mirror of
https://github.com/msberends/AMR.git
synced 2026-09-27 21:38:23 +02:00
Compare commits
140
Commits
v1.6.0
...
e63defe324
@@ -1,3 +1,4 @@
|
||||
^.*\.RData$
|
||||
^.*\.Rproj$
|
||||
^\.Renviron$
|
||||
^\.Rprofile$
|
||||
@@ -22,8 +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
|
||||
|
||||
@@ -50,128 +50,115 @@ jobs:
|
||||
fail-fast: false
|
||||
matrix:
|
||||
config:
|
||||
- {os: macOS-latest, r: 'devel', allowfail: false}
|
||||
- {os: macOS-latest, r: 'release', allowfail: false}
|
||||
- {os: macOS-latest, r: 'oldrel', allowfail: false}
|
||||
|
||||
- {os: windows-latest, r: 'devel', allowfail: false}
|
||||
- {os: windows-latest, r: 'release', allowfail: false}
|
||||
- {os: windows-latest, r: 'oldrel', allowfail: false}
|
||||
|
||||
- {os: ubuntu-20.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
- {os: ubuntu-20.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
- {os: ubuntu-20.04, r: 'oldrel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
# test all systems against all released versions of R >= 3.0, we support them all!
|
||||
- {os: macOS-latest, r: 'devel', allowfail: true}
|
||||
- {os: macOS-latest, r: '4.1', allowfail: false}
|
||||
- {os: 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"}
|
||||
- {os: ubuntu-20.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
- {os: ubuntu-20.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
- {os: ubuntu-20.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
- {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
- {os: ubuntu-20.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
- {os: ubuntu-20.04, r: '3.3', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
# - {os: ubuntu-20.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
# - {os: ubuntu-20.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
- {os: ubuntu-20.04, r: '3.0', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
|
||||
- {os: ubuntu-16.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
|
||||
- {os: ubuntu-16.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
|
||||
- {os: ubuntu-16.04, r: 'oldrel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
|
||||
- {os: ubuntu-16.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
|
||||
- {os: ubuntu-16.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
|
||||
- {os: ubuntu-16.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
|
||||
- {os: ubuntu-16.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
|
||||
- {os: ubuntu-16.04, r: '3.3', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
|
||||
# - {os: ubuntu-16.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
|
||||
# - {os: ubuntu-16.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
|
||||
- {os: ubuntu-16.04, r: '3.0', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
|
||||
|
||||
- {os: ubuntu-20.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
- {os: ubuntu-20.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
- {os: 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 }}
|
||||
|
||||
R_REPOSITORIES: "https://cran.rstudio.com"
|
||||
|
||||
steps:
|
||||
- uses: actions/checkout@v2
|
||||
|
||||
- uses: r-lib/actions/setup-r@master
|
||||
- uses: r-lib/actions/setup-r@v1
|
||||
with:
|
||||
r-version: ${{ matrix.config.r }}
|
||||
|
||||
- uses: r-lib/actions/setup-pandoc@master
|
||||
|
||||
- name: Query dependencies
|
||||
if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
|
||||
run: |
|
||||
install.packages('remotes')
|
||||
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
|
||||
shell: Rscript {0}
|
||||
|
||||
- name: Cache R packages
|
||||
if: runner.os != 'Windows' && matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
|
||||
uses: actions/cache@v1
|
||||
with:
|
||||
path: ${{ env.R_LIBS_USER }}
|
||||
key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-3-${{ hashFiles('.github/depends.Rds') }}
|
||||
restore-keys: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-3-
|
||||
|
||||
- uses: r-lib/actions/setup-pandoc@v1
|
||||
|
||||
- name: Install Linux dependencies
|
||||
if: runner.os == 'Linux' && matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
|
||||
env:
|
||||
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
|
||||
run: |
|
||||
Rscript -e "remotes::install_github('r-hub/sysreqs')"
|
||||
sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
|
||||
sudo -s eval "$sysreqs"
|
||||
|
||||
- name: Install Linux dependencies on old R versions
|
||||
if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2'
|
||||
env:
|
||||
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
|
||||
if: runner.os == 'Linux'
|
||||
# update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
|
||||
# we don't want to depend on the sysreqs pkg here, as it requires a quite new R version
|
||||
# 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
|
||||
sudo apt install -y libssl-dev libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev
|
||||
|
||||
- name: Restore cached R packages
|
||||
# this step will add the step 'Post Restore cached R packages' on a succesful run
|
||||
uses: actions/cache@v2
|
||||
with:
|
||||
path: ${{ env.R_LIBS_USER }}
|
||||
key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-v4
|
||||
|
||||
- name: Install macOS dependencies
|
||||
if: matrix.config.os == 'macOS-latest' && matrix.config.r == 'devel'
|
||||
- name: Unpack AMR and install R dependencies
|
||||
if: always()
|
||||
run: |
|
||||
brew install mariadb-connector-c
|
||||
|
||||
- name: Install package dependencies
|
||||
if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
|
||||
run: |
|
||||
remotes::install_deps(dependencies = TRUE)
|
||||
remotes::install_cran("rcmdcheck")
|
||||
shell: Rscript {0}
|
||||
|
||||
- name: Session info
|
||||
tar -xf data-raw/AMR_latest.tar.gz
|
||||
Rscript -e "source('data-raw/_install_deps.R')"
|
||||
shell: bash
|
||||
|
||||
- name: Show session info
|
||||
if: always()
|
||||
run: |
|
||||
options(width = 100)
|
||||
utils::sessionInfo()
|
||||
as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
|
||||
shell: Rscript {0}
|
||||
|
||||
- name: Run R CMD check
|
||||
if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
|
||||
env:
|
||||
_R_CHECK_CRAN_INCOMING_: false
|
||||
run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
|
||||
shell: Rscript {0}
|
||||
|
||||
- name: Run R CMD check on older R versions
|
||||
- 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
|
||||
Rscript -e "writeLines(readLines('AMR/DESCRIPTION')[!grepl('VignetteBuilder', readLines('AMR/DESCRIPTION'))], 'AMR/DESCRIPTION2')"
|
||||
rm AMR/DESCRIPTION
|
||||
mv AMR/DESCRIPTION2 AMR/DESCRIPTION
|
||||
shell: bash
|
||||
|
||||
- name: Run R CMD check
|
||||
if: always()
|
||||
env:
|
||||
_R_CHECK_CRAN_INCOMING_: false
|
||||
_R_CHECK_FORCE_SUGGESTS_: false
|
||||
_R_CHECK_DEPENDS_ONLY_: true
|
||||
_R_CHECK_LENGTH_1_CONDITION_: verbose
|
||||
_R_CHECK_LENGTH_1_LOGIC2_: verbose
|
||||
# during 'R CMD check', R_LIBS_USER will be overwritten, so:
|
||||
R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
|
||||
R_RUN_TINYTEST: true
|
||||
run: |
|
||||
R CMD check data-raw/AMR_latest.tar.gz --no-manual --no-build-vignettes
|
||||
|
||||
- name: Show testthat output
|
||||
if: always()
|
||||
run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
|
||||
R CMD check --no-manual --run-donttest --run-dontrun AMR
|
||||
shell: bash
|
||||
|
||||
- name: Upload check results
|
||||
if: failure()
|
||||
uses: actions/upload-artifact@master
|
||||
- name: Show unit tests output
|
||||
if: always()
|
||||
run: |
|
||||
find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
|
||||
shell: bash
|
||||
|
||||
- name: Upload artifacts
|
||||
if: always()
|
||||
uses: actions/upload-artifact@v2
|
||||
with:
|
||||
name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
|
||||
path: check
|
||||
name: artifacts-${{ matrix.config.os }}-r${{ matrix.config.r }}
|
||||
path: AMR.Rcheck
|
||||
|
||||
@@ -26,10 +26,11 @@
|
||||
on:
|
||||
push:
|
||||
branches:
|
||||
- master
|
||||
- development
|
||||
- main
|
||||
pull_request:
|
||||
branches:
|
||||
- master
|
||||
- main
|
||||
|
||||
name: code-coverage
|
||||
|
||||
@@ -41,31 +42,48 @@ jobs:
|
||||
steps:
|
||||
- uses: actions/checkout@v2
|
||||
|
||||
- uses: r-lib/actions/setup-r@master
|
||||
|
||||
- uses: r-lib/actions/setup-pandoc@master
|
||||
- uses: r-lib/actions/setup-r@v1
|
||||
with:
|
||||
r-version: release
|
||||
|
||||
- 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: |
|
||||
install.packages('remotes')
|
||||
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
|
||||
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
|
||||
writeLines(paste(format(Sys.Date(), "week %V %Y"), sprintf("R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/week-R-version")
|
||||
shell: Rscript {0}
|
||||
|
||||
- name: Cache R packages
|
||||
uses: actions/cache@v1
|
||||
|
||||
- name: Restore cached R packages
|
||||
# this step will add the step 'Post Restore cached R packages' on a succesful run
|
||||
uses: actions/cache@v2
|
||||
with:
|
||||
path: ${{ env.R_LIBS_USER }}
|
||||
key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
|
||||
restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
|
||||
key: ${{ matrix.config.os }}-${{ hashFiles('.github/week-R-version') }}-v4
|
||||
|
||||
- name: Install dependencies
|
||||
- name: Unpack AMR and install R dependencies
|
||||
run: |
|
||||
install.packages(c("remotes"))
|
||||
remotes::install_deps(dependencies = TRUE)
|
||||
remotes::install_cran("covr")
|
||||
tar -xf data-raw/AMR_latest.tar.gz
|
||||
Rscript -e "source('data-raw/_install_deps.R')"
|
||||
shell: bash
|
||||
|
||||
- name: Show session info
|
||||
run: |
|
||||
options(width = 100)
|
||||
utils::sessionInfo()
|
||||
as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
|
||||
shell: Rscript {0}
|
||||
|
||||
- name: Test coverage
|
||||
run: 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"), quiet = FALSE)
|
||||
env:
|
||||
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
|
||||
R_RUN_TINYTEST: true
|
||||
run: |
|
||||
install.packages("covr", repos = "https://cran.rstudio.com/")
|
||||
library(AMR)
|
||||
library(tinytest)
|
||||
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
|
||||
|
||||
+83
-59
@@ -1,68 +1,92 @@
|
||||
Package: AMR
|
||||
Version: 1.6.0
|
||||
Date: 2021-03-14
|
||||
Version: 1.7.1.9062
|
||||
Date: 2021-12-06
|
||||
Title: Antimicrobial Resistance Data Analysis
|
||||
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
|
||||
data analysis and to work with microbial and antimicrobial properties by
|
||||
using evidence-based methods and reliable reference data such as LPSN
|
||||
<doi:10.1099/ijsem.0.004332>.
|
||||
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 the analysis and prediction of Antimicrobial
|
||||
Resistance (AMR) and to work with microbial and antimicrobial properties by
|
||||
using evidence-based methods, like those defined by Leclercq et al. (2013)
|
||||
<doi:10.1111/j.1469-0691.2011.03703.x> and containing reference data such as
|
||||
LPSN <doi:10.1099/ijsem.0.004332>.
|
||||
Depends:
|
||||
R (>= 3.0.0)
|
||||
Suggests:
|
||||
cleaner,
|
||||
curl,
|
||||
dplyr,
|
||||
ggplot2,
|
||||
knitr,
|
||||
microbenchmark,
|
||||
pillar,
|
||||
readxl,
|
||||
rmarkdown,
|
||||
rstudioapi,
|
||||
rvest,
|
||||
skimr,
|
||||
testthat,
|
||||
tidyr,
|
||||
xml2
|
||||
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)
|
||||
|
||||
@@ -1,9 +1,11 @@
|
||||
# Generated by roxygen2: do not edit by hand
|
||||
|
||||
S3method("!",mic)
|
||||
S3method("!=",ab_selector)
|
||||
S3method("!=",mic)
|
||||
S3method("%%",mic)
|
||||
S3method("%/%",mic)
|
||||
S3method("&",ab_selector)
|
||||
S3method("&",mic)
|
||||
S3method("*",mic)
|
||||
S3method("+",mic)
|
||||
@@ -11,6 +13,7 @@ S3method("-",mic)
|
||||
S3method("/",mic)
|
||||
S3method("<",mic)
|
||||
S3method("<=",mic)
|
||||
S3method("==",ab_selector)
|
||||
S3method("==",mic)
|
||||
S3method(">",mic)
|
||||
S3method(">=",mic)
|
||||
@@ -33,16 +36,23 @@ S3method("[[<-",mic)
|
||||
S3method("[[<-",mo)
|
||||
S3method("[[<-",rsi)
|
||||
S3method("^",mic)
|
||||
S3method("|",ab_selector)
|
||||
S3method("|",mic)
|
||||
S3method(abs,mic)
|
||||
S3method(acos,mic)
|
||||
S3method(acosh,mic)
|
||||
S3method(all,ab_selector)
|
||||
S3method(all,ab_selector_any_all)
|
||||
S3method(all,mic)
|
||||
S3method(any,ab_selector)
|
||||
S3method(any,ab_selector_any_all)
|
||||
S3method(any,mic)
|
||||
S3method(as.data.frame,ab)
|
||||
S3method(as.data.frame,mo)
|
||||
S3method(as.double,mic)
|
||||
S3method(as.integer,mic)
|
||||
S3method(as.list,custom_eucast_rules)
|
||||
S3method(as.list,custom_mdro_guideline)
|
||||
S3method(as.matrix,mic)
|
||||
S3method(as.numeric,mic)
|
||||
S3method(as.rsi,data.frame)
|
||||
@@ -57,6 +67,9 @@ S3method(barplot,disk)
|
||||
S3method(barplot,mic)
|
||||
S3method(barplot,rsi)
|
||||
S3method(c,ab)
|
||||
S3method(c,ab_selector)
|
||||
S3method(c,custom_eucast_rules)
|
||||
S3method(c,custom_mdro_guideline)
|
||||
S3method(c,disk)
|
||||
S3method(c,mic)
|
||||
S3method(c,mo)
|
||||
@@ -97,6 +110,7 @@ S3method(plot,rsi)
|
||||
S3method(print,ab)
|
||||
S3method(print,bug_drug_combinations)
|
||||
S3method(print,catalogue_of_life_version)
|
||||
S3method(print,custom_eucast_rules)
|
||||
S3method(print,custom_mdro_guideline)
|
||||
S3method(print,disk)
|
||||
S3method(print,mic)
|
||||
@@ -108,7 +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)
|
||||
@@ -137,34 +155,50 @@ S3method(unique,mo)
|
||||
S3method(unique,rsi)
|
||||
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)
|
||||
export(betalactams)
|
||||
export(brmo)
|
||||
export(bug_drug_combinations)
|
||||
export(carbapenems)
|
||||
@@ -184,28 +218,13 @@ export(count_all)
|
||||
export(count_df)
|
||||
export(count_resistant)
|
||||
export(count_susceptible)
|
||||
export(custom_eucast_rules)
|
||||
export(custom_mdro_guideline)
|
||||
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_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)
|
||||
@@ -227,12 +246,15 @@ export(is.mo)
|
||||
export(is.rsi)
|
||||
export(is.rsi.eligible)
|
||||
export(is_new_episode)
|
||||
export(key_antibiotics)
|
||||
export(key_antibiotics_equal)
|
||||
export(italicise_taxonomy)
|
||||
export(italicize_taxonomy)
|
||||
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)
|
||||
@@ -272,15 +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)
|
||||
@@ -292,11 +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)
|
||||
|
||||
@@ -1,5 +1,146 @@
|
||||
# AMR 1.6.0
|
||||
# `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
|
||||
* 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
|
||||
example_isolates[, carbapenems()] # base R
|
||||
example_isolates %>% select(carbapenems()) # dplyr
|
||||
|
||||
# filter rows for resistance in any carbapenem
|
||||
example_isolates[any(carbapenems() == "R"), ] # base R
|
||||
example_isolates %>% filter(any(carbapenems() == "R")) # dplyr
|
||||
example_isolates %>% filter(if_any(carbapenems(), ~.x == "R")) # dplyr (formal)
|
||||
|
||||
# filter rows for resistance in all carbapenems
|
||||
example_isolates[all(carbapenems() == "R"), ] # base R
|
||||
example_isolates[carbapenems() == "R", ]
|
||||
example_isolates %>% filter(all(carbapenems() == "R")) # dplyr
|
||||
example_isolates %>% filter(carbapenems() == "R")
|
||||
```
|
||||
|
||||
### 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.
|
||||
* The `first_isolate()` function gained the argument `method` that has to be "phenotype-based", "episode-based", "patient-based", or "isolate-based". The old behaviour is equal to "episode-based". The new default is "phenotype-based" if antimicrobial test results are available, and "episode-based" otherwise. This new default will yield slightly more isolates for selection (which is a good thing).
