole Ceftezole Cephtezol
|
||||
Ce(f|ph)tizoxime TRUE TRUE TRUE FALSE Ceftizoxim Ceftizoxim Ceftizoxima Cephtizoxime Céphtizoxime Cephtizoxime Cephtizoxim
|
||||
Ce(f|ph)triaxone TRUE TRUE TRUE FALSE Ceftriaxon Ceftriaxon Ceftriaxona Ceftriaxone Céphtriaxone Cefhtriaxone Cephtriaxon
|
||||
Ce(f|ph)uroxime TRUE TRUE TRUE FALSE Cefuroxim Cefuroxim Cefuroxima Cefuroxima Céphuroxime Cephuroxime Cephuroxim
|
||||
Ce(f|ph)uroxime/metronidazole TRUE TRUE TRUE FALSE Cefuroxim/Metronidazol Cefuroxim/andere antibacteriele middelen Cefuroxima/metronidazol Cefuroxima/metronidazolo Céphuroxime/métronidazole Cephuroxime/metronidazol Cefuroxim/metronidazol
|
||||
Chloramphenicol FALSE TRUE TRUE FALSE Chloramphenicol Chlooramfenicol Cloranfenicol Cloramfenicolo Chloramphénicol Cloranfenicol Kloramfenicol
|
||||
Chlortetracycline FALSE TRUE TRUE FALSE Chlortetracyclin Chloortetracycline Clortetraciclina Clorotetraciclina Chlortétracycline Chlortetracycline Chlortetracyclin
|
||||
Cinoxacin FALSE TRUE TRUE FALSE Cinoxacin Cinoxacine Cinoxacina Cinoxacina Cinoxacine Cinoxacin Cinoxacin
|
||||
Ciprofloxacin FALSE TRUE TRUE FALSE Ciprofloxacin Ciprofloxacine Ciprofloxacina Ciprofloxacina Ciprofloxacine Ciprofloxacin Ciprofloxacin
|
||||
Clarithromycin FALSE TRUE TRUE FALSE Clarithromycin Claritromycine Claritromicina Claritromicina Clarithromycine Claritromicina Clarithromycin
|
||||
Clavulanic acid FALSE TRUE TRUE FALSE Clavulansäure Clavulaanzuur Ácido clavulánico Acido clavulanico Acide clavulanique Ácido clavulânico Clavulansyre
|
||||
clavulanic acid FALSE TRUE TRUE FALSE Clavulansäure clavulaanzuur ácido clavulánico acido clavulanico acide clavulanique ácido clavulânico clavulansyre
|
||||
Clindamycin FALSE TRUE TRUE FALSE Clindamycin Clindamycine Clindamicina Clindamicina Clindamycine Clindamicina Clindamycin
|
||||
Clometocillin FALSE TRUE TRUE FALSE Clometocillin Clometocilline Clometocilina Clometocillina Clométocilline Clometocillin Clometocillin
|
||||
Clotrimazole FALSE TRUE TRUE FALSE Clotrimazol Clotrimazol Clotrimazol Clotrimazolo Clotrimazole Clotrimazole Clotrimazol
|
||||
Cloxacillin FALSE TRUE TRUE FALSE Cloxacillin Cloxacilline Cloxacilina Cloxacillina Cloxacilline Cloxacillin Cloxacillin
|
||||
Colistin FALSE TRUE TRUE FALSE Colistin Colistine Colistina Colistina Colistine Colistin Colistin
|
||||
Dapsone FALSE TRUE TRUE FALSE Dapson Dapson Dapsona Dapsone Dapsone Dapsone Dapson
|
||||
Daptomycin FALSE TRUE TRUE FALSE Daptomycin Daptomycine Daptomicina Daptomicina Daptomycine Daptomicina Daptomycin
|
||||
Dibekacin FALSE TRUE TRUE FALSE Dibekacin Dibekacine Dibekacina Dibekacin Dibekacine Dibekacin Dibekacin
|
||||
Dicloxacillin FALSE TRUE TRUE FALSE Dicloxacillin Dicloxacilline Dicloxacilina Dicloxacillina Dicloxacilline Dicloxacilina Dicloxacillin
|
||||
Dirithromycin FALSE TRUE TRUE FALSE Dirithromycin Diritromycine Diritromicina Diritromicina Dirithromycine Diritromicina Dirithromycin
|
||||
Econazole FALSE TRUE TRUE FALSE Econazol Econazol Econazol Econazolo Econazole Econazole Econazol
|
||||
Enoxacin FALSE TRUE TRUE FALSE Enoxacin Enoxacine Enoxacina Enoxacina Enoxacine Enoxacin Enoxacin
|
||||
Epicillin FALSE TRUE TRUE FALSE Epicillin Epicilline Epicilina Epicillina Epicilline Epicilina Epicillin
|
||||
Erythromycin FALSE TRUE TRUE FALSE Erythromycin Erytromycine Eritromicina Eritromicina Erythromycine Eritromicina Erythromycin
|
||||
Ethambutol/isoniazid FALSE TRUE TRUE FALSE Ethambutol/Isoniazid Ethambutol/isoniazide Etambutol/isoniazida Etambutolo/isoniazide Ethambutol/isoniazide Ethambutol/isoniazid Ethambutol/isoniazid