|
||||
* Since fungal isolates can also be selected, the functions `key_antibiotics()` and `key_antibiotics_equal()` are now deprecated in favour of the `key_antimicrobials()` and `antimicrobials_equal()` functions. Also, the new `all_antimicrobials()` function works like the old `key_antibiotics()` function, but includes any column with antimicrobial test results. Using `key_antimicrobials()` still only selects six preferred antibiotics for Gram-negatives, six for Gram-positives, and six universal antibiotics. It has a new `antifungal` argument to set antifungal agents (antimycotics).
|
||||
* Using `type == "points"` in the `first_isolate()` function for phenotype-based selection will now consider all antimicrobial drugs in the data set, using the new `all_antimicrobials()`
|
||||
* The `first_isolate()` function can now take a vector of values for `col_keyantibiotics` and can have an episode length of `Inf`
|
||||
* Since the phenotype-based method is the new default, `filter_first_isolate()` renders the `filter_first_weighted_isolate()` function redundant. For this reason, `filter_first_weighted_isolate()` is now deprecated.
|
||||
* The documentation of the `first_isolate()` and `key_antimicrobials()` functions has been completely rewritten.
|
||||
* Function `betalactams()` as additional antbiotic column selector and function `filter_betalactams()` as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.
|
||||
* A `ggplot()` method for `resistance_predict()`
|
||||
|
||||
|
||||
### Changed
|
||||
* `bug_drug_combinations()` now supports grouping using the `dplyr` package
|
||||
* Custom MDRO guidelines (`mdro()`, `custom_mdro_guideline()`):
|
||||
* Custom MDRO guidelines can now be combined with other custom MDRO guidelines using `c()`
|
||||
* Fix for applying the rules; in previous versions, rows were interpreted according to the last matched rule. Now, rows are interpreted according to the first matched rule
|
||||
* Fix for `age_groups()` for persons aged zero
|
||||
* The `example_isolates` data set now contains some (fictitious) zero-year old patients
|
||||
* Fix for minor translation errors
|
||||
* Printing of microbial codes in a `data.frame` or `tibble` now gives a warning if the data contains old microbial codes (from a previous AMR package version)
|
||||
* Extended the `like()` functions:
|
||||
* Now checks if `pattern` is a *valid* regular expression
|
||||
* Added `%unlike%` and `%unlike_case%` (as negations of the existing `%like%` and `%like_case%`). This greatly improves readability:
|
||||
```r
|
||||
if (!grepl("EUCAST", guideline)) ...
|
||||
# same:
|
||||
if (guideline %unlike% "EUCAST") ...
|
||||
```
|
||||
* Altered the RStudio addin, so it now iterates over `%like%` -> `%unlike%` -> `%like_case%` -> `%unlike_case%` if you keep pressing your keyboard shortcut
|
||||
* Fixed an installation error on R-3.0
|
||||
* Added `info` argument to `as.mo()` to turn on/off the progress bar
|
||||
* Fixed a bug where `col_mo` in some functions (esp. `eucast_rules()` and `mdro()`) could not be a column name of the `microorganisms` data set as it would throw an error
|
||||
* Fix for transforming numeric values to RSI (`as.rsi()`) when the `vctrs` package is loaded (i.e., when using tidyverse)
|
||||
* Colour fix for using `barplot()` on an RSI class
|
||||
* Added 25 common system codes for bacteria to the `microorganisms.codes` data set
|
||||
* Added 16 common system codes for antimicrobial agents to the `antibiotics` data set
|
||||
* Fix for using `skimr::skim()` on classes `mo`, `mic` and `disk` when using the just released `dplyr` v1.0.6
|
||||
* Updated `skimr::skim()` usage for MIC values to also include 25th and 75th percentiles
|
||||
* Fix for plotting missing MIC/disk diffusion values
|
||||
* Updated join functions to always use `dplyr` join functions if the `dplyr` package is installed - now also preserving grouped variables
|
||||
* Antibiotic class selectors (such as `cephalosporins()`) now maintain the column order from the original data
|
||||
* Fix for selecting columns using `fluoroquinolones()`
|
||||
* `age()` now vectorises over both `x` and `reference`
|
||||
|
||||
### Other
|
||||
* As requested by CRAN administrators: decreased package size by 3 MB in costs of a slower loading time of the package
|
||||
* 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
|
||||
|
||||
### 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.
|
||||
@@ -59,7 +200,7 @@
|
||||
```
|
||||
|
||||
### Changed
|
||||
* Updated the bacterial taxonomy to 3 March 2021 (using [LSPN](https://lpsn.dsmz.de))
|
||||
* Updated the bacterial taxonomy to 3 March 2021 (using [LPSN](https://lpsn.dsmz.de))
|
||||
* Added 3,372 new species and 1,523 existing species became synomyms
|
||||
* The URL of a bacterial species (`mo_url()`) will now lead to https://lpsn.dsmz.de
|
||||
* Big update for plotting classes `rsi`, `<mic>`, and `<disk>`:
|
||||
@@ -377,7 +518,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
|
||||
|
||||
### New
|
||||
* Support for the newest [EUCAST Clinical Breakpoint Tables v.10.0](https://www.eucast.org/clinical_breakpoints/), valid from 1 January 2020. This affects translation of MIC and disk zones using `as.rsi()` and inferred resistance and susceptibility using `eucast_rules()`.
|
||||
* The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt>. This **allows for machine reading these guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file [can be found here](https://github.com/msberends/AMR/blob/master/data-raw/read_EUCAST.R).
|
||||
* The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt>. This **allows for machine reading these guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file [can be found here](https://github.com/msberends/AMR/blob/main/data-raw/read_EUCAST.R).
|
||||
* Support for LOINC and SNOMED codes
|
||||
* Support for LOINC codes in the `antibiotics` data set. Use `ab_loinc()` to retrieve LOINC codes, or use a LOINC code for input in any `ab_*` function:
|
||||
```r
|
||||
@@ -694,7 +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
|
||||
@@ -718,7 +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`
|
||||
@@ -835,7 +976,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
|
||||
* Emphasised in manual that penicillin is meant as benzylpenicillin (ATC [J01CE01](https://www.whocc.no/atc_ddd_index/?code=J01CE01))
|
||||
* New info is returned when running this function, stating exactly what has been changed or added. Use `eucast_rules(..., verbose = TRUE)` to get a data set with all changed per bug and drug combination.
|
||||
* Removed data sets `microorganisms.oldDT`, `microorganisms.prevDT`, `microorganisms.unprevDT` and `microorganismsDT` since they were no longer needed and only contained info already available in the `microorganisms` data set
|
||||
* Added 65 antibiotics to the `antibiotics` data set, from the [Pharmaceuticals Community Register](http://ec.europa.eu/health/documents/community-register/html/atc.htm) of the European Commission
|
||||
* Added 65 antibiotics to the `antibiotics` data set, from the [Pharmaceuticals Community Register](https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm) of the European Commission
|
||||
* Removed columns `atc_group1_nl` and `atc_group2_nl` from the `antibiotics` data set
|
||||
* Functions `atc_ddd()` and `atc_groups()` have been renamed `atc_online_ddd()` and `atc_online_groups()`. The old functions are deprecated and will be removed in a future version.
|
||||
* Function `guess_mo()` is now deprecated in favour of `as.mo()` and will be removed in future versions
|
||||
@@ -1229,7 +1370,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
|
||||
* Added [ORCID](https://orcid.org) of authors to DESCRIPTION file
|
||||
* Added unit testing with the `testthat` package
|
||||
* Added build tests for Linux and macOS using Travis CI (https://travis-ci.org/msberends/AMR)
|
||||
* Added line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/master/R)
|
||||
* Added line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/main/R)
|
||||
|
||||
# AMR 0.1.1
|
||||
|
||||
|
||||
+338
-167
@@ -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
|
||||
@@ -71,7 +143,49 @@ addin_insert_in <- function() {
|
||||
|
||||
# No export, no Rd
|
||||
addin_insert_like <- function() {
|
||||
import_fn("insertText", "rstudioapi")(" %like% ")
|
||||
# we want Shift + Ctrl/Cmd + L to iterate over %like%, %unlike%, %like_case%, and %unlike_case%
|
||||
|
||||
getActiveDocumentContext <- import_fn("getActiveDocumentContext", "rstudioapi")
|
||||
insertText <- import_fn("insertText", "rstudioapi")
|
||||
modifyRange <- import_fn("modifyRange", "rstudioapi")
|
||||
document_range <- import_fn("document_range", "rstudioapi")
|
||||
document_position <- import_fn("document_position", "rstudioapi")
|
||||
|
||||
context <- getActiveDocumentContext()
|
||||
current_row <- context$selection[[1]]$range$end[1]
|
||||
current_col <- context$selection[[1]]$range$end[2]
|
||||
current_row_txt <- context$contents[current_row]
|
||||
if (is.null(current_row) || current_row_txt %unlike% "%(un)?like") {
|
||||
insertText(" %like% ")
|
||||
return(invisible())
|
||||
}
|
||||
|
||||
pos_preceded_by <- function(txt) {
|
||||
if (tryCatch(substr(current_row_txt, current_col - nchar(trimws(txt, which = "right")), current_col) == trimws(txt, which = "right"),
|
||||
error = function(e) FALSE)) {
|
||||
return(TRUE)
|
||||
}
|
||||
tryCatch(substr(current_row_txt, current_col - nchar(txt), current_col) %like% paste0("^", txt),
|
||||
error = function(e) FALSE)
|
||||
}
|
||||
replace_pos <- function(old, with) {
|
||||
modifyRange(document_range(document_position(current_row, current_col - nchar(old)),
|
||||
document_position(current_row, current_col)),
|
||||
text = with,
|
||||
id = context$id)
|
||||
}
|
||||
|
||||
if (pos_preceded_by(" %like% ")) {
|
||||
replace_pos(" %like% ", with = " %unlike% ")
|
||||
} else if (pos_preceded_by(" %unlike% ")) {
|
||||
replace_pos(" %unlike% ", with = " %like_case% ")
|
||||
} else if (pos_preceded_by(" %like_case% ")) {
|
||||
replace_pos(" %like_case% ", with = " %unlike_case% ")
|
||||
} else if (pos_preceded_by(" %unlike_case% ")) {
|
||||
replace_pos(" %unlike_case% ", with = " %like% ")
|
||||
} else {
|
||||
insertText(" %like% ")
|
||||
}
|
||||
}
|
||||
|
||||
check_dataset_integrity <- function() {
|
||||
@@ -87,11 +201,13 @@ check_dataset_integrity <- function() {
|
||||
} else {
|
||||
plural <- c(" is", "s", "")
|
||||
}
|
||||
warning_("The following data set", plural[1],
|
||||
" overwritten by your global environment and prevent", plural[2],
|
||||
" the AMR package from working correctly: ",
|
||||
vector_and(overwritten, quotes = "'"),
|
||||
".\nPlease rename your object", plural[3], ".", call = FALSE)
|
||||
if (message_not_thrown_before("dataset_overwritten")) {
|
||||
warning_("The following data set", plural[1],
|
||||
" overwritten by your global environment and prevent", plural[2],
|
||||
" the AMR package from working correctly: ",
|
||||
vector_and(overwritten, quotes = "'"),
|
||||
".\nPlease rename your object", plural[3], ".", call = FALSE)
|
||||
}
|
||||
}
|
||||
# check if other packages did not overwrite our data sets
|
||||
valid_microorganisms <- TRUE
|
||||
@@ -125,67 +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,
|
||||
microorganisms.translation$mo_old)))) {
|
||||
# take first <mo> column
|
||||
found <- colnames(x)[vapply(FUN.VALUE = logical(1), x, is.mo)]
|
||||
} else if ("mo" %in% colnames_formatted &
|
||||
suppressWarnings(all(x$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 == "keyantibiotics") {
|
||||
if (any(colnames(x) %like% "^key.*(ab|antibiotics)")) {
|
||||
found <- sort(colnames(x)[colnames(x) %like% "^key.*(ab|antibiotics)"])[1]
|
||||
if (type %in% c("keyantibiotics", "keyantimicrobials")) {
|
||||
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
|
||||
@@ -198,23 +320,35 @@ 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
|
||||
}
|
||||
|
||||
is_possibly_regex <- function(x) {
|
||||
tryCatch(vapply(FUN.VALUE = character(1), strsplit(x, ""),
|
||||
function(y) any(y %in% c("$", "(", ")", "*", "+", "-", ".", "?", "[", "]", "^", "{", "|", "}", "\\"), na.rm = TRUE)),
|
||||
error = function(e) rep(TRUE, length(x)))
|
||||
is_valid_regex <- function(x) {
|
||||
regex_at_all <- tryCatch(vapply(FUN.VALUE = logical(1),
|
||||
X = strsplit(x, ""),
|
||||
FUN = function(y) any(y %in% c("$", "(", ")", "*", "+", "-",
|
||||
".", "?", "[", "]", "^", "{",
|
||||
"|", "}", "\\"),
|
||||
na.rm = TRUE),
|
||||
USE.NAMES = FALSE),
|
||||
error = function(e) rep(TRUE, length(x)))
|
||||
regex_valid <- vapply(FUN.VALUE = logical(1),
|
||||
X = x,
|
||||
FUN = function(y) !"try-error" %in% class(try(grepl(y, "", perl = TRUE),
|
||||
silent = TRUE)),
|
||||
USE.NAMES = FALSE)
|
||||
regex_at_all & regex_valid
|
||||
}
|
||||
|
||||
stop_ifnot_installed <- function(package) {
|
||||
@@ -223,8 +357,8 @@ stop_ifnot_installed <- function(package) {
|
||||
vapply(FUN.VALUE = character(1), package, function(pkg)
|
||||
tryCatch(get(".packageName", envir = asNamespace(pkg)),
|
||||
error = function(e) {
|
||||
if (package == "rstudioapi") {
|
||||
stop("This function only works in RStudio.", call. = FALSE)
|
||||
if (pkg == "rstudioapi") {
|
||||
stop("This function only works in RStudio when using R >= 3.2.", call. = FALSE)
|
||||
} else if (pkg != "base") {
|
||||
stop("This requires the '", pkg, "' package.",
|
||||
"\nTry to install it with: install.packages(\"", pkg, "\")",
|
||||
@@ -234,6 +368,18 @@ stop_ifnot_installed <- function(package) {
|
||||
return(invisible())
|
||||
}
|
||||
|
||||
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))
|
||||
} else {
|
||||
out <- requireNamespace(pkg, quietly = TRUE)
|
||||
}
|
||||
if (!is.null(min_version)) {
|
||||
out <- out && utils::packageVersion(pkg) >= min_version
|
||||
}
|
||||
isTRUE(out)
|
||||
}
|
||||
|
||||
import_fn <- function(name, pkg, error_on_fail = TRUE) {
|
||||
if (isTRUE(error_on_fail)) {
|
||||
stop_ifnot_installed(pkg)
|
||||
@@ -265,7 +411,7 @@ word_wrap <- function(...,
|
||||
msg <- paste0(c(...), collapse = "")
|
||||
|
||||
if (isTRUE(as_note)) {
|
||||
msg <- paste0("NOTE: ", gsub("^note:? ?", "", msg, ignore.case = TRUE))
|
||||
msg <- paste0(pkg_env$info_icon, " ", gsub("^note:? ?", "", msg, ignore.case = TRUE))
|
||||
}
|
||||
|
||||
if (msg %like% "\n") {
|
||||
@@ -280,6 +426,9 @@ word_wrap <- function(...,
|
||||
collapse = "\n"))
|
||||
}
|
||||
|
||||
# correct for operators (will add the space later on)
|
||||
ops <- "([,./><\\]\\[])"
|
||||
msg <- gsub(paste0(ops, " ", ops), "\\1\\2", msg, perl = TRUE)
|
||||
# we need to correct for already applied style, that adds text like "\033[31m\"
|
||||
msg_stripped <- font_stripstyle(msg)
|
||||
# where are the spaces now?
|
||||
@@ -296,11 +445,13 @@ word_wrap <- function(...,
|
||||
# put it together
|
||||
msg <- unlist(strsplit(msg, " "))
|
||||
msg[replace_spaces] <- paste0(msg[replace_spaces], "\n")
|
||||
# add space around operators again
|
||||
msg <- gsub(paste0(ops, ops), "\\1 \\2", msg, perl = TRUE)
|
||||
msg <- paste0(msg, collapse = " ")
|
||||
msg <- gsub("\n ", "\n", msg, fixed = TRUE)
|
||||
|
||||
if (msg_stripped %like% "^NOTE: ") {
|
||||
indentation <- 6 + extra_indent
|
||||
if (msg_stripped %like% "\u2139 ") {
|
||||
indentation <- 2 + extra_indent
|
||||
} else if (msg_stripped %like% "^=> ") {
|
||||
indentation <- 3 + extra_indent
|
||||
} else {
|
||||
@@ -309,7 +460,7 @@ word_wrap <- function(...,
|
||||
msg <- gsub("\n", paste0("\n", strrep(" ", indentation)), msg, fixed = TRUE)
|
||||
# remove trailing empty characters
|
||||
msg <- gsub("(\n| )+$", "", msg)
|
||||
|
||||
|
||||
if (length(add_fn) > 0) {
|
||||
if (!is.list(add_fn)) {
|
||||
add_fn <- list(add_fn)
|
||||
@@ -322,6 +473,9 @@ word_wrap <- function(...,
|
||||
# format backticks
|
||||
msg <- gsub("(`.+?`)", font_grey_bg("\\1"), msg)
|
||||
|
||||
# clean introduced whitespace between fullstops
|
||||
msg <- gsub("[.] +[.]", "..", msg)
|
||||
|
||||
msg
|
||||
}
|
||||
|
||||
@@ -403,7 +557,7 @@ stop_ifnot <- function(expr, ..., call = TRUE) {
|
||||
ifelse(!is.na(y), y, NA))
|
||||
}
|
||||
|
||||
class_integrity_check <- function(value, type, check_vector) {
|
||||
return_after_integrity_check <- function(value, type, check_vector) {
|
||||
if (!all(value[!is.na(value)] %in% check_vector)) {
|
||||
warning_(paste0("invalid ", type, ", NA generated"), call = FALSE)
|
||||
value[!value %in% check_vector] <- NA
|
||||
@@ -437,19 +591,35 @@ dataset_UTF8_to_ASCII <- function(df) {
|
||||
}
|
||||
|
||||
# for eucast_rules() and mdro(), creates markdown output with URLs and names
|
||||
create_ab_documentation <- function(ab) {
|
||||
create_eucast_ab_documentation <- function() {
|
||||
x <- trimws(unique(toupper(unlist(strsplit(EUCAST_RULES_DF$then_change_these_antibiotics, ",")))))
|
||||
ab <- 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 `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 {
|
||||
val <- as.rsi(NA)
|
||||
}
|
||||
ab <- c(ab, val)
|
||||
}
|
||||
ab <- unique(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)
|
||||
ab <- ab[order(ab_names)]
|
||||
ab_names <- ab_names[order(ab_names)]
|
||||
atcs <- ab_atc(ab)
|
||||
atcs[!is.na(atcs)] <- paste0("[", atcs[!is.na(atcs)], "](", ab_url(ab[!is.na(atcs)]), ")")
|
||||
atcs[is.na(atcs)] <- "no ATC code"
|
||||
out <- paste0(ab_names, " (`", ab, "`, ", atcs, ")", collapse = ", ")
|
||||
atc_txt <- paste0("[", atcs[!is.na(atcs)], "](", ab_url(ab), ")")
|
||||
out <- paste0(ab_names, " (`", ab, "`, ", atc_txt, ")", collapse = ", ")
|
||||
substr(out, 1, 1) <- toupper(substr(out, 1, 1))
|
||||
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)) {
|
||||
@@ -465,6 +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))
|
||||
}
|
||||
@@ -477,11 +650,12 @@ 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) {
|
||||
format_class <- function(class, plural = FALSE) {
|
||||
class.bak <- class
|
||||
class[class == "numeric"] <- "number"
|
||||
class[class == "integer"] <- "whole number"
|
||||
@@ -495,17 +669,15 @@ format_class <- function(class, plural) {
|
||||
ifelse(plural, "s", ""))
|
||||
# exceptions
|
||||
class[class == "logical"] <- ifelse(plural, "a vector of `TRUE`/`FALSE`", "`TRUE` or `FALSE`")
|
||||
if ("data.frame" %in% class) {
|
||||
class <- "a data set"
|
||||
}
|
||||
class[class == "data.frame"] <- "a data set"
|
||||
if ("list" %in% class) {
|
||||
class <- "a list"
|
||||
}
|
||||
if ("matrix" %in% class) {
|
||||
class <- "a matrix"
|
||||
}
|
||||
if ("isolate_identifier" %in% class) {
|
||||
class <- "created with isolate_identifier()"
|
||||
if ("custom_eucast_rules" %in% class) {
|
||||
class <- "input created with `custom_eucast_rules()`"
|
||||
}
|
||||
if (any(c("mo", "ab", "rsi") %in% class)) {
|
||||
class <- paste0("of class <", class[1L], ">")
|
||||
@@ -522,6 +694,7 @@ meet_criteria <- function(object,
|
||||
looks_like = NULL,
|
||||
is_in = NULL,
|
||||
is_positive = NULL,
|
||||
is_positive_or_zero = NULL,
|
||||
is_finite = NULL,
|
||||
contains_column_class = NULL,
|
||||
allow_NULL = FALSE,
|
||||
@@ -583,29 +756,37 @@ meet_criteria <- function(object,
|
||||
object <- tolower(object)
|
||||
is_in <- tolower(is_in)
|
||||
}
|
||||
stop_ifnot(all(object %in% is_in, na.rm = TRUE), "argument `", obj_name,
|
||||
"` must be ",
|
||||
ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1, "either ", ""),
|
||||
stop_ifnot(all(object %in% is_in, na.rm = TRUE), "argument `", obj_name, "` ",
|
||||
ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1,
|
||||
"must be either ",
|
||||
"must only contain values "),
|
||||
vector_or(is_in, quotes = !isTRUE(any(c("double", "numeric", "integer") %in% allow_class))),
|
||||
ifelse(allow_NA == TRUE, ", or NA", ""),
|
||||
call = call_depth)
|
||||
}
|
||||
if (!is.null(is_positive)) {
|
||||
if (isTRUE(is_positive)) {
|
||||
stop_if(is.numeric(object) && !all(object > 0, na.rm = TRUE), "argument `", obj_name,
|
||||
"` must ",
|
||||
ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1,
|
||||
"be a positive number",
|
||||
"all be positive numbers"),
|
||||
" (higher than zero)",
|
||||
"be a number higher than zero",
|
||||
"all be numbers higher than zero"),
|
||||
call = call_depth)
|
||||
}
|
||||
if (!is.null(is_finite)) {
|
||||
if (isTRUE(is_positive_or_zero)) {
|
||||
stop_if(is.numeric(object) && !all(object >= 0, na.rm = TRUE), "argument `", obj_name,
|
||||
"` must ",
|
||||
ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1,
|
||||
"be zero or a positive number",
|
||||
"all be zero or numbers higher than zero"),
|
||||
call = call_depth)
|
||||
}
|
||||
if (isTRUE(is_finite)) {
|
||||
stop_if(is.numeric(object) && !all(is.finite(object[!is.na(object)]), na.rm = TRUE), "argument `", obj_name,
|
||||
"` must ",
|
||||
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)) {
|
||||
@@ -630,57 +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)) {
|
||||
return(out)
|
||||
return(structure(out, type = "dplyr_cur_data_all"))
|
||||
}
|
||||
}
|
||||
|
||||
if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2) {
|
||||
# R-3.0 and R-3.1 do not have an `x` element in the call stack, rendering this function useless
|
||||
if (is.na(arg_name)) {
|
||||
# like in carbapenems() etc.
|
||||
warning_("this function can only be used in R >= 3.2", call = call)
|
||||
return(data.frame())
|
||||
} else {
|
||||
stop_("argument `", arg_name, "` is missing with no default", call = call)
|
||||
}
|
||||
}
|
||||
|
||||
# try a (base R) method, by going over the complete system call stack with sys.frames()
|
||||
not_set <- TRUE
|
||||
frms <- lapply(sys.frames(), function(el) {
|
||||
if (not_set == TRUE && ".Generic" %in% names(el)) {
|
||||
if (tryCatch(".data" %in% names(el) && is.data.frame(el$`.data`), error = function(e) FALSE)) {
|
||||
# dplyr? - an element `.data` will be in the system call stack
|
||||
# will be used in dplyr::select() (but not in dplyr::filter(), dplyr::mutate() or dplyr::summarise())
|
||||
not_set <<- FALSE
|
||||
el$`.data`
|
||||
} else if (tryCatch(any(c("x", "xx") %in% names(el)), error = function(e) FALSE)) {
|
||||
# otherwise try base R:
|
||||
# an element `x` will be in this environment for only cols, e.g. `example_isolates[, carbapenems()]`
|
||||
# an element `xx` will be in this environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
|
||||
if (tryCatch(is.data.frame(el$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$x, type = "base_R"))
|
||||
}
|
||||
} else {
|
||||
NULL
|
||||
}
|
||||
})
|
||||
|
||||
vars_df <- tryCatch(frms[[which(!vapply(FUN.VALUE = logical(1), frms, is.null))]], error = function(e) NULL)
|
||||
if (is.data.frame(vars_df)) {
|
||||
return(vars_df)
|
||||
}
|
||||
|
||||
# nothing worked, so:
|
||||
# no data.frame found, so an error must be returned:
|
||||
if (is.na(arg_name)) {
|
||||
if (isTRUE(is.numeric(call))) {
|
||||
fn <- as.character(sys.call(call + 1)[1])
|
||||
@@ -692,10 +848,11 @@ get_current_data <- function(arg_name, call) {
|
||||
} else {
|
||||
examples <- ""
|
||||
}
|
||||
stop_("this function must be used inside valid dplyr selection verbs or inside a data.frame call",
|
||||
stop_("this function must be used inside a `dplyr` verb or `data.frame` call",
|
||||
examples,
|
||||
call = call)
|
||||
} else {
|
||||
# mimic a base R error that the argument is missing
|
||||
stop_("argument `", arg_name, "` is missing with no default", call = call)
|
||||
}
|
||||
}
|
||||
@@ -710,19 +867,19 @@ get_current_column <- function() {
|
||||
}
|
||||
}
|
||||
|
||||
# cur_column() doesn't always work (only allowed for conditions set by dplyr), but it's probably still possible:
|
||||
frms <- lapply(sys.frames(), function(el) {
|
||||
if ("i" %in% names(el)) {
|
||||
if ("tibble_vars" %in% names(el)) {
|
||||
# cur_column() doesn't always work (only allowed for certain conditions set by dplyr), but it's probably still possible:
|
||||
frms <- lapply(sys.frames(), function(env) {
|
||||
if (!is.null(env$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 {
|
||||
@@ -740,7 +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")
|
||||
}
|
||||
|
||||
@@ -749,30 +906,30 @@ 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") {
|
||||
# unit tests will keep the same call and environment - give them a unique ID
|
||||
call <- paste0(sample(c(c(0:9), letters[1:6]), size = 64, replace = TRUE), collapse = "")
|
||||
}
|
||||
c(envir = gsub("<environment: (.*)>", "\\1", utils::capture.output(sys.frames()[[1]])),
|
||||
call = paste0(deparse(sys.calls()[[1]]), collapse = ""))
|
||||
call = call)
|
||||
}
|
||||
}
|
||||
|
||||
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))
|
||||
}
|
||||
|
||||
reset_all_thrown_messages <- function() {
|
||||
# for unit tests, where the environment and highest system call do not change
|
||||
pkg_env_contents <- ls(envir = pkg_env)
|
||||
rm(list = pkg_env_contents[pkg_env_contents %like% "^thrown_msg."],
|
||||
envir = pkg_env)
|
||||
# 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() {
|
||||
@@ -790,7 +947,7 @@ has_colour <- function() {
|
||||
if (Sys.getenv("RSTUDIO", "") == "") {
|
||||
return(FALSE)
|
||||
}
|
||||
if ((cols <- Sys.getenv("RSTUDIO_CONSOLE_COLOR", "")) != "" && !is.na(as.numeric(cols))) {
|
||||
if ((cols <- Sys.getenv("RSTUDIO_CONSOLE_COLOR", "")) != "" && !is.na(as.double(cols))) {
|
||||
return(TRUE)
|
||||
}
|
||||
tryCatch(get("isAvailable", envir = asNamespace("rstudioapi"))(), error = function(e) return(FALSE)) &&
|
||||
@@ -867,12 +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)()$dark, error = function(e) FALSE)) {
|
||||
# similar to HTML #444444
|
||||
try_colour(..., before = "\033[48;5;238m", after = "\033[49m", collapse = collapse)
|
||||
} else {
|
||||
# similar to HTML #eeeeee
|
||||
try_colour(..., before = "\033[48;5;254m", after = "\033[49m", collapse = collapse)
|
||||
# similar to HTML #f0f0f0
|
||||
try_colour(..., before = "\033[48;5;255m", after = "\033[49m", collapse = collapse)
|
||||
}
|
||||
}
|
||||
font_green_bg <- function(..., collapse = " ") {
|
||||
@@ -913,8 +1070,8 @@ font_stripstyle <- function(x) {
|
||||
gsub("(?:(?:\\x{001b}\\[)|\\x{009b})(?:(?:[0-9]{1,3})?(?:(?:;[0-9]{0,3})*)?[A-M|f-m])|\\x{001b}[A-M]", "", x, perl = TRUE)
|
||||
}
|
||||
|
||||
progress_ticker <- function(n = 1, n_min = 0, ...) {
|
||||
if (!interactive() || n < n_min) {
|
||||
progress_ticker <- function(n = 1, n_min = 0, print = TRUE, ...) {
|
||||
if (print == FALSE || n < n_min) {
|
||||
pb <- list()
|
||||
pb$tick <- function() {
|
||||
invisible()
|
||||
@@ -1011,7 +1168,7 @@ s3_register <- function(generic, class, method = NULL) {
|
||||
|
||||
# works exactly like round(), but rounds `round2(44.55, 1)` to 44.6 instead of 44.5
|
||||
# and adds decimal zeroes until `digits` is reached when force_zero = TRUE
|
||||
round2 <- function(x, digits = 0, force_zero = TRUE) {
|
||||
round2 <- function(x, digits = 1, force_zero = TRUE) {
|
||||
x <- as.double(x)
|
||||
# https://stackoverflow.com/a/12688836/4575331
|
||||
val <- (trunc((abs(x) * 10 ^ digits) + 0.5) / 10 ^ digits) * sign(x)
|
||||
@@ -1056,11 +1213,14 @@ percentage <- function(x, digits = NULL, ...) {
|
||||
if (is.null(digits)) {
|
||||
digits <- getdecimalplaces(x)
|
||||
}
|
||||
if (is.null(digits) || is.na(digits) || !is.numeric(digits)) {
|
||||
digits <- 2
|
||||
}
|
||||
|
||||
# round right: percentage(0.4455) and format(as.percentage(0.4455), 1) should return "44.6%", not "44.5%"
|
||||
x_formatted <- format(round2(as.double(x), digits = digits + 2) * 100,
|
||||
scientific = FALSE,
|
||||
digits = digits,
|
||||
digits = max(1, digits),
|
||||
nsmall = digits,
|
||||
...)