|
||||
Fleroxacin FALSE TRUE TRUE FALSE Fleroxacin Fleroxacine Fleroxacina Fleroxacina Fléroxacine Fleroxacina Fleroxacin
|
||||
Flucloxacillin FALSE TRUE TRUE FALSE Flucloxacillin Flucloxacilline Flucloxacilina Flucloxacillina Flucloxacilline Flucloxacillin Flucloxacillin
|
||||
Fluconazole FALSE TRUE TRUE FALSE Fluconazol Fluconazol Fluconazol Fluconazolo Fluconazole Fluconazole Fluconazol
|
||||
Flucytosine FALSE TRUE TRUE FALSE Flucytosin Fluorocytosine Flucitosina Flucytosine Flucytosine Flucytosine Flucytosin
|
||||
Flurithromycin FALSE TRUE TRUE FALSE Flurithromycin Fluritromycine Fluritromicina Fluritromicina Flurithromycine Fluritromicina Flurithromycin
|
||||
Fosfomycin FALSE TRUE TRUE FALSE Fosfomycin Fosfomycine Fosfomicina Fosfomicina Fosfomycine Fosfomycin Fosfomycin
|
||||
Fusidic acid FALSE TRUE TRUE FALSE Fusidinsäure Fusidinezuur Ácido fusídico Acido fusidico Acide fusidique Ácido fusídico Fusidinsyre
|
||||
Gatifloxacin FALSE TRUE TRUE FALSE Gatifloxacin Gatifloxacine Gatifloxacina Gatifloxacina Gatifloxacine Gatifloxacin Gatifloxacin
|
||||
Gemifloxacin FALSE TRUE TRUE FALSE Gemifloxacin Gemifloxacine Gemifloxacina Gemifloxacina Gemifloxacine Gemifloxacin Gemifloxacin
|
||||
Gentamicin FALSE TRUE TRUE FALSE Gentamicin Gentamicine Gentamicina Gentamicina Gentamicine Gentamicina Gentamicin
|
||||
Grepafloxacin FALSE TRUE TRUE FALSE Grepafloxacin Grepafloxacine Grepafloxacina Grepafloxacina Grepafloxacine Grepafloxacin Grepafloxacin
|
||||
Hachimycin FALSE TRUE TRUE FALSE Hachimycin Hachimycine Hachimycin Hachimycin Hachimycine Hachimycin Hachimycin
|
||||
Hetacillin FALSE TRUE TRUE FALSE Hetacillin Hetacilline Hetacilina Hetacillin Hétacilline Hetacillin Hetacillin
|
||||
Imipenem/cilastatin FALSE TRUE TRUE FALSE Imipenem/Cilastatin Imipenem/enzymremmer Imipenem/cilastatina Imipenem/cilastatina Imipénème/cilastatine Imipenem/coteltelatina Imipenem/cilastatin
|
||||
Inosine pranobex FALSE TRUE TRUE FALSE Inosin-Pranobex Inosiplex Inosina pranobex Inosina pranobex Inosine pranobex Pranobex inosine Inosin pranobex
|
||||
Isepamicin FALSE TRUE TRUE FALSE Isepamicin Isepamicine Isepamicina Isepamicina Isepamicine Isepamicina Isepamicin
|
||||
Isoconazole FALSE TRUE TRUE FALSE Isoconazol Isoconazol Isoconazol Isoconazolo Isoconazole Isoconazole Isoconazol
|
||||
Isoniazid FALSE TRUE TRUE FALSE Isoniazid Isoniazide Isoniazida Isoniazide Isoniazide Isoniazid Isoniazid
|
||||
Itraconazole FALSE TRUE TRUE FALSE Itraconazol Itraconazol Itraconazol Itraconazolo Itraconazole Itraconazole Itraconazol
|
||||
Josamycin FALSE TRUE TRUE FALSE Josamycin Josamycine Josamicina Josamicina Josamycine Josamycin Josamycin
|
||||
Kanamycin FALSE TRUE TRUE FALSE Kanamycin Kanamycine Kanamicina Kanamicina Kanamycine Kanamycin Kanamycin
|
||||
Ketoconazole FALSE TRUE TRUE FALSE Ketoconazol Ketoconazol Ketoconazol Ketoconazolo Kétoconazole Ketoconazole Ketoconazol
|
||||
Levofloxacin FALSE TRUE TRUE FALSE Levofloxacin Levofloxacine Levofloxacina Levofloxacina Lévofloxacine Levofloxacin Levofloxacin
|
||||
Lincomycin FALSE TRUE TRUE FALSE Lincomycin Lincomycine Lincomicina Lincomicina Lincomycine Lincomycin Lincomycin
|
||||
Lomefloxacin FALSE TRUE TRUE FALSE Lomefloxacin Lomefloxacine Lomefloxacina Lomefloxacina Loméfloxacine Lomefloxacin Lomefloxacin
|
||||
Lysozyme FALSE TRUE TRUE FALSE Lysozym Lysozym Lisozima Lisozima Lysozyme Lysozyme Lysozym
|
||||
Mandelic acid FALSE TRUE TRUE FALSE Mandelsäure Amandelzuur Ácido mandélico Acido mandelico Acide mandélique Ácido mandélico Mandelinsyre