|
||||
x_formatted <- paste0(x_formatted, "%")
|
||||
@@ -1080,15 +1240,15 @@ percentage <- function(x, digits = NULL, ...) {
|
||||
}
|
||||
|
||||
time_start_tracking <- function() {
|
||||
pkg_env$time_start <- round(as.numeric(Sys.time()) * 1000)
|
||||
pkg_env$time_start <- round(as.double(Sys.time()) * 1000)
|
||||
}
|
||||
|
||||
time_track <- function(name = NULL) {
|
||||
paste("(until now:", trimws(round(as.numeric(Sys.time()) * 1000) - pkg_env$time_start), "ms)")
|
||||
paste("(until now:", trimws(round(as.double(Sys.time()) * 1000) - pkg_env$time_start), "ms)")
|
||||
}
|
||||
|
||||
# prevent dependency on package 'backports'
|
||||
# these functions were not available in previous versions of R (last checked: R 4.0.3)
|
||||
# prevent dependency on package 'backports' ----
|
||||
# these functions were not available in previous versions of R (last checked: R 4.1.0)
|
||||
# see here for the full list: https://github.com/r-lib/backports
|
||||
strrep <- function(x, times) {
|
||||
x <- as.character(x)
|
||||
@@ -1102,14 +1262,13 @@ strrep <- function(x, times) {
|
||||
paste0(replicate(times, x), collapse = "")
|
||||
}, list(x = x, times = times), MoreArgs = list()), use.names = FALSE)
|
||||
}
|
||||
trimws <- function(x, which = c("both", "left", "right")) {
|
||||
trimws <- function(x, which = c("both", "left", "right"), whitespace = "[ \t\r\n]") {
|
||||
which <- match.arg(which)
|
||||
mysub <- function(re, x) sub(re, "", x, perl = TRUE)
|
||||
if (which == "left")
|
||||
return(mysub("^[ \t\r\n]+", x))
|
||||
if (which == "right")
|
||||
return(mysub("[ \t\r\n]+$", x))
|
||||
mysub("[ \t\r\n]+$", mysub("^[ \t\r\n]+", x))
|
||||
switch(which,
|
||||
left = mysub(paste0("^", whitespace, "+"), x),
|
||||
right = mysub(paste0(whitespace, "+$"), x),
|
||||
both = mysub(paste0(whitespace, "+$"), mysub(paste0("^", whitespace, "+"), x)))
|
||||
}
|
||||
isFALSE <- function(x) {
|
||||
is.logical(x) && length(x) == 1L && !is.na(x) && !x
|
||||
@@ -1135,3 +1294,15 @@ isNamespaceLoaded <- function(pkg) {
|
||||
lengths <- function(x, use.names = TRUE) {
|
||||
vapply(x, length, FUN.VALUE = NA_integer_, USE.NAMES = use.names)
|
||||
}
|
||||
|
||||
if (getRversion() < "3.1") {
|
||||
# R-3.0 does not contain these functions, set them here to prevent installation failure
|
||||
# (required for extension of the <mic> class)
|
||||
cospi <- function(...) 1
|
||||
sinpi <- function(...) 1
|
||||
tanpi <- function(...) 1
|
||||
}
|
||||
dir.exists <- function (paths) {
|
||||
x = base::file.info(paths)$isdir
|
||||
!is.na(x) & x
|
||||
}
|
||||
|
||||
@@ -27,13 +27,13 @@
|
||||
#'
|
||||
#' Use this function to determine the antibiotic code of one or more antibiotics. The data set [antibiotics] will be searched for abbreviations, official names and synonyms (brand names).
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param x character vector to determine to antibiotic ID
|
||||
#' @param flag_multiple_results logical to indicate whether a note should be printed to the console that probably more than one antibiotic code or name can be retrieved from a single input value.
|
||||
#' @param info logical to indicate whether a progress bar should be printed
|
||||
#' @param x a [character] vector to determine to antibiotic ID
|
||||
#' @param flag_multiple_results a [logical] to indicate whether a note should be printed to the console that probably more than one antibiotic code or name can be retrieved from a single input value.
|
||||
#' @param info a [logical] to indicate whether a progress bar should be printed, defaults to `TRUE` only in interactive mode
|
||||
#' @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:
|
||||
#'
|
||||
@@ -50,7 +50,7 @@
|
||||
#'
|
||||
#' WHONET 2019 software: \url{http://www.whonet.org/software.html}
|
||||
#'
|
||||
#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}
|
||||
#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
|
||||
#' @aliases ab
|
||||
#' @return A [character] [vector] with additional class [`ab`]
|
||||
#' @seealso
|
||||
@@ -82,7 +82,7 @@
|
||||
#' # they use as.ab() internally:
|
||||
#' ab_name("J01FA01") # "Erythromycin"
|
||||
#' ab_name("eryt") # "Erythromycin"
|
||||
#'
|
||||
#' \donttest{
|
||||
#' if (require("dplyr")) {
|
||||
#'
|
||||
#' # you can quickly rename <rsi> columns using dplyr >= 1.0.0:
|
||||
@@ -90,7 +90,8 @@
|
||||
#' rename_with(as.ab, where(is.rsi))
|
||||
#'
|
||||
#' }
|
||||
as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
|
||||
#' }
|
||||
as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
|
||||
meet_criteria(x, allow_class = c("character", "numeric", "integer", "factor"), allow_NA = TRUE)
|
||||
meet_criteria(flag_multiple_results, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(info, allow_class = "logical", has_length = 1)
|
||||
@@ -100,6 +101,11 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
|
||||
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)
|
||||
@@ -109,28 +115,12 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
|
||||
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?$)", "", x, ignore.case = TRUE, perl = TRUE)
|
||||
# penicillin is a special case: we call it so, but then mean benzylpenicillin
|
||||
x[x %like_case% "^PENICILLIN" & x %unlike_case% "[ /+-]"] <- "benzylpenicillin"
|
||||
x_bak_clean <- x
|
||||
if (already_regex == FALSE) {
|
||||
x_bak_clean <- generalise_antibiotic_name(x_bak_clean)
|
||||
@@ -154,13 +144,29 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
|
||||
found[1L]
|
||||
}
|
||||
|
||||
if (initial_search == TRUE) {
|
||||
progress <- progress_ticker(n = length(x), n_min = ifelse(isTRUE(info), 25, length(x) + 1)) # start if n >= 25
|
||||
# Fill in names, AB codes, CID codes and ATC codes directly (`x` is already clean and uppercase)
|
||||
known_names <- x %in% AB_lookup$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()
|
||||
}
|
||||
@@ -169,8 +175,6 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
|
||||
next
|
||||
}
|
||||
if (identical(x[i], "") |
|
||||
# no short names:
|
||||
nchar(x[i]) <= 2 |
|
||||
# prevent "bacteria" from coercing to TMP, since Bacterial is a brand name of it:
|
||||
identical(tolower(x[i]), "bacteria")) {
|
||||
x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
|
||||
@@ -190,34 +194,6 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
|
||||
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$generalised_loinc,
|
||||
function(s) x[i] %in% s))
|
||||
@@ -238,7 +214,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
|
||||
|
||||
# exact abbreviation
|
||||
abbr_found <- unlist(lapply(AB_lookup$generalised_abbreviations,
|
||||
function(s) x[i] %in% s))
|
||||
# require at least 2 characters for abbreviations
|
||||
function(s) x[i] %in% s & nchar(x[i]) >= 2))
|
||||
found <- antibiotics$ab[abbr_found == TRUE]
|
||||
if (length(found) > 0) {
|
||||
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
|
||||
@@ -252,6 +229,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
|
||||
}
|
||||
x_spelling <- x[i]
|
||||
if (already_regex == FALSE) {
|
||||
|
||||
x_spelling <- gsub("[IY]+", "[IY]+", x_spelling, perl = TRUE)
|
||||
x_spelling <- gsub("(C|K|Q|QU|S|Z|X|KS)+", "(C|K|Q|QU|S|Z|X|KS)+", x_spelling, perl = TRUE)
|
||||
x_spelling <- gsub("(PH|F|V)+", "(PH|F|V)+", x_spelling, perl = TRUE)
|
||||
@@ -296,7 +274,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
|
||||
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
|
||||
next
|
||||
}
|
||||
|
||||
|
||||
# INITIAL SEARCH - More uncertain results ----
|
||||
|
||||
if (initial_search == TRUE && fast_mode == FALSE) {
|
||||
@@ -325,9 +303,9 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
|
||||
function(y) {
|
||||
for (i in seq_len(length(y))) {
|
||||
for (lang in LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED != "en"]) {
|
||||
y[i] <- ifelse(tolower(y[i]) %in% tolower(translations_file[, lang, drop = TRUE]),
|
||||
translations_file[which(tolower(translations_file[, lang, drop = TRUE]) == tolower(y[i]) &
|
||||
!isFALSE(translations_file$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])
|
||||
}
|
||||
}
|
||||
@@ -389,7 +367,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
|
||||
|
||||
# first 5 except for cephalosporins, then first 7 (those cephalosporins all start quite the same!)
|
||||
found <- suppressWarnings(as.ab(substr(x[i], 1, 5), initial_search = FALSE))
|
||||
if (!is.na(found) && !ab_group(found, initial_search = FALSE) %like% "cephalosporins") {
|
||||
if (!is.na(found) && ab_group(found, initial_search = FALSE) %unlike% "cephalosporins") {
|
||||
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
|
||||
next
|
||||
}
|
||||
@@ -461,14 +439,14 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
|
||||
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)
|
||||
@@ -477,14 +455,10 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
|
||||
if (length(x_unknown) > 0 & fast_mode == FALSE) {
|
||||
warning_("These values could not be coerced to a valid antimicrobial ID: ",
|
||||
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_
|
||||
}
|
||||
@@ -552,7 +526,7 @@ as.data.frame.ab <- function(x, ...) {
|
||||
"[<-.ab" <- function(i, j, ..., value) {
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(i)
|
||||
class_integrity_check(y, "antimicrobial code", antibiotics$ab)
|
||||
return_after_integrity_check(y, "antimicrobial code", antibiotics$ab)
|
||||
}
|
||||
#' @method [[<- ab
|
||||
#' @export
|
||||
@@ -560,15 +534,16 @@ as.data.frame.ab <- function(x, ...) {
|
||||
"[[<-.ab" <- function(i, j, ..., value) {
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(i)
|
||||
class_integrity_check(y, "antimicrobial code", antibiotics$ab)
|
||||
return_after_integrity_check(y, "antimicrobial code", antibiotics$ab)
|
||||
}
|
||||
#' @method c ab
|
||||
#' @export
|
||||
#' @noRd
|
||||
c.ab <- function(x, ...) {
|
||||
c.ab <- function(...) {
|
||||
x <- list(...)[[1L]]
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(x)
|
||||
class_integrity_check(y, "antimicrobial code", antibiotics$ab)
|
||||
return_after_integrity_check(y, "antimicrobial code", antibiotics$ab)
|
||||
}
|
||||
|
||||
#' @method unique ab
|
||||
@@ -580,6 +555,15 @@ unique.ab <- function(x, incomparables = FALSE, ...) {
|
||||
y
|
||||
}
|
||||
|
||||
#' @method rep ab
|
||||
#' @export
|
||||
#' @noRd
|
||||
rep.ab <- function(x, ...) {
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(x)
|
||||
y
|
||||
}
|
||||
|
||||
generalise_antibiotic_name <- function(x) {
|
||||
x <- toupper(x)
|
||||
# remove suffices
|
||||
|
||||
+648
-142
@@ -23,18 +23,32 @@
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Antibiotic Class Selectors
|
||||
#' Antibiotic Selectors
|
||||
#'
|
||||
#' These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
|
||||
#' These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group, without the need to define the columns or antibiotic abbreviations. In short, if you have a column name that resembles an antimicrobial agent, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "CZO" and "J01DB04" will all be picked up by [cephalosporins()].