|
||||
Metampicillin FALSE TRUE TRUE FALSE Metampicillin Metampicilline Metampicilina Metampicillina Métampicilline Metampicilina Metampicillin
|
||||
Meticillin FALSE TRUE TRUE FALSE Meticillin Meticilline Meticilina Meticillina Méticilline Meticillin Meticillin
|
||||
Metisazone FALSE TRUE TRUE FALSE Metisazon Metisazon Metisazona Metisazone Métisazone Metisazone Metisazon
|
||||
Metronidazole FALSE TRUE TRUE FALSE Metronidazol Metronidazol Metronidazol Metronidazolo Métronidazole Metronidazol Metronidazol
|
||||
Mezlocillin FALSE TRUE TRUE FALSE Mezlocillin Mezlocilline Mezlocilina Mezlocillina Mezlocilline Mezlocillin Mezlocillin
|
||||
Micafungin FALSE TRUE TRUE FALSE Micafungin Micafungine Micafungina Micafungin Micafungine Micafungin Micafungin
|
||||
Miconazole FALSE TRUE TRUE FALSE Miconazol Miconazol Miconazol Miconazolo Miconazole Miconazole Miconazol
|
||||
Midecamycin FALSE TRUE TRUE FALSE Midecamycin Midecamycine Midecamicina Midecamicina Midecamycine Midecamycin Midecamycin
|
||||
Miocamycin FALSE TRUE TRUE FALSE Miocamycin Miocamycine Miocamycin Miocamicina Miocamycine Miocamicina Miocamycin
|
||||
Moxifloxacin FALSE TRUE TRUE FALSE Moxifloxacin Moxifloxacine Moxifloxacina Moxifloxacin Moxifloxacine Moxifloxacina Moxifloxacin
|
||||
Mupirocin FALSE TRUE TRUE FALSE Mupirocin Mupirocine Mupirocina Mupirocina Mupirocine Mupirocina Mupirocin
|
||||
Nalidixic acid FALSE TRUE TRUE FALSE Nalidixinsäure Nalidixinezuur Ácido nalidíxico Acido nalidixico Acide nalidixique Ácido nalidíxico Nalidixinsyre
|
||||
Neomycin FALSE TRUE TRUE FALSE Neomycin Neomycine Neomicina Neomicina Néomycine Neomicina Neomycin
|
||||
Netilmicin FALSE TRUE TRUE FALSE Netilmicin Netilmicine Netilmicina Netilmicin Netilmicine Netilmicin Netilmicin
|
||||
Nitrofurantoin FALSE TRUE TRUE FALSE Nitrofurantoin Nitrofurantoine Nitrofurantoína Nitrofurantoina Nitrofurantoïne Nitrofurantoína Nitrofurantoin
|
||||
Norfloxacin FALSE TRUE TRUE FALSE Norfloxacin Norfloxacine Norfloxacina Norfloxacina Norfloxacine Norfloxacin Norfloxacin
|
||||
Novobiocin FALSE TRUE TRUE FALSE Novobiocin Novobiocine Novobiocina Novobiocin Novobiocine Novobiocin Novobiocin
|
||||
Nystatin FALSE TRUE TRUE FALSE Nystatin Nystatine Nistatina Nystatin Nystatine Nystatin Nystatin
|
||||
Ofloxacin FALSE TRUE TRUE FALSE Ofloxacin Ofloxacine Ofloxacina Ofloxacin Ofloxacine Ofloxacin Ofloxacin
|
||||
Oleandomycin FALSE TRUE TRUE FALSE Oleandomycin Oleandomycine Oleandomicina Oleandomicina Oleandomycine Oleandomicina Oleandomycin
|
||||
Ornidazole FALSE TRUE TRUE FALSE Ornidazol Ornidazol Ornidazol Ornidazolo Ornidazole Ornidazole Ornidazol
|
||||
Oxacillin FALSE TRUE TRUE FALSE Oxacillin Oxacilline Oxacilina Oxacillina Oxacilline Oxacillin Oxacillin
|
||||
Oxolinic acid FALSE TRUE TRUE FALSE Oxolinsäure Oxolinezuur Ácido oxolínico Acido ossolinico Acide oxolinique Ácido oxolínico Oxolinsyre
|
||||
Oxytetracycline FALSE TRUE TRUE FALSE Oxytetracyclin Oxytetracycline Oxitetraciclina Ossitetraciclina Oxytétracycline Oxitetraciclina Oxytetracyclin
|
||||
Pazufloxacin FALSE TRUE TRUE FALSE Pazufloxacin Pazufloxacine Pazufloxacina Pazufloxacin Pazufloxacine Pazufloxacin Pazufloxacin
|
||||
Pefloxacin FALSE TRUE TRUE FALSE Pefloxacin Pefloxacine Pefloxacina Pefloxacina Péfloxacine Pefloxacin Pefloxacin
|
||||
Penamecillin FALSE TRUE TRUE FALSE Penamecillin Penamecilline Penamecilina Penamecillina Pénamécilline Penamecilina Penamecillin
|
||||