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param only_rsi_columns a logical to indicate whether only columns of class `<rsi>` must be selected (defaults to `FALSE`), see [as.rsi()]
|
||||
#' @inheritParams filter_ab_class
|
||||
#' @details \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 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 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()]
|
||||
#' @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 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.
|
||||
#' All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the [antibiotics] data set. This means that a selector such as [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
|
||||
#'
|
||||
#' The [ab_class()] function can be used to filter/select on a manually defined antibiotic class. It searches for results in the [antibiotics] data set within the columns `group`, `atc_group1` and `atc_group2`.
|
||||
#'
|
||||
#' The [ab_selector()] function can be used to internally filter the [antibiotics] data set on any results, see *Examples*. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.
|
||||
#'
|
||||
#' The [administrable_per_os()] and [administrable_iv()] functions also rely on the [antibiotics] data set - antibiotic columns will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the [antibiotics] data set.
|
||||
#'
|
||||
#' @section Full list of supported (antibiotic) classes:
|
||||
#'
|
||||
#' `r paste0(" * ", na.omit(sapply(DEFINED_AB_GROUPS, function(ab) ifelse(tolower(gsub("^AB_", "", ab)) %in% ls(envir = asNamespace("AMR")), paste0("[", tolower(gsub("^AB_", "", ab)), "()] can select: \\cr ", vector_and(paste0(ab_name(eval(parse(text = ab), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), " (", eval(parse(text = ab), envir = asNamespace("AMR")), ")"), quotes = FALSE, sort = TRUE)), character(0)), USE.NAMES = FALSE)), "\n", collapse = "")`
|
||||
#' @rdname antibiotic_class_selectors
|
||||
#' @seealso [filter_ab_class()] for the `filter()` equivalent.
|
||||
#' @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!
|
||||
@@ -42,13 +56,62 @@
|
||||
#' # `example_isolates` is a data set available in the AMR package.
|
||||
#' # See ?example_isolates.
|
||||
#'
|
||||
#' # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
|
||||
#' # base R ------------------------------------------------------------------
|
||||
#'
|
||||
#' # select columns 'IPM' (imipenem) and 'MEM' (meropenem)
|
||||
#' example_isolates[, carbapenems()]
|
||||
#' # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
|
||||
#'
|
||||
#' # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
|
||||
#' example_isolates[, c("mo", aminoglycosides())]
|
||||
#'
|
||||
#' # select only antibiotic columns with DDDs for oral treatment
|
||||
#' example_isolates[, administrable_per_os()]
|
||||
#'
|
||||
#' # filter using any() or all()
|
||||
#' example_isolates[any(carbapenems() == "R"), ]
|
||||
#' subset(example_isolates, any(carbapenems() == "R"))
|
||||
#'
|
||||
#' # filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
|
||||
#' example_isolates[any(carbapenems()), ]
|
||||
#' example_isolates[all(carbapenems()), ]
|
||||
#'
|
||||
#' # filter with multiple antibiotic selectors using c()
|
||||
#' example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]
|
||||
#'
|
||||
#' # filter + select in one go: get penicillins in 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{
|
||||
#' if (require("dplyr")) {
|
||||
#'
|
||||
#' # get AMR for all aminoglycosides e.g., per hospital:
|
||||
#' 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 %>%
|
||||
#' select(carbapenems())
|
||||
@@ -57,11 +120,24 @@
|
||||
#' example_isolates %>%
|
||||
#' select(mo, aminoglycosides())
|
||||
#'
|
||||
#' # any() and all() work in dplyr's filter() too:
|
||||
#' example_isolates %>%
|
||||
#' filter(any(aminoglycosides() == "R"),
|
||||
#' all(cephalosporins_2nd() == "R"))
|
||||
#'
|
||||
#' # also works with c():
|
||||
#' example_isolates %>%
|
||||
#' filter(any(c(carbapenems(), aminoglycosides()) == "R"))
|
||||
#'
|
||||
#' # not setting any/all will automatically apply all():
|
||||
#' example_isolates %>%
|
||||
#' filter(aminoglycosides() == "R")
|
||||
#' #> i Assuming a filter on all 4 aminoglycosides.
|
||||
#'
|
||||
#' # this will select columns 'mo' and all antimycobacterial drugs ('RIF'):
|
||||
#' example_isolates %>%
|
||||
#' select(mo, ab_class("mycobact"))
|
||||
#'
|
||||
#'
|
||||
#' # get bug/drug combinations for only macrolides in Gram-positives:
|
||||
#' example_isolates %>%
|
||||
#' filter(mo_is_gram_positive()) %>%
|
||||
@@ -69,165 +145,595 @@
|
||||
#' 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 equal:
|
||||
#' # (though the row names on the first are more correct)
|
||||
#' example_isolates %>% filter_carbapenems("R", "all")
|
||||
#' example_isolates %>% filter(across(carbapenems(), ~. == "R"))
|
||||
#' # with dplyr 1.0.0 and higher (that adds 'across()'), this is all equal:
|
||||
#' 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
|
||||
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)
|
||||
|
||||
if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2) {
|
||||
warning_("antibiotic class selectors such as ", function_name,
|
||||
"() require R version 3.2 or later - you have ", R.version.string,
|
||||
call = FALSE)
|
||||
return(NULL)
|
||||
}
|
||||
ab_selector <- function(filter,
|
||||
only_rsi_columns = FALSE,
|
||||
only_treatable = TRUE,
|
||||
...) {
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
|
||||
|
||||
# get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
|
||||
# but it only takes a couple of milliseconds
|
||||
vars_df <- get_current_data(arg_name = NA, call = -2)
|
||||
# to improve speed, get_column_abx() will only run once when e.g. in a select or group call
|
||||
ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE)
|
||||
call <- substitute(filter)
|
||||
agents <- tryCatch(AMR::antibiotics[which(eval(call, envir = AMR::antibiotics)), "ab", drop = TRUE],
|
||||
error = function(e) stop_(e$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)
|
||||
|
||||
# improve speed here so it will only run once when e.g. in one select call
|
||||
if (!identical(pkg_env$ab_selector, unique_call_id())) {
|
||||
ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns)
|
||||
pkg_env$ab_selector <- unique_call_id()
|
||||
pkg_env$ab_selector_cols <- ab_in_data
|
||||
} else {
|
||||
ab_in_data <- pkg_env$ab_selector_cols
|
||||
# to improve speed, get_column_abx() will only run once when e.g. in a select or group call
|
||||
ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE)
|
||||
|
||||
# untreatable drugs
|
||||
untreatable <- antibiotics[which(antibiotics$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), ")")
|
||||
# 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)$ab
|
||||
ab_group <- find_ab_group(ab_class_args)
|
||||
function_name <- "ab_class"
|
||||
examples <- paste0(" (such as ", find_ab_names(ab_class_args, 2), ")")
|
||||
}
|
||||
|
||||
# get the columns with a group names in the chosen ab class
|
||||
agents <- ab_in_data[names(ab_in_data) %in% ab_reference$ab]
|
||||
if (message_not_thrown_before(function_name)) {
|
||||
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
|
||||
#' @export
|
||||
#' @noRd
|
||||
c.ab_selector <- function(...) {
|
||||
structure(unlist(lapply(list(...), as.character)),
|
||||
class = c("ab_selector", "character"))
|
||||
}
|
||||
|
||||
all_any_ab_selector <- function(type, ..., na.rm = TRUE) {
|
||||
cols_ab <- c(...)
|
||||
result <- cols_ab[toupper(cols_ab) %in% c("R", "S", "I")]
|
||||
if (length(result) == 0) {
|
||||
message_("Filtering ", type, " of columns ", vector_and(font_bold(cols_ab, collapse = NULL), quotes = "'"), ' to contain value "R", "S" or "I"')
|
||||
result <- c("R", "S", "I")
|
||||
}
|
||||
cols_ab <- cols_ab[!cols_ab %in% result]
|
||||
df <- get_current_data(arg_name = NA, call = -3)
|
||||
|
||||
if (type == "all") {
|
||||
scope_fn <- all
|
||||
} else {
|
||||
scope_fn <- any
|
||||
}
|
||||
|
||||
x_transposed <- as.list(as.data.frame(t(df[, cols_ab, drop = FALSE]), stringsAsFactors = FALSE))
|
||||
vapply(FUN.VALUE = logical(1),
|
||||
X = x_transposed,
|
||||
FUN = function(y) scope_fn(y %in% result, na.rm = na.rm),
|
||||
USE.NAMES = FALSE)
|
||||
}
|
||||
|
||||
#' @method all ab_selector
|
||||
#' @export
|
||||
#' @noRd
|
||||
all.ab_selector <- function(..., na.rm = FALSE) {
|
||||
all_any_ab_selector("all", ..., na.rm = na.rm)
|
||||
}
|
||||
|
||||
#' @method any ab_selector
|
||||
#' @export
|
||||
#' @noRd
|
||||
any.ab_selector <- function(..., na.rm = FALSE) {
|
||||
all_any_ab_selector("any", ..., na.rm = na.rm)
|
||||
}
|
||||
|
||||
|
||||
#' @method all ab_selector_any_all
|
||||
#' @export
|
||||
#' @noRd
|
||||
all.ab_selector_any_all <- function(..., na.rm = FALSE) {
|
||||
# this is all() on a logical vector from `==.ab_selector` or `!=.ab_selector`
|
||||
# e.g., example_isolates %>% filter(all(carbapenems() == "R"))
|
||||
# so just return the vector as is, only correcting for na.rm
|
||||
out <- unclass(c(...))
|
||||
if (na.rm == TRUE) {
|
||||
out <- out[!is.na(out)]
|
||||
}
|
||||
out
|
||||
}
|
||||
|
||||
#' @method any ab_selector_any_all
|
||||
#' @export
|
||||
#' @noRd
|
||||
any.ab_selector_any_all <- function(..., na.rm = FALSE) {
|
||||
# this is any() on a logical vector from `==.ab_selector` or `!=.ab_selector`
|
||||
# e.g., example_isolates %>% filter(any(carbapenems() == "R"))
|
||||
# so just return the vector as is, only correcting for na.rm
|
||||
out <- unclass(c(...))
|
||||
if (na.rm == TRUE) {
|
||||
out <- out[!is.na(out)]
|
||||
}
|
||||
out
|
||||
}
|
||||
|
||||
#' @method == ab_selector
|
||||
#' @export
|
||||
#' @noRd
|
||||
`==.ab_selector` <- function(e1, e2) {
|
||||
calls <- as.character(match.call())
|
||||
fn_name <- calls[2]
|
||||
fn_name <- gsub("^(c\\()(.*)(\\))$", "\\2", fn_name)
|
||||
if (is_any(fn_name)) {
|
||||
type <- "any"
|
||||
} else if (is_all(fn_name)) {
|
||||
type <- "all"
|
||||
} else {
|
||||
type <- "all"
|
||||
if (length(e1) > 1) {
|
||||
message_("Assuming a filter on ", type, " ", length(e1), " ", gsub("[\\(\\)]", "", fn_name),
|
||||
". Wrap around `all()` or `any()` to prevent this note.")
|
||||
}
|
||||
}
|
||||
structure(all_any_ab_selector(type = type, e1, e2),
|
||||
class = c("ab_selector_any_all", "logical"))
|
||||
}
|
||||
|
||||
#' @method != ab_selector
|
||||
#' @export
|
||||
#' @noRd
|
||||
`!=.ab_selector` <- function(e1, e2) {
|
||||
calls <- as.character(match.call())
|
||||
fn_name <- calls[2]
|
||||
fn_name <- gsub("^(c\\()(.*)(\\))$", "\\2", fn_name)
|
||||
if (is_any(fn_name)) {
|
||||
type <- "any"
|
||||
} else if (is_all(fn_name)) {
|
||||
type <- "all"
|
||||
} else {
|
||||
type <- "all"
|
||||
if (length(e1) > 1) {
|
||||
message_("Assuming a filter on ", type, " ", length(e1), " ", gsub("[\\(\\)]", "", fn_name),
|
||||
". Wrap around `all()` or `any()` to prevent this note.")
|
||||
}
|
||||
}
|
||||
# this is `!=`, so turn around the values
|
||||
rsi <- c("R", "S", "I")
|
||||
e2 <- rsi[rsi != e2]
|
||||
structure(all_any_ab_selector(type = type, e1, e2),
|
||||
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)
|
||||
syscall %like% paste0("[^_a-zA-Z0-9]any\\(", "(c\\()?", el1)
|
||||
}
|
||||
is_all <- function(el1) {
|
||||
syscall <- paste0(trimws(deparse(sys.calls()[[1]])), collapse = " ")
|
||||
el1 <- gsub("(.*),.*", "\\1", el1)
|
||||
syscall %like% paste0("[^_a-zA-Z0-9]all\\(", "(c\\()?", el1)
|
||||
}
|
||||
|
||||
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) {
|
||||
ab_group <- gsub("[^a-zA-Z|0-9]", ".*", ab_group)
|
||||
|
||||
# try popular first, they have DDDs
|
||||
drugs <- antibiotics[which((!is.na(antibiotics$iv_ddd) | !is.na(antibiotics$oral_ddd)) &
|
||||
antibiotics$name %unlike% " " &
|
||||
antibiotics$group %like% ab_group &
|
||||
antibiotics$ab %unlike% "[0-9]$"), ]$name
|
||||
if (length(drugs) < n) {
|
||||
# now try it all
|
||||
drugs <- antibiotics[which((antibiotics$group %like% ab_group |
|
||||
antibiotics$atc_group1 %like% ab_group |
|
||||
antibiotics$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) {
|
||||
message_("No antimicrobial agents of class ", ab_group, " found", examples, ".")
|
||||
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 <- 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_("Selecting ", ab_group, ": ",
|
||||
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),
|
||||
as_note = FALSE,
|
||||
extra_indent = 6)
|
||||
vector_and(agents_formatted, quotes = FALSE, sort = FALSE))
|
||||
}
|
||||
remember_thrown_message(function_name)
|
||||
}
|
||||
unname(agents)
|
||||
}
|
||||
|
||||
+7
-4
@@ -29,16 +29,17 @@
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param text text to analyse
|
||||
#' @param type type of property to search for, either `"drug"`, `"dose"` or `"administration"`, see *Examples*
|
||||
#' @param collapse character to pass on to `paste(, collapse = ...)` to only return one character per element of `text`, see *Examples*
|
||||
#' @param collapse a [character] to pass on to `paste(, collapse = ...)` to only return one [character] per element of `text`, see *Examples*
|
||||
#' @param translate_ab if `type = "drug"`: a column name of the [antibiotics] data set to translate the antibiotic abbreviations to, using [ab_property()]. Defaults to `FALSE`. Using `TRUE` is equal to using "name".
|
||||
#' @param thorough_search logical to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to `TRUE` will take considerably more time than when using `FALSE`. At default, it will turn `TRUE` when all input elements contain a maximum of three words.
|
||||
#' @param thorough_search a [logical] to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to `TRUE` will take considerably more time than when using `FALSE`. At default, it will turn `TRUE` when all input elements contain a maximum of three words.
|
||||
#' @param info a [logical] to indicate whether a progress bar should be printed, defaults to `TRUE` only in interactive mode
|
||||
#' @param ... arguments passed on to [as.ab()]
|
||||
#' @details This function is also internally used by [as.ab()], although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the [as.ab()] function may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems.
|
||||
#'
|
||||
#' ## Argument `type`
|
||||
#' At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses [as.ab()] internally, it will correct for misspelling.
|
||||
#'
|
||||
#' With `type = "dose"` (or similar, like "dosing", "doses"), all text elements will be searched for numeric values that are higher than 100 and do not resemble years. The output will be numeric. It supports any unit (g, mg, IE, etc.) and multiple values in one clinical text, see *Examples*.
|
||||
#' With `type = "dose"` (or similar, like "dosing", "doses"), all text elements will be searched for [numeric] values that are higher than 100 and do not resemble years. The output will be [numeric]. It supports any unit (g, mg, IE, etc.) and multiple values in one clinical text, see *Examples*.
|
||||
#'
|
||||
#' With `type = "administration"` (or abbreviations, like "admin", "adm"), all text elements will be searched for a form of drug administration. It supports the following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal and vaginal. Abbreviations for oral (such as 'po', 'per os') will become "oral", all values for intravenous (such as 'iv', 'intraven') will become "iv". It supports multiple values in one clinical text, see *Examples*.
|
||||
#'
|
||||
@@ -92,6 +93,7 @@ ab_from_text <- function(text,
|
||||
collapse = NULL,
|
||||
translate_ab = FALSE,
|
||||
thorough_search = NULL,
|
||||
info = interactive(),
|
||||
...) {
|
||||
if (missing(type)) {
|
||||
type <- type[1L]
|
||||
@@ -102,12 +104,13 @@ ab_from_text <- function(text,
|
||||
meet_criteria(collapse, has_length = 1, allow_NULL = TRUE)
|
||||
meet_criteria(translate_ab, allow_NULL = FALSE) # get_translate_ab() will be more informative about what's allowed
|
||||
meet_criteria(thorough_search, allow_class = "logical", has_length = 1, allow_NULL = TRUE)
|
||||
meet_criteria(info, allow_class = "logical", has_length = 1)
|
||||
|
||||
type <- tolower(trimws(type))
|
||||
|
||||
text <- tolower(as.character(text))
|
||||
text_split_all <- strsplit(text, "[ ;.,:\\|]")
|
||||
progress <- progress_ticker(n = length(text_split_all), n_min = 5)
|
||||
progress <- progress_ticker(n = length(text_split_all), n_min = 5, print = info)
|
||||
on.exit(close(progress))
|
||||
|
||||
if (type %like% "(drug|ab|anti)") {
|
||||
|
||||
+226
-52
@@ -28,23 +28,28 @@
|
||||
#' Use these functions to return a specific property of an antibiotic from the [antibiotics] data set. All input values will be evaluated internally with [as.ab()].