Penicillin FALSE TRUE TRUE FALSE Penicillin Penicilline Penicilina Penicillina Pénicilline Penicilina Penicillin
|
||||
Pheneticillin FALSE TRUE TRUE FALSE Pheneticillin Feneticilline Feneticilina Feneticillina Phénéticilline Pheneticillin Pheneticillin
|
||||
Phenoxymethylpenicillin FALSE TRUE TRUE FALSE Phenoxymethylpenicillin Fenoxymethylpenicilline Fenoximetilpenicilina Fenossimetilpenicillina Phénoxyméthylpénicilline Fenoximetilpenicilina Phenoxymethylpenicillin
|
||||
Pipemidic acid FALSE TRUE TRUE FALSE Pipemidinsäure Pipemidinezuur Ácido pipemídico Acido pipemidico Acide pipémidique Ácido pipemídico Pipemidinsyre
|
||||
Piperacillin FALSE TRUE TRUE FALSE Piperacillin Piperacilline Piperacilina Piperacillina Pipéracilline Piperacilina Piperacillin
|
||||
Piperacillin/beta-lactamase inhibitor FALSE TRUE TRUE FALSE Piperacillin/Beta-Lactamase-Hemmer Piperacilline/enzymremmer Piperacilina/inhib. de la beta-lactamasa Piperacillina/inib. d. beta-lattamasi Pipéracilline/inhib. de bêta-lactamase Piperacilina/inibid. da beta-lactamase Piperacillin/beta-lactamasehæmmer
|
||||
Piromidic acid FALSE TRUE TRUE FALSE Piromidinsäure Piromidinezuur Ácido piromídico Acido piromidico Acide piromidique Ácido piromídico Piromidinsyre
|
||||
Pivampicillin FALSE TRUE TRUE FALSE Pivampicillin Pivampicilline Pivampicilina Pivampicillina Pivampicilline Pivampicilina Pivampicillin
|
||||
Polymyxin B FALSE TRUE TRUE FALSE Polymyxin B Polymyxine B Polimixina B Polimixina B Polymyxine B Polimixina B Polymyxin B
|
||||
Posaconazole FALSE TRUE TRUE FALSE Posaconazol Posaconazol Posaconazol Posaconazolo Posaconazole Posaconazole Posaconazol
|
||||
Pristinamycin FALSE TRUE TRUE FALSE Pristinamycin Pristinamycine Pristinamicina Pristinamicina Pristinamycine Pristinamicina Pristinamycin
|
||||
Procaine benzylpenicillin FALSE TRUE TRUE FALSE Procain-Benzylpenicillin Benzylpenicillineprocaine Bencilpenicilina procaína Procaina benzilpenicillina Procaïne benzylpénicilline Procaína benzilpenicilina Prokainbenzylpenicillin
|
||||
Propicillin FALSE TRUE TRUE FALSE Propicillin Propicilline Propicilina Propicillina Propicilline Propicilina Propicillin
|
||||
Prulifloxacin FALSE TRUE TRUE FALSE Prulifloxacin Prulifloxacine Prulifloxacina Prulifloxacina Prulifloxacine Prulifloxacina Prulifloxacin
|
||||
Quinupristin/dalfopristin FALSE TRUE TRUE FALSE Quinupristin/Dalfopristin Quinupristine/dalfopristine Quinupristina/dalfopristina Quinupristina/dalfopristina Quinupristine/dalfopristine Quinupristin/dalfopristin Quinupristin/dalfopristin
|
||||
Ribostamycin FALSE TRUE TRUE FALSE Ribostamycin Ribostamycine Ribostamicina Ribostamicina Ribostamycine Ribostamicina Ribostamycin
|
||||
Rifabutin FALSE TRUE TRUE FALSE Rifabutin Rifabutine Rifabutina Rifabutina Rifabutine Rifabutin Rifabutin
|
||||
Rifampicin FALSE TRUE TRUE FALSE Rifampicin Rifampicine Rifampicina Rifampicina Rifampicine Rifampicina Rifampicin
|
||||
Rifampicin/pyrazinamide/ethambutol/isoniazid FALSE TRUE TRUE FALSE Rifampicin/Pyrazinamid/Ethambutol/Isoniazid Rifampicine/pyrazinamide/ethambutol/isoniazide Rifampicina/pirazinamida/etambutol/isoniazida Rifampicina/pirazinamide/etambutolo/isoniazide Rifampicine/pyrazinamide/éthambutol/isoniazide Rifampicina/pirazinamida/etambutol/isoniazida Rifampicin/pyrazinamid/ethambutol/isoniazid
|
||||
Rifampicin/pyrazinamide/isoniazid FALSE TRUE TRUE FALSE Rifampicin/Pyrazinamid/Isoniazid Rifampicine/pyrazinamide/isoniazide Rifampicina/pirazinamida/isoniazida Rifampicina/pirazinamide/isoniazide Rifampicine/pyrazinamide/isoniazide Rifampicina/pirazinamida/isoniazida Rifampicin/pyrazinamid/isoniazid
|
||||
Rifampicin/isoniazid FALSE TRUE TRUE FALSE Rifampicin/Isoniazid Rifampicine/isoniazide Rifampicina/isoniazida Rifampicina/isoniazide Rifampicine/isoniazide Rifampicina/isoniazida Rifampicin/isoniazid
|
||||
Rifamycin FALSE TRUE TRUE FALSE Rifamycin Rifamycine Rifamicina Rifamicina Rifamycine Rifamycin Rifamycin
|
||||
Rifaximin FALSE TRUE TRUE FALSE Rifaximin Rifaximine Rifaximina Rifaximina Rifaximine Rifaximin Rifaximin
|
||||
Rokitamycin FALSE TRUE TRUE FALSE Rokitamycin Rokitamycine Rokitamicina Rokitamicina Rokitamycine Rokitamycin Rokitamycin
|
||||
Rosoxacin FALSE TRUE TRUE FALSE Rosoxacin Rosoxacine Rosoxacina Rosoxacina Rosoxacine Rosoxacina Rosoxacin
|
||||
Roxithromycin FALSE TRUE TRUE FALSE Roxithromycin Roxitromycine Roxitromicina Roxitromicina Roxithromycine Roxitromicina Roxithromycin
|
||||
Rufloxacin FALSE TRUE TRUE FALSE Rufloxacin Rufloxacine Rufloxacina Rufloxacina Rufloxacine Rufloxacin Rufloxacin
|
||||
Sisomicin FALSE TRUE TRUE FALSE Sisomicin Sisomicine Sisomicina Sisomicina Sisomicine Sisomicina Sisomicin
|
||||
Sodium aminosalicylate FALSE TRUE TRUE FALSE Natrium-Aminosalicylat Aminosalicylzuur Aminosalicilato de sodio Sodio aminosalicilato Aminosalicylate de sodium Aminosalicilato de sódio Natriumaminosalicylat
|
||||
Sparfloxacin FALSE TRUE TRUE FALSE Sparfloxacin Sparfloxacine Esparfloxacina Sparfloxacina Sparfloxacine Sparfloxacin Sparfloxacin
|
||||
Spectinomycin FALSE TRUE TRUE FALSE Spectinomycin Spectinomycine Espectinomicina Spectinomycin Spectinomycine Spectinomycin Spectinomycin
|
||||
Spiramycin FALSE TRUE TRUE FALSE Spiramycin Spiramycine Espiramicina Spiramicina Spiramycine Spiramycin Spiramycin
|
||||
Spiramycin/metronidazole FALSE TRUE TRUE FALSE Spiramycin/Metronidazol Spiramycine/metronidazol Espiramicina/metronidazol Spiramicina/metronidazolo Spiramycine/métronidazole Spiramycin/metronidazol Spiramycin/metronidazol
|
||||
Staphylococcus immunoglobulin FALSE TRUE TRUE FALSE Staphylococcus-Immunoglobulin Stafylokokkenimmunoglobuline Inmunoglobulina estafilocócica Immunoglobulina per stafilococco Immunoglobuline staphylococcique Imunoglobulina de Staphylococcus Stafylokok-immunglobulin
|
||||
Streptoduocin FALSE TRUE TRUE FALSE Streptoduocin Streptoduocine Estreptoduocina Streptoduocin Streptoduocine Estreptoduocina Streptoduocin
|
||||
Streptomycin FALSE TRUE TRUE FALSE Streptomycin Streptomycine Estreptomicina Streptomicina Streptomycine Streptomycin Streptomycin
|
||||
Streptomycin/isoniazid FALSE TRUE TRUE FALSE Streptomycin/Isoniazid Streptomycine/isoniazide Estreptomicina/isoniazida Streptomicina/isoniazide Streptomycine/isoniazide Streptomicina/isoniazida Streptomycin/isoniazid
|
||||
Sulbenicillin FALSE TRUE TRUE FALSE Sulbenicillin Sulbenicilline Sulbenicilina Sulbenicillina Sulbenicilline Sulbenicilina Sulbenicillin
|
||||
Sulfadiazine/tetroxoprim FALSE TRUE TRUE FALSE Sulfadiazin/Tetroxoprim Sulfadiazine/tetroxoprim Sulfadiazina/tetroxoprim Sulfadiazina/tetroxoprim Sulfadiazine/tetroxoprime Sulfadiazina/tetroxoprim Sulfadiazin/tetroxoprim
|
||||
Sulfadiazine/trimethoprim FALSE TRUE TRUE FALSE Sulfadiazin/Trimethoprim Sulfadiazine/trimethoprim Sulfadiazina/trimetoprima Sulfadiazina/trimetoprim Sulfadiazine/triméthoprime Sulfadiazina/trimethoprim Sulfadiazin/trimethoprim
|
||||
Sulfadimidine/trimethoprim FALSE TRUE TRUE FALSE Sulfadimidin/Trimethoprim Sulfadimidine/trimethoprim Sulfadimidina/trimetoprima Sulfadimidina/trimetoprim Sulfadimidine/triméthoprime Sulfadimidina/trimethoprim Sulfadimidin/trimethoprim