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param x any (vector of) text that can be coerced to a valid antibiotic code with [as.ab()]
|
||||
#' @param tolower 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 tolower a [logical] to indicate whether the first [character] of every output should be transformed to a lower case [character]. This will lead to e.g. "polymyxin B" and not "polymyxin b".
|
||||
#' @param property one of the column names of one of the [antibiotics] data set: `vector_or(colnames(antibiotics), sort = FALSE)`.
|
||||
#' @param language language of the returned text, defaults to system language (see [get_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation.
|
||||
#' @param 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
|
||||
#'
|
||||
@@ -88,12 +93,39 @@
|
||||
#' 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)
|
||||
meet_criteria(tolower, allow_class = "logical", has_length = 1)
|
||||
|
||||
x <- translate_AMR(ab_validate(x = x, property = "name", ...), language = language)
|
||||
x <- translate_AMR(ab_validate(x = x, property = "name", ...), language = language, only_affect_ab_names = TRUE)
|
||||
if (tolower == TRUE) {
|
||||
# use perl to only transform the first character
|
||||
# as we want "polymyxin B", not "polymyxin b"
|
||||
@@ -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, ...) {
|
||||
@@ -142,7 +166,37 @@ ab_tradenames <- function(x, ...) {
|
||||
ab_group <- function(x, language = get_locale(), ...) {
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
translate_AMR(ab_validate(x = x, property = "group", ...), language = language)
|
||||
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
|
||||
@@ -150,7 +204,7 @@ ab_group <- function(x, language = get_locale(), ...) {
|
||||
ab_atc_group1 <- function(x, language = get_locale(), ...) {
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
translate_AMR(ab_validate(x = x, property = "atc_group1", ...), language = language)
|
||||
translate_AMR(ab_validate(x = x, property = "atc_group1", ...), language = language, only_affect_ab_names = TRUE)
|
||||
}
|
||||
|
||||
#' @rdname ab_property
|
||||
@@ -158,7 +212,7 @@ ab_atc_group1 <- function(x, language = get_locale(), ...) {
|
||||
ab_atc_group2 <- function(x, language = get_locale(), ...) {
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
translate_AMR(ab_validate(x = x, property = "atc_group2", ...), language = language)
|
||||
translate_AMR(ab_validate(x = x, property = "atc_group2", ...), language = language, only_affect_ab_names = TRUE)
|
||||
}
|
||||
|
||||
#' @rdname ab_property
|
||||
@@ -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)
|
||||
}
|
||||
}
|
||||
|
||||
@@ -27,12 +27,14 @@
|
||||
#'
|
||||
#' Calculates age in years based on a reference date, which is the sytem date at default.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param x date(s), will be coerced with [as.POSIXlt()]
|
||||
#' @param reference reference date(s) (defaults to today), will be coerced with [as.POSIXlt()]
|
||||
#' @param exact a logical to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of [year-to-date](https://en.wikipedia.org/wiki/Year-to-date) (YTD) of `x` by the number of days in the year of `reference` (either 365 or 366).
|
||||
#' @param na.rm a logical to indicate whether missing values should be removed
|
||||
#' @param x date(s), [character] (vectors) will be coerced with [as.POSIXlt()]
|
||||
#' @param reference reference date(s) (defaults to today), [character] (vectors) will be coerced with [as.POSIXlt()]
|
||||
#' @param exact a [logical] to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of [year-to-date](https://en.wikipedia.org/wiki/Year-to-date) (YTD) of `x` by the number of days in the year of `reference` (either 365 or 366).
|
||||
#' @param na.rm a [logical] to indicate whether missing values should be removed
|
||||
#' @param ... arguments passed on to [as.POSIXlt()], such as `origin`
|
||||
#' @details Ages below 0 will be returned as `NA` with a warning. Ages above 120 will only give a warning.
|
||||
#'
|
||||
#' This function vectorises over both `x` and `reference`, meaning that either can have a length of 1 while the other argument has a larger length.
|
||||
#' @return An [integer] (no decimals) if `exact = FALSE`, a [double] (with decimals) otherwise
|
||||
#' @seealso To split ages into groups, use the [age_groups()] function.
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
@@ -53,8 +55,13 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
|
||||
meet_criteria(na.rm, allow_class = "logical", has_length = 1)
|
||||
|
||||
if (length(x) != length(reference)) {
|
||||
stop_if(length(reference) != 1, "`x` and `reference` must be of same length, or `reference` must be of length 1.")
|
||||
reference <- rep(reference, length(x))
|
||||
if (length(x) == 1) {
|
||||
x <- rep(x, length(reference))
|
||||
} else if (length(reference) == 1) {
|
||||
reference <- rep(reference, length(x))
|
||||
} else {
|
||||
stop_("`x` and `reference` must be of same length, or `reference` must be of length 1.")
|
||||
}
|
||||
}
|
||||
x <- as.POSIXlt(x, ...)
|
||||
reference <- as.POSIXlt(reference, ...)
|
||||
@@ -68,21 +75,26 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
|
||||
# add decimals
|
||||
if (exact == TRUE) {
|
||||
# get dates of `x` when `x` would have the year of `reference`
|
||||
x_in_reference_year <- as.POSIXlt(paste0(format(reference, "%Y"), format(x, "-%m-%d")))
|
||||
x_in_reference_year <- as.POSIXlt(paste0(format(as.Date(reference), "%Y"),
|
||||
format(as.Date(x), "-%m-%d")),
|
||||
format = "%Y-%m-%d")
|
||||
# get differences in days
|
||||
n_days_x_rest <- as.double(difftime(reference, x_in_reference_year, units = "days"))
|
||||
n_days_x_rest <- as.double(difftime(as.Date(reference),
|
||||
as.Date(x_in_reference_year),
|
||||
units = "days"))
|
||||
# get numbers of days the years of `reference` has for a reliable denominator
|
||||
n_days_reference_year <- as.POSIXlt(paste0(format(reference, "%Y"), "-12-31"))$yday + 1
|
||||
n_days_reference_year <- as.POSIXlt(paste0(format(as.Date(reference), "%Y"), "-12-31"),
|
||||
format = "%Y-%m-%d")$yday + 1
|
||||
# add decimal parts of year
|
||||
mod <- n_days_x_rest / n_days_reference_year
|
||||
# negative mods are cases where `x_in_reference_year` > `reference` - so 'add' a year
|
||||
mod[mod < 0] <- 1 + mod[mod < 0]
|
||||
mod[!is.na(mod) & mod < 0] <- mod[!is.na(mod) & mod < 0] + 1
|
||||
# and finally add to ages
|
||||
ages <- ages + mod
|
||||
}
|
||||
|
||||
if (any(ages < 0, na.rm = TRUE)) {
|
||||
ages[ages < 0] <- NA
|
||||
ages[!is.na(ages) & ages < 0] <- NA
|
||||
warning_("NAs introduced for ages below 0.", call = TRUE)
|
||||
}
|
||||
if (any(ages > 120, na.rm = TRUE)) {
|
||||
@@ -93,7 +105,11 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
|
||||
ages <- ages[!is.na(ages)]
|
||||
}
|
||||
|
||||
ages
|
||||
if (exact == TRUE) {
|
||||
as.double(ages)
|
||||
} else {
|
||||
as.integer(ages)
|
||||
}
|
||||
}
|
||||
|
||||
#' Split Ages into Age Groups
|
||||
@@ -105,7 +121,7 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
|
||||
#' @param na.rm a [logical] to indicate whether missing values should be removed
|
||||
#' @details To split ages, the input for the `split_at` argument can be:
|
||||
#'
|
||||
#' * A numeric vector. A value of e.g. `c(10, 20)` will split `x` on 0-9, 10-19 and 20+. A value of only `50` will split `x` on 0-49 and 50+.
|
||||
#' * A [numeric] vector. A value of e.g. `c(10, 20)` will split `x` on 0-9, 10-19 and 20+. A value of only `50` will split `x` on 0-49 and 50+.
|
||||
#' The default is to split on young children (0-11), youth (12-24), young adults (25-54), middle-aged adults (55-74) and elderly (75+).
|
||||
#' * A character:
|
||||
#' - `"children"` or `"kids"`, equivalent of: `c(0, 1, 2, 4, 6, 13, 18)`. This will split on 0, 1, 2-3, 4-5, 6-12, 13-17 and 18+.
|
||||
@@ -149,8 +165,8 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
|
||||
#' }
|
||||
#' }
|
||||
age_groups <- function(x, split_at = c(12, 25, 55, 75), na.rm = FALSE) {
|
||||
meet_criteria(x, allow_class = c("numeric", "integer"), is_positive = TRUE, is_finite = TRUE)
|
||||
meet_criteria(split_at, allow_class = c("numeric", "integer", "character"), is_positive = TRUE, is_finite = TRUE)
|
||||
meet_criteria(x, allow_class = c("numeric", "integer"), is_positive_or_zero = TRUE, is_finite = TRUE)
|
||||
meet_criteria(split_at, allow_class = c("numeric", "integer", "character"), is_positive_or_zero = TRUE, is_finite = TRUE)
|
||||
meet_criteria(na.rm, allow_class = "logical", has_length = 1)
|
||||
|
||||
if (any(x < 0, na.rm = TRUE)) {
|
||||
|
||||
@@ -54,14 +54,14 @@
|
||||
#' @section Reference Data Publicly Available:
|
||||
#' All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this `AMR` package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find [all download links on our website](https://msberends.github.io/AMR/articles/datasets.html), which is automatically updated with every code change.
|
||||
#' @section Read more on Our Website!:
|
||||
#' On our website <https://msberends.github.io/AMR/> you can find [a comprehensive tutorial](https://msberends.github.io/AMR/articles/AMR.html) about how to conduct AMR data analysis, the [complete documentation of all functions](https://msberends.github.io/AMR/reference/) and [an example analysis using WHONET data](https://msberends.github.io/AMR/articles/WHONET.html). As we would like to better understand the backgrounds and needs of our users, please [participate in our survey](https://msberends.github.io/AMR/survey.html)!
|
||||
#' On our website <https://msberends.github.io/AMR/> you can find [a comprehensive tutorial](https://msberends.github.io/AMR/articles/AMR.html) about how to conduct AMR data analysis, the [complete documentation of all functions](https://msberends.github.io/AMR/reference/) and [an example analysis using WHONET data](https://msberends.github.io/AMR/articles/WHONET.html).
|
||||
#' @section Contact Us:
|
||||
#' For suggestions, comments or questions, please contact us at:
|
||||
#'
|
||||
#' Matthijs S. Berends \cr
|
||||
#' m.s.berends \[at\] umcg \[dot\] nl \cr
|
||||
#' University of Groningen
|
||||
#' Department of Medical Microbiology
|
||||
#' Department of Medical Microbiology and Infection Prevention \cr
|
||||
#' University Medical Center Groningen \cr
|
||||
#' Post Office Box 30001 \cr
|
||||
#' 9700 RB Groningen \cr
|
||||
|
||||
+54
-33
@@ -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.
|
||||
@@ -56,7 +56,7 @@
|
||||
#' - `"TU"` = thousand units
|
||||
#' - `"MU"` = million units
|
||||
#' - `"mmol"` = millimole
|
||||
#' - `"ml"` = milliliter (e.g. eyedrops)
|
||||
#' - `"ml"` = millilitre (e.g. eyedrops)
|
||||
#'
|
||||
#' **N.B. This function requires an internet connection and only works if the following packages are installed: `curl`, `rvest`, `xml2`.**
|
||||
#' @export
|
||||
@@ -65,13 +65,16 @@
|
||||
#' @source <https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/>
|
||||
#' @examples
|
||||
#' \donttest{
|
||||
#' # oral DDD (Defined Daily Dose) of amoxicillin
|
||||
#' atc_online_property("J01CA04", "DDD", "O")
|
||||
#' 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")
|
||||
#' # parenteral DDD (Defined Daily Dose) of amoxicillin
|
||||
#' atc_online_property("J01CA04", "DDD", "P")
|
||||
#'
|
||||
#' atc_online_property("J01CA04", property = "groups") # search hierarchical groups of amoxicillin
|
||||
#' atc_online_property("J01CA04", property = "groups") # search hierarchical groups of amoxicillin
|
||||
#' }
|
||||
#' }
|
||||
atc_online_property <- function(atc_code,
|
||||
property,
|
||||
@@ -79,7 +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?://")
|
||||
@@ -95,8 +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()) {
|
||||
@@ -106,12 +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") {
|
||||
@@ -136,15 +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
|
||||
@@ -152,15 +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
|
||||
@@ -168,15 +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]
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -204,3 +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", ...)