|
||||
Sulfafurazole FALSE TRUE TRUE FALSE Sulfafurazol Sulfafurazol Sulfafurazol Sulfafurazolo Sulfafurazole Sulfafurazole Sulfafurazol
|
||||
Sulfaisodimidine FALSE TRUE TRUE FALSE Sulfaisodimidin Sulfisomidine Sulfaisodimidina Sulfaisodimidina Sulfaisodimidine Sulfaisodimidina Sulfaisodimidin
|
||||
Sulfalene FALSE TRUE TRUE FALSE Sulfalene Sulfaleen Sulfaleno Sulfalene Sulfalène Sulfaleno Sulfalen
|
||||
Sulfamazone FALSE TRUE TRUE FALSE Sulfamazon Sulfamazon Sulfamazona Sulfamazone Sulfamazone Sulfamazona Sulfamazon
|
||||
Sulfamerazine/trimethoprim FALSE TRUE TRUE FALSE Sulfamerazin/Trimethoprim Sulfamerazine/trimethoprim Sulfamerazina/trimetoprima Sulfamerazina/trimetoprim Sulfamérazine/triméthoprime Sulfamerazina/trimethoprim Sulfamerazin/trimethoprim
|
||||
Sulfamethizole FALSE TRUE TRUE FALSE Sulfamethizol Sulfamethizol Sulfametozol Sulfamethizolo Sulfaméthizole Sulfametizole Sulfamethizol
|
||||
Sulfamethoxazole FALSE TRUE TRUE FALSE Sulfamethoxazol Sulfamethoxazol Sulfametoxazol Sulfametossazolo Sulfaméthoxazole Sulfamethoxazole Sulfamethoxazol
|
||||
Sulfamethoxazole/trimethoprim FALSE TRUE TRUE FALSE Sulfamethoxazol/Trimethoprim Sulfamethoxazol/trimethoprim Sulfametoxazol/trimetoprima Sulfametossazolo/trimetoprim Sulfaméthoxazole/triméthoprime Sulfametoxazol/trimethoprim Sulfamethoxazol/trimethoprim
|
||||
Sulfametoxydiazine FALSE TRUE TRUE FALSE Sulfametoxydiazin Sulfamethoxydiazine Sulfametoxidiazina Sulfametoxydiazine Sulfamétoxydiazine Sulfametoxidiazina Sulfametoxydiazin
|
||||
Sulfametrole/trimethoprim FALSE TRUE TRUE FALSE Sulfametrole/Trimethoprim Sulfametrol/trimethoprim Sulfametrol/trimetoprima Sulfametrole/trimetoprim Sulfamétrole/triméthoprime Sulfametrole/trimethoprim Sulfametrol/trimethoprim
|
||||
Sulfamoxole FALSE TRUE TRUE FALSE Sulfamoxol Sulfamoxol Sulfamoxole Sulfamoxolo Sulfamoxole Sulfamoxole Sulfamoxol
|
||||
Sulfamoxole/trimethoprim FALSE TRUE TRUE FALSE Sulfamoxol/Trimethoprim Sulfamoxol/trimethoprim Sulfamoxol/trimetoprima Sulfamoxolo/trimetoprim Sulfamoxole/triméthoprime Sulfamoxole/trimethoprim Sulfamoxol/trimethoprim
|
||||
Sulfaperin FALSE TRUE TRUE FALSE Sulfaperin Sulfaperine Sulfametoxazol Sulfaperin Sulfapérine Sulfaperin Sulfaperin
|
||||
Sulfaphenazole FALSE TRUE TRUE FALSE Sulfaphenazol Sulfafenazol Sulfafenazol Sulfafenazolo Sulfaphénazole Sulfafenazol Sulfaphenazol
|
||||
Sulfathiazole FALSE TRUE TRUE FALSE Sulfathiazol Sulfathiazol Sulfatiazol Sulfathiazole Sulfathiazole Sulfatazol Sulfathiazol
|
||||
Sulfathiourea FALSE TRUE TRUE FALSE Sulfathioharnstoff Sulfathioureum Sulfathiourea Sulfathiourea Sulfathiourée Sulfathiourea Sulfathiourea
|
||||
Sultamicillin FALSE TRUE TRUE FALSE Sultamicillin Sultamicilline Sultamicilina Sultamicillina Sultamicilline Sultamicillin Sultamicillin
|
||||
Talampicillin FALSE TRUE TRUE FALSE Talampicillin Talampicilline Talampicilina Talampicillina Talampicilline Talampicilina Talampicillin
|
||||
Teicoplanin FALSE TRUE TRUE FALSE Teicoplanin Teicoplanine Teicoplanina Teicoplanina Teicoplanine Teicoplanin Teicoplanin
|
||||
Telithromycin FALSE TRUE TRUE FALSE Telithromycin Telitromycine Telitromicina Telitromicina Télithromycine Telitromicina Telithromycin
|
||||
Temafloxacin FALSE TRUE TRUE FALSE Temafloxacin Temafloxacine Temafloxacina Temafloxacina Temafloxacine Temafloxacin Temafloxacin
|
||||
Temocillin FALSE TRUE TRUE FALSE Temocillin Temocilline Temocilina Temocillina Temocillin Temocillin Temocillin
|
||||
Tenofovir disoproxil FALSE TRUE TRUE FALSE Tenofovir Disoproxil Tenofovir Tenofovir disoproxil Tenofovir disoproxil Tenofovir disoproxil Tenofovir disoproxil Tenofovir disoproxil
|
||||
Terizidone FALSE TRUE TRUE FALSE Terizidon Terizidon Terizidona Terizidone Terizidone Terizidone Terizidon
|
||||
Thiamphenicol FALSE TRUE TRUE FALSE Thiamphenicol Thiamfenicol Tiamfenicol Tiamfenicolo Thiamphénicol Tiamfenicol Thiamphenicol
|
||||
Thioacetazone/isoniazid FALSE TRUE TRUE FALSE Thioacetazon/Isoniazid Thioacetazon/isoniazide Tioacetazona/isoniazida Tioacetazone/isoniazide Thioacétazone/isoniazide Thioacetazone/isoniazid Thioacetazon/isoniazid
|
||||
Ticarcillin FALSE TRUE TRUE FALSE Ticarcillin Ticarcilline Ticarcilina Ticarcillina Ticarcilline Ticarcilina Ticarcillin
|
||||
Ticarcillin/beta-lactamase inhibitor FALSE TRUE TRUE FALSE Ticarcillin/Beta-Lactamase-Hemmer Ticarcilline/enzymremmer Ticarcilina/inhib. de la betalactamasa Ticarcillina/inib. d. beta-lattamasi Ticarcilline/inhib. de bêta-lactamase Ticarcilina/inibid. da beta-lactamase Ticarcillin/beta-lactamasehæmmer
|
||||
Ticarcillin/clavulanic acid FALSE TRUE TRUE FALSE Ticarcillin/Clavulansäure Ticarcilline/clavulaanzuur Ticarcilina/ácido clavulánico Ticarcillina/acido clavulanico Ticarcilline/acide clavulanique Ticarcilina/ácido clavulanico Ticarcillin/clavulansyre
|
||||
Tinidazole FALSE TRUE TRUE FALSE Tinidazol Tinidazol Tinidazol Tinidazolo Tinidazole Tinidazole Tinidazol
|
||||
Tobramycin FALSE TRUE TRUE FALSE Tobramycin Tobramycine Tobramicina Tobramicina Tobramycine Tobramycin Tobramycin
|
||||
Trimethoprim/sulfamethoxazole FALSE TRUE TRUE FALSE Trimethoprim/Sulfamethoxazol Cotrimoxazol Trimetoprima/sulfametoxazol Trimetoprim/sulfametossazolo Triméthoprime/sulfaméthoxazole Trimethoprim/sulfametoxazol Trimethoprim/sulfamethoxazol
|
||||
Troleandomycin FALSE TRUE TRUE FALSE Troleandomycin Troleandomycine Troleandomicina Troleandomicina Troleandomycine Troleandomicina Troleandomycin
|
||||
Trovafloxacin FALSE TRUE TRUE FALSE Trovafloxacin Trovafloxacine Trovafloxacina Trovafloxacin Trovafloxacine Trovafloxacin Trovafloxacin
|
||||
Vancomycin FALSE TRUE TRUE FALSE Vancomycin Vancomycine Vancomicina Vancomicina Vancomycine Vancomycin Vancomycin
|
||||
Voriconazole FALSE TRUE TRUE FALSE Voriconazol Voriconazol Voriconazol Voriconazolo Voriconazole Voriconazol Voriconazol
|
||||
Aminoglycosides FALSE TRUE TRUE FALSE Aminoglykoside Aminoglycosiden Aminoglucósidos Aminoglicosidi Aminoglycosides Aminoglycosides Aminoglykosider
|
||||
Amphenicols FALSE TRUE TRUE FALSE Amphenicole Amfenicolen Anfenicoles Amphenicols Amphénicols Anfenicóis Amphenicoler
|
||||
Antifungals/antimycotics FALSE TRUE TRUE FALSE Antimykotika/Antimykotika Antifungica/antimycotica Antifúngicos/antimicóticos Antifungini/antimicotici Antifongiques/antimycotiques Antifúngicos/antimicóticos Antimykotika/antimykotika
|
||||
Antimycobacterials FALSE TRUE TRUE FALSE Antimykobakterielle Mittel Antimycobacteriele middelen Antimicrobianos Antimicobatterici Antimycobactériens Antimycobacterials Antimycobakterier
|
||||
Beta-lactams/penicillins FALSE TRUE TRUE FALSE Beta-Lactame/Penicilline Beta-lactams/penicillines Beta-lactámicos/penicilinas Beta-lattami/penicilline Bêta-lactamines/pénicillines Beta-lactâmicas/penicilinas Beta-lactamer/penicilliner
|
||||
Cephalosporins (1st gen.) FALSE TRUE TRUE FALSE Cephalosporine (1. Gen.) Cefalosporines (1e gen.) Cefalosporinas (1er gen.) Cefalosporine (1° gen.) Céphalosporines (1ère génération) Cefalosporinas (1º género) Cefalosporiner (1. gen.)