|
||||
}
|
||||
|
||||
+2
-1
@@ -35,13 +35,14 @@
|
||||
#' @export
|
||||
#' @examples
|
||||
#' availability(example_isolates)
|
||||
#'
|
||||
#' \donttest{
|
||||
#' if (require("dplyr")) {
|
||||
#' example_isolates %>%
|
||||
#' filter(mo == as.mo("E. coli")) %>%
|
||||
#' select_if(is.rsi) %>%
|
||||
#' availability()
|
||||
#' }
|
||||
#' }
|
||||
availability <- function(tbl, width = NULL) {
|
||||
meet_criteria(tbl, allow_class = "data.frame")
|
||||
meet_criteria(width, allow_class = c("numeric", "integer"), has_length = 1, allow_NULL = TRUE, is_positive = TRUE, is_finite = TRUE)
|
||||
|
||||
+100
-38
@@ -25,14 +25,14 @@
|
||||
|
||||
#' 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 logical to indicate whether values R and I should be summed
|
||||
#' @param add_ab_group logical to indicate where the group of the antimicrobials must be included as a first column
|
||||
#' @param remove_intrinsic_resistant logical to indicate that rows and columns with 100% resistance for all tested antimicrobials must be removed from the table
|
||||
#' @param FUN function to call on the `mo` column to transform the microorganism IDs, defaults to [mo_shortname()]
|
||||
#' @param translate_ab character of length 1 containing column names of the [antibiotics] data set
|
||||
#' @param combine_IR a [logical] to indicate whether values R and I should be summed
|
||||
#' @param add_ab_group a [logical] to indicate where the group of the antimicrobials must be included as a first column
|
||||
#' @param remove_intrinsic_resistant [logical] to indicate that rows and columns with 100% resistance for all tested antimicrobials must be removed from the table
|
||||
#' @param FUN the function to call on the `mo` column to transform the microorganism codes, defaults to [mo_shortname()]
|
||||
#' @param translate_ab a [character] of length 1 containing column names of the [antibiotics] data set
|
||||
#' @param ... arguments passed on to `FUN`
|
||||
#' @inheritParams rsi_df
|
||||
#' @inheritParams base::formatC
|
||||
@@ -74,42 +74,87 @@ bug_drug_combinations <- function(x,
|
||||
stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found")
|
||||
}
|
||||
|
||||
x_class <- class(x)
|
||||
x.bak <- x
|
||||
x <- as.data.frame(x, stringsAsFactors = FALSE)
|
||||
x[, col_mo] <- FUN(x[, col_mo, drop = TRUE], ...)
|
||||
x <- x[, c(col_mo, names(which(vapply(FUN.VALUE = logical(1), x, is.rsi)))), drop = FALSE]
|
||||
|
||||
unique_mo <- sort(unique(x[, col_mo, drop = TRUE]))
|
||||
|
||||
out <- data.frame(mo = character(0),
|
||||
ab = character(0),
|
||||
S = integer(0),
|
||||
I = integer(0),
|
||||
R = integer(0),
|
||||
total = integer(0),
|
||||
stringsAsFactors = FALSE)
|
||||
|
||||
for (i in seq_len(length(unique_mo))) {
|
||||
# filter on MO group and only select R/SI columns
|
||||
x_mo_filter <- x[which(x[, col_mo, drop = TRUE] == unique_mo[i]), names(which(vapply(FUN.VALUE = logical(1), x, is.rsi))), drop = FALSE]
|
||||
# turn and merge everything
|
||||
pivot <- lapply(x_mo_filter, function(x) {
|
||||
m <- as.matrix(table(x))
|
||||
data.frame(S = m["S", ], I = m["I", ], R = m["R", ], stringsAsFactors = FALSE)
|
||||
})
|
||||
merged <- do.call(rbind, pivot)
|
||||
out_group <- data.frame(mo = unique_mo[i],
|
||||
ab = rownames(merged),
|
||||
S = merged$S,
|
||||
I = merged$I,
|
||||
R = merged$R,
|
||||
total = merged$S + merged$I + merged$R,
|
||||
stringsAsFactors = FALSE)
|
||||
out <- rbind(out, out_group, stringsAsFactors = FALSE)
|
||||
# select only groups and antibiotics
|
||||
if (is_null_or_grouped_tbl(x.bak)) {
|
||||
data_has_groups <- TRUE
|
||||
groups <- setdiff(names(attributes(x.bak)$groups), ".rows")
|
||||
x <- x[, c(groups, col_mo, colnames(x)[vapply(FUN.VALUE = logical(1), x, is.rsi)]), drop = FALSE]
|
||||
} else {
|
||||
data_has_groups <- FALSE
|
||||
x <- x[, c(col_mo, names(which(vapply(FUN.VALUE = logical(1), x, is.rsi)))), drop = FALSE]
|
||||
}
|
||||
|
||||
set_clean_class(out,
|
||||
new_class = c("bug_drug_combinations", x_class))
|
||||
run_it <- function(x) {
|
||||
out <- data.frame(mo = character(0),
|
||||
ab = character(0),
|
||||
S = integer(0),
|
||||
I = integer(0),
|
||||
R = integer(0),
|
||||
total = integer(0),
|
||||
stringsAsFactors = FALSE)
|
||||
if (data_has_groups) {
|
||||
group_values <- unique(x[, which(colnames(x) %in% groups), drop = FALSE])
|
||||
rownames(group_values) <- NULL
|
||||
x <- x[, which(!colnames(x) %in% groups), drop = FALSE]
|
||||
}
|
||||
|
||||
for (i in seq_len(length(unique_mo))) {
|
||||
# filter on MO group and only select R/SI columns
|
||||
x_mo_filter <- x[which(x[, col_mo, drop = TRUE] == unique_mo[i]), names(which(vapply(FUN.VALUE = logical(1), x, is.rsi))), drop = FALSE]
|
||||
# turn and merge everything
|
||||
pivot <- lapply(x_mo_filter, function(x) {
|
||||
m <- as.matrix(table(x))
|
||||
data.frame(S = m["S", ], I = m["I", ], R = m["R", ], stringsAsFactors = FALSE)
|
||||
})
|
||||
merged <- do.call(rbind, pivot)
|
||||
out_group <- data.frame(mo = rep(unique_mo[i], NROW(merged)),
|
||||
ab = rownames(merged),
|
||||
S = merged$S,
|
||||
I = merged$I,
|
||||
R = merged$R,
|
||||
total = merged$S + merged$I + merged$R,
|
||||
stringsAsFactors = FALSE)
|
||||
if (data_has_groups) {
|
||||
if (nrow(group_values) < nrow(out_group)) {
|
||||
# repeat group_values for the number of rows in out_group
|
||||
repeated <- rep(seq_len(nrow(group_values)),
|
||||
each = nrow(out_group) / nrow(group_values))
|
||||
group_values <- group_values[repeated, , drop = FALSE]
|
||||
}
|
||||
out_group <- cbind(group_values, out_group)
|
||||
}
|
||||
out <- rbind(out, out_group, stringsAsFactors = FALSE)
|
||||
}
|
||||
out
|
||||
}
|
||||
# based on pm_apply_grouped_function
|
||||
apply_group <- function(.data, fn, groups, drop = FALSE, ...) {
|
||||
grouped <- pm_split_into_groups(.data, groups, drop)
|
||||
res <- do.call(rbind, unname(lapply(grouped, fn, ...)))
|
||||
if (any(groups %in% colnames(res))) {
|
||||
class(res) <- c("grouped_data", class(res))
|
||||
res <- pm_set_groups(res, groups[groups %in% colnames(res)])
|
||||
}
|
||||
res
|
||||
}
|
||||
|
||||
if (data_has_groups) {
|
||||
out <- apply_group(x, "run_it", groups)
|
||||
rownames(out) <- NULL
|
||||
set_clean_class(out,
|
||||
new_class = c("grouped", "bug_drug_combinations", "data.frame"))
|
||||
} else {
|
||||
out <- run_it(x)
|
||||
rownames(out) <- NULL
|
||||
set_clean_class(out,
|
||||
new_class = c("bug_drug_combinations", "data.frame"))
|
||||
}
|
||||
}
|
||||
|
||||
#' @method format bug_drug_combinations
|
||||
@@ -137,6 +182,21 @@ format.bug_drug_combinations <- function(x,
|
||||
meet_criteria(decimal.mark, allow_class = "character", has_length = 1)
|
||||
meet_criteria(big.mark, allow_class = "character", has_length = 1)
|
||||
|
||||
if (inherits(x, "grouped")) {
|
||||
# bug_drug_combinations() has been run on groups, so de-group here
|
||||
warning_("formatting the output of `bug_drug_combinations()` does not support grouped variables, they are ignored", call = FALSE)
|
||||
idx <- split(seq_len(nrow(x)), paste0(x$mo, "%%", x$ab))
|
||||
x <- data.frame(mo = gsub("(.*)%%(.*)", "\\1", names(idx)),
|
||||
ab = gsub("(.*)%%(.*)", "\\2", names(idx)),
|
||||
S = sapply(idx, function(i) sum(y$S[i], na.rm = TRUE)),
|
||||
I = sapply(idx, function(i) sum(y$I[i], na.rm = TRUE)),
|
||||
R = sapply(idx, function(i) sum(y$R[i], na.rm = TRUE)),
|
||||
total = sapply(idx, function(i) sum(y$S[i], na.rm = TRUE) +
|
||||
sum(y$I[i], na.rm = TRUE) +
|
||||
sum(y$R[i], na.rm = TRUE)),
|
||||
stringsAsFactors = FALSE)
|
||||
}
|
||||
|
||||
x <- as.data.frame(x, stringsAsFactors = FALSE)
|
||||
x <- subset(x, total >= minimum)
|
||||
|
||||
@@ -158,7 +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]
|
||||
}
|
||||
@@ -249,7 +309,9 @@ format.bug_drug_combinations <- function(x,
|
||||
print.bug_drug_combinations <- function(x, ...) {
|
||||
x_class <- class(x)
|
||||
print(set_clean_class(x,
|
||||
new_class = x_class[x_class != "bug_drug_combinations"]),
|
||||
new_class = x_class[!x_class %in% c("bug_drug_combinations", "grouped")]),
|
||||
...)
|
||||
message_("Use 'format()' on this result to get a publishable/printable format.", as_note = FALSE)
|
||||
message_("Use 'format()' on this result to get a publishable/printable format.",
|
||||
ifelse(inherits(x, "grouped"), " Note: The grouping variable(s) will be ignored.", ""),
|
||||
as_note = FALSE)
|
||||
}
|
||||
|
||||
@@ -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$n_total_synonyms, big.mark = ","), "\n\n",
|
||||
"See for more info ?microorganisms and ?catalogue_of_life.\n"))
|
||||
"See for more info ", font_grey_bg("`?microorganisms`"), " and ", font_grey_bg("`?catalogue_of_life`"), ".\n"))
|
||||
}
|
||||
|
||||
@@ -72,7 +72,7 @@
|
||||
#' count_susceptible(example_isolates$AMX)
|
||||
#' susceptibility(example_isolates$AMX) * n_rsi(example_isolates$AMX)
|
||||
#'
|
||||
#'
|
||||
#' \donttest{
|
||||
#' if (require("dplyr")) {
|
||||
#' example_isolates %>%
|
||||
#' group_by(hospital_id) %>%
|
||||
@@ -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.
|
||||
@@ -106,82 +112,97 @@
|
||||
#' group_by(hospital_id) %>%
|
||||
#' count_df(translate = FALSE)
|
||||
#' }
|
||||
#' }
|
||||
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
|
||||
@@ -195,11 +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))
|
||||
}
|
||||
|
||||
@@ -0,0 +1,255 @@
|
||||
# ==================================================================== #
|
||||
# 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/ #
|
||||
# ==================================================================== #
|
||||
|
||||
#' 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 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.
|
||||
#'
|
||||
#' @section How it works:
|
||||
#'
|
||||
#' ### Basics
|
||||
#'
|
||||
#' If you are familiar with the [`case_when()`][dplyr::case_when()] function of the `dplyr` package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule itself is written *before* the tilde (`~`) and the consequence of the rule is written *after* the tilde:
|
||||
#'
|
||||
#' ```
|
||||
#' x <- custom_eucast_rules(TZP == "S" ~ aminopenicillins == "S",
|
||||
#' TZP == "R" ~ aminopenicillins == "R")
|
||||
#' ```
|
||||
#'
|
||||
#' These are two custom EUCAST rules: if TZP (piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must be made "R". These rules can also be printed to the console, so it is immediately clear how they work:
|
||||
#'
|
||||
#' ```
|
||||
#' x
|
||||
#' #> A set of custom EUCAST rules:
|
||||
#' #>
|
||||
#' #> 1. If TZP is S then set to S:
|
||||
#' #> amoxicillin (AMX), ampicillin (AMP)
|
||||
#' #>
|
||||
#' #> 2. If TZP is R then set to R:
|
||||
#' #> amoxicillin (AMX), ampicillin (AMP)
|
||||
#' ```
|
||||
#'
|
||||
#' The rules (the part *before* the tilde, in above example `TZP == "S"` and `TZP == "R"`) must be evaluable in your data set: it should be able to run as a filter in your data set without errors. This means for the above example that the column `TZP` must exist. We will create a sample data set and test the rules set:
|
||||
#'
|
||||
#' ```
|
||||
#' df <- data.frame(mo = c("E. coli", "K. pneumoniae"),
|
||||
#' TZP = "R",
|
||||
#' amox = "",
|
||||
#' AMP = "")
|
||||
#' df
|
||||
#' #> mo TZP amox AMP
|
||||
#' #> 1 E. coli R
|
||||
#' #> 2 K. pneumoniae R
|
||||
#'
|
||||
#' eucast_rules(df, rules = "custom", custom_rules = x)
|
||||
#' #> mo TZP amox AMP
|
||||
#' #> 1 E. coli R R R
|
||||
#' #> 2 K. pneumoniae R R R
|
||||
#' ```
|
||||
#'
|
||||
#' ### Using taxonomic properties in rules
|
||||
#'
|
||||
#' There is one exception in variables used for the rules: all column names of the [microorganisms] data set can also be used, but do not have to exist in the data set. These column names are: `r vector_and(colnames(microorganisms), quote = "``", sort = FALSE)`. Thus, this next example will work as well, despite the fact that the `df` data set does not contain a column `genus`:
|
||||
#'
|
||||
#' ```
|
||||
#' y <- custom_eucast_rules(TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",
|
||||
#' TZP == "R" & genus == "Klebsiella" ~ aminopenicillins == "R")
|
||||
#'
|
||||
#' eucast_rules(df, rules = "custom", custom_rules = y)
|
||||
#' #> mo TZP amox AMP
|
||||
#' #> 1 E. coli R
|
||||
#' #> 2 K. pneumoniae R R R
|
||||
#' ```
|
||||
#'
|
||||
#' ### 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 agents that will be matched when running the rule.
|
||||
#'
|
||||
#' `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
|
||||
#' @examples
|
||||
#' x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
|
||||
#' AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
|
||||
#' eucast_rules(example_isolates,
|
||||
#' rules = "custom",
|
||||
#' custom_rules = x,
|
||||
#' info = FALSE)
|
||||
#'
|
||||
#' # combine rule sets
|
||||
#' x2 <- c(x,
|
||||
#' custom_eucast_rules(TZP == "R" ~ carbapenems == "R"))
|
||||
#' x2
|
||||
custom_eucast_rules <- function(...) {
|
||||
|
||||
dots <- tryCatch(list(...),
|
||||
error = function(e) "error")
|
||||
stop_if(identical(dots, "error"),
|
||||
"rules must be a valid formula inputs (e.g., using '~'), see `?custom_eucast_rules`")
|
||||
n_dots <- length(dots)
|
||||
stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using `?custom_eucast_rules`.")