|
||||
Cephalosporins (2nd gen.) FALSE TRUE TRUE FALSE Cephalosporine (2. Gen.) Cefalosporines (2e gen.) Cefalosporinas (2do gen.) Cefalosporine (2° gen.) Céphalosporines (2ème génération) Cefalosporinas (2ª gen.) Cefalosporiner (2. gen.)
|
||||
Cephalosporins (3rd gen.) FALSE TRUE TRUE FALSE Cephalosporine (3. Gen.) Cefalosporines (3e gen.) Cefalosporinas (3er gen.) Cefalosporine (3° gen.) Céphalosporines (3ème génération) Cefalosporinas (3ª gen.) Cefalosporiner (3. gen.)
|
||||
Cephalosporins (4th gen.) FALSE TRUE TRUE FALSE Cephalosporine (4. Gen.) Cefalosporines (4e gen.) Cefalosporinas (4ª gen.) Cefalosporine (4° gen.) Céphalosporines (4ème génération) Cefalosporinas (4.ª gen.) Cefalosporiner (4. gen.)
|
||||
Cephalosporins (5th gen.) FALSE TRUE TRUE FALSE Cephalosporine (5. Gen.) Cefalosporines (5e gen.) Cefalosporinas (5º gen.) Cefalosporine (5° gen.) Céphalosporines (5e gén.) Cefalosporinas (5.ª gen.) Cefalosporiner (5. gen.)
|
||||
Cephalosporins (unclassified gen.) FALSE TRUE TRUE FALSE Cephalosporine (unklassifiziert) Cefalosporines (ongeclassificeerd) Cefalosporinas (gen. no clasificado) Cefalosporine (gen. non classificato) Céphalosporines (genre non classifié) Cefalosporinas (não classificado gen.) Cefalosporiner (uklassificeret gen.)
|
||||
Cephalosporins FALSE TRUE TRUE FALSE Cephalosporine Cefalosporines Cefalosporinas Cefalosporine Céphalosporines Cefalosporinas Cefalosporiner
|
||||
Glycopeptides FALSE TRUE TRUE FALSE Glykopeptide Glycopeptiden Glicopéptidos Glicopeptidi Glycopeptides Glycopeptides Glykopeptider
|
||||
Macrolides/lincosamides FALSE TRUE TRUE FALSE Makrolide/Linkosamide Macroliden/lincosamiden Macrólidos/lincosamidas Macrolidi/lincosamidi Macrolides/lincosamides Macrolides/lincosamidas Makrolider/lincosamider
|
||||
Other antibacterials FALSE TRUE TRUE FALSE Andere Antibiotika Overige antibiotica Otros antibacterianos Altri antibatterici Autres antibactériens Outros antibacterianos Andre antibakterielle stoffer
|
||||
Polymyxins FALSE TRUE TRUE FALSE Polymyxine Polymyxines Polimixinas Polimixine Polymyxines Polimixinas Polymyxiner
|
||||
Quinolones FALSE TRUE TRUE FALSE Quinolone Quinolonen Quinolonas Chinoloni Quinolones Quinolones Kinoloner
|
||||
|
||||
|
@@ -7,5 +7,5 @@ microorganisms.codes[which(microorganisms.codes$code == "ENT"), "mo"] <- as.mo("
|
||||
microorganisms.codes[which(microorganisms.codes$code == "STR"), "mo"] <- as.mo("streptococcus")
|
||||
microorganisms.codes[which(microorganisms.codes$code == "CDF"), "mo"] <- as.mo("clostridium difficile")
|
||||
microorganisms.codes[which(microorganisms.codes$code == "HA-"), "mo"] <- as.mo("haemophilus influenzae")
|
||||
usethis::use_data(microorganisms.codes, overwrite = TRUE)
|
||||
usethis::use_data(microorganisms.codes, overwrite = TRUE, version = 2)
|
||||
rm(microorganisms.codes)
|
||||
|
||||
Binary file not shown.
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user