|
||||
out <- vector("list", n_dots)
|
||||
for (i in seq_len(n_dots)) {
|
||||
stop_ifnot(inherits(dots[[i]], "formula"),
|
||||
"rule ", i, " must be a valid formula input (e.g., using '~'), see `?custom_eucast_rules`")
|
||||
|
||||
# Query
|
||||
qry <- dots[[i]][[2]]
|
||||
if (inherits(qry, "call")) {
|
||||
qry <- as.expression(qry)
|
||||
}
|
||||
qry <- as.character(qry)
|
||||
# these will prevent vectorisation, so replace them:
|
||||
qry <- gsub("&&", "&", qry, fixed = TRUE)
|
||||
qry <- gsub("||", "|", qry, fixed = TRUE)
|
||||
# format nicely, setting spaces around operators
|
||||
qry <- gsub(" *([&|+-/*^><==]+) *", " \\1 ", qry)
|
||||
qry <- gsub(" ?, ?", ", ", qry)
|
||||
qry <- gsub("'", "\"", qry, fixed = TRUE)
|
||||
out[[i]]$query <- as.expression(qry)
|
||||
|
||||
# Resulting rule
|
||||
result <- dots[[i]][[3]]
|
||||
stop_ifnot(deparse(result) %like% "==",
|
||||
"the result of rule ", i, " (the part after the `~`) must contain `==`, such as in `... ~ ampicillin == \"R\"`, see `?custom_eucast_rules`")
|
||||
result_group <- as.character(result)[[2]]
|
||||
if (paste0("AB_", toupper(result_group), "S") %in% DEFINED_AB_GROUPS) {
|
||||
# support for e.g. 'aminopenicillin' if user meant 'aminopenicillins'
|
||||
result_group <- paste0(result_group, "s")
|
||||
}
|
||||
if (paste0("AB_", toupper(result_group)) %in% DEFINED_AB_GROUPS) {
|
||||
result_group <- eval(parse(text = paste0("AB_", toupper(result_group))), envir = asNamespace("AMR"))
|
||||
} else {
|
||||
result_group <- tryCatch(
|
||||
suppressWarnings(as.ab(result_group,
|
||||
fast_mode = TRUE,
|
||||
flag_multiple_results = FALSE)),
|
||||
error = function(e) NA_character_)
|
||||
}
|
||||
|
||||
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(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),
|
||||
"the resulting value of rule ", i, " must be either \"R\", \"S\", \"I\" or NA")
|
||||
result_value <- as.rsi(result_value)
|
||||
|
||||
out[[i]]$result_group <- result_group
|
||||
out[[i]]$result_value <- result_value
|
||||
}
|
||||
|
||||
names(out) <- paste0("rule", seq_len(n_dots))
|
||||
set_clean_class(out, new_class = c("custom_eucast_rules", "list"))
|
||||
}
|
||||
|
||||
#' @method c custom_eucast_rules
|
||||
#' @noRd
|
||||
#' @export
|
||||
c.custom_eucast_rules <- function(x, ...) {
|
||||
if (length(list(...)) == 0) {
|
||||
return(x)
|
||||
}
|
||||
out <- unclass(x)
|
||||
for (e in list(...)) {
|
||||
out <- c(out, unclass(e))
|
||||
}
|
||||
names(out) <- paste0("rule", seq_len(length(out)))
|
||||
set_clean_class(out, new_class = c("custom_eucast_rules", "list"))
|
||||
}
|
||||
|
||||
#' @method as.list custom_eucast_rules
|
||||
#' @noRd
|
||||
#' @export
|
||||
as.list.custom_eucast_rules <- function(x, ...) {
|
||||
c(x, ...)
|
||||
}
|
||||
|
||||
#' @method print custom_eucast_rules
|
||||
#' @export
|
||||
#' @noRd
|
||||
print.custom_eucast_rules <- function(x, ...) {
|
||||
cat("A set of custom EUCAST rules:\n")
|
||||
for (i in seq_len(length(x))) {
|
||||
rule <- x[[i]]
|
||||
rule$query <- format_custom_query_rule(rule$query)
|
||||
if (is.na(rule$result_value)) {
|
||||
val <- font_red("<NA>")
|
||||
} else if (rule$result_value == "R") {
|
||||
val <- font_rsi_R_bg(font_black(" R "))
|
||||
} else if (rule$result_value == "S") {
|
||||
val <- font_rsi_S_bg(font_black(" S "))
|
||||
} else {
|
||||
val <- font_rsi_I_bg(font_black(" I "))
|
||||
}
|
||||
agents <- paste0(font_blue(ab_name(rule$result_group, language = NULL, tolower = TRUE),
|
||||
collapse = NULL),
|
||||
" (", rule$result_group, ")")
|
||||
agents <- sort(agents)
|
||||
rule_if <- word_wrap(paste0(i, ". ", font_bold("If "), font_blue(rule$query), font_bold(" then "),
|
||||
"set to {result}:"),
|
||||
extra_indent = 5)
|
||||
rule_if <- gsub("{result}", val, rule_if, fixed = TRUE)
|
||||
rule_then <- paste0(" ", word_wrap(paste0(agents, collapse = ", "), extra_indent = 5))
|
||||
cat("\n ", rule_if, "\n", rule_then, "\n", sep = "")
|
||||
}
|
||||
}
|
||||
|
||||
format_custom_query_rule <- function(query, colours = has_colour()) {
|
||||
query <- gsub(" & ", font_black(font_bold(" and ")), query, fixed = TRUE)
|
||||
query <- gsub(" | ", font_black(" or "), query, fixed = TRUE)
|
||||
query <- gsub(" + ", font_black(" plus "), query, fixed = TRUE)
|
||||
query <- gsub(" - ", font_black(" minus "), query, fixed = TRUE)
|
||||
query <- gsub(" / ", font_black(" divided by "), query, fixed = TRUE)
|
||||
query <- gsub(" * ", font_black(" times "), query, fixed = TRUE)
|
||||
query <- gsub(" == ", font_black(" is "), query, fixed = TRUE)
|
||||
query <- gsub(" > ", font_black(" is higher than "), query, fixed = TRUE)
|
||||
query <- gsub(" < ", font_black(" is lower than "), query, fixed = TRUE)
|
||||
query <- gsub(" >= ", font_black(" is higher than or equal to "), query, fixed = TRUE)
|
||||
query <- gsub(" <= ", font_black(" is lower than or equal to "), query, fixed = TRUE)
|
||||
query <- gsub(" ^ ", font_black(" to the power of "), query, fixed = TRUE)
|
||||
query <- gsub(" %in% ", font_black(" is one of "), query, fixed = TRUE)
|
||||
query <- gsub(" %like% ", font_black(" resembles "), query, fixed = TRUE)
|
||||
if (colours == TRUE) {
|
||||
query <- gsub('"R"', font_rsi_R_bg(font_black(" R ")), query, fixed = TRUE)
|
||||
query <- gsub('"S"', font_rsi_S_bg(font_black(" S ")), query, fixed = TRUE)
|
||||
query <- gsub('"I"', font_rsi_I_bg(font_black(" I ")), query, fixed = TRUE)
|
||||
}
|
||||
# replace the black colour 'stops' with blue colour 'starts'
|
||||
query <- gsub("\033[39m", "\033[34m", as.character(query), fixed = TRUE)
|
||||
# start with blue
|
||||
query <- paste0("\033[34m", query)
|
||||
if (colours == FALSE) {
|
||||
query <- font_stripstyle(query)
|
||||
}
|
||||
query
|
||||
}
|
||||
@@ -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
|
||||
@@ -55,23 +55,23 @@
|
||||
#' - `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>
|
||||
#'
|
||||
#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <http://ec.europa.eu/health/documents/community-register/html/atc.htm>
|
||||
#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm>
|
||||
#' @inheritSection AMR Reference Data Publicly Available
|
||||
#' @inheritSection WHOCC WHOCC
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
@@ -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
|
||||
@@ -98,27 +98,28 @@
|
||||
#' @details
|
||||
#' Please note that entries are only based on the Catalogue of Life and the LPSN (see below). Since these sources incorporate entries based on (recent) publications in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), it can happen that the year of publication is sometimes later than one might expect.
|
||||
#'
|
||||
#' For example, *Staphylococcus pettenkoferi* was described for the first time in Diagnostic Microbiology and Infectious Disease in 2002 (\doi{10.1016/s0732-8893(02)00399-1}), but it was not before 2007 that a publication in IJSEM followed (\doi{10.1099/ijs.0.64381-0}). Consequently, the AMR package returns 2007 for `mo_year("S. pettenkoferi")`.
|
||||
#' For example, *Staphylococcus pettenkoferi* was described for the first time in Diagnostic Microbiology and Infectious Disease in 2002 (\doi{10.1016/s0732-8893(02)00399-1}), but it was not before 2007 that a publication in IJSEM followed (\doi{10.1099/ijs.0.64381-0}). Consequently, the `AMR` package returns 2007 for `mo_year("S. pettenkoferi")`.
|
||||
#'
|
||||
#' ## Manual additions
|
||||
#' For convenience, some entries were added manually:
|
||||
#'
|
||||
#' - 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.
|
||||
#'
|
||||
@@ -178,9 +179,9 @@
|
||||
#' @format A [data.frame] with `r format(nrow(example_isolates), big.mark = ",")` observations and `r ncol(example_isolates)` variables:
|
||||
#' - `date`\cr date of receipt at the laboratory
|
||||
#' - `hospital_id`\cr ID of the hospital, from A to D
|
||||
#' - `ward_icu`\cr logical to determine if ward is an intensive care unit
|
||||
#' - `ward_clinical`\cr logical to determine if ward is a regular clinical ward
|
||||
#' - `ward_outpatient`\cr logical to determine if ward is an outpatient clinic
|
||||
#' - `ward_icu`\cr [logical] to determine if ward is an intensive care unit
|
||||
#' - `ward_clinical`\cr [logical] to determine if ward is a regular clinical ward
|
||||
#' - `ward_outpatient`\cr [logical] to determine if ward is an outpatient clinic
|
||||
#' - `age`\cr age of the patient
|
||||
#' - `gender`\cr gender of the patient
|
||||
#' - `patient_id`\cr ID of the patient
|
||||
@@ -217,8 +218,8 @@
|
||||
#' - `Sex`\cr Fictitious gender of patient
|
||||
#' - `Age`\cr Fictitious age of patient
|
||||
#' - `Age category`\cr Age group, can also be looked up using [age_groups()]
|
||||
#' - `Date of admission`\cr Date of hospital admission
|
||||
#' - `Specimen date`\cr Date when specimen was received at laboratory
|
||||
#' - `Date of admission`\cr [Date] of hospital admission
|
||||
#' - `Specimen date`\cr [Date] when specimen was received at laboratory
|
||||
#' - `Specimen type`\cr Specimen type or group
|
||||
#' - `Specimen type (Numeric)`\cr Translation of `"Specimen type"`
|
||||
#' - `Reason`\cr Reason of request with Differential Diagnosis
|
||||
@@ -231,7 +232,7 @@
|
||||
#' - `MRSA screening test`\cr Microorganism is possible MRSA?
|
||||
#' - `Inducible clindamycin resistance`\cr Clindamycin can be induced?
|
||||
#' - `Comment`\cr Other comments
|
||||
#' - `Date of data entry`\cr Date this data was entered in WHONET
|
||||
#' - `Date of data entry`\cr [Date] this data was entered in WHONET
|
||||
#' - `AMP_ND10:CIP_EE`\cr `r sum(vapply(FUN.VALUE = logical(1), WHONET, is.rsi))` different antibiotics. You can lookup the abbreviations in the [antibiotics] data set, or use e.g. [`ab_name("AMP")`][ab_name()] to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using [as.rsi()].
|
||||
#' @inheritSection AMR Reference Data Publicly Available
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
@@ -239,7 +240,7 @@
|
||||
|
||||
#' Data Set for R/SI Interpretation
|
||||
#'
|
||||
#' Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`) and EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`). Use [as.rsi()] to transform MICs or disks measurements to R/SI values.
|
||||
#' Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`). Use [as.rsi()] to transform MICs or disks measurements to R/SI values.
|
||||
#' @format A [data.frame] with `r format(nrow(rsi_translation), big.mark = ",")` observations and `r ncol(rsi_translation)` variables:
|
||||
#' - `guideline`\cr Name of the guideline
|
||||
#' - `method`\cr Either `r vector_or(rsi_translation$method)`
|
||||
@@ -250,8 +251,8 @@
|
||||
#' - `disk_dose`\cr Dose of the used disk diffusion method
|
||||
#' - `breakpoint_S`\cr Lowest MIC value or highest number of millimetres that leads to "S"
|
||||
#' - `breakpoint_R`\cr Highest MIC value or lowest number of millimetres that leads to "R"
|
||||
#' - `uti`\cr A logical value (`TRUE`/`FALSE`) to indicate whether the rule applies to a urinary tract infection (UTI)
|
||||
#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt>. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically.
|
||||
#' - `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/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]
|
||||
@@ -263,18 +264,20 @@
|
||||
#' @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
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
#' @examples
|
||||
#' \donttest{
|
||||
#' if (require("dplyr")) {
|
||||
#' intrinsic_resistant %>%
|
||||
#' filter(antibiotic == "Vancomycin", microorganism %like% "Enterococcus") %>%
|
||||
#' pull(microorganism)
|
||||
#' # [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
|
||||
#' }
|
||||
#' }
|
||||
"intrinsic_resistant"
|
||||
|
||||
#' Data Set with Treatment Dosages as Defined by EUCAST
|
||||
|
||||
+3
-16
@@ -25,23 +25,10 @@
|
||||
|
||||
#' 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).
|
||||
#' 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).
|
||||
#' @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
|
||||
}
|
||||
# @export
|
||||
NULL
|
||||
|
||||
@@ -29,7 +29,7 @@
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @rdname as.disk
|
||||
#' @param x vector
|
||||
#' @param na.rm a logical indicating whether missing values should be removed
|
||||
#' @param na.rm a [logical] indicating whether missing values should be removed
|
||||
#' @details Interpret disk values as RSI values with [as.rsi()]. It supports guidelines from EUCAST and CLSI.
|
||||
#' @return An [integer] with additional class [`disk`]
|
||||
#' @aliases disk
|
||||
@@ -85,7 +85,7 @@ as.disk <- function(x, na.rm = FALSE) {
|
||||
fixed = TRUE)
|
||||
x_clean <- gsub(remove, "", x, ignore.case = TRUE, fixed = fixed)
|
||||
# remove everything that is not a number or dot
|
||||
as.numeric(gsub("[^0-9.]+", "", x_clean))
|
||||
as.double(gsub("[^0-9.]+", "", x_clean))
|
||||
}
|
||||
|
||||
# round up and make it an integer
|
||||
@@ -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) {
|
||||
@@ -182,11 +188,8 @@ print.disk <- function(x, ...) {
|
||||
#' @method c disk
|
||||
#' @export
|
||||
#' @noRd
|
||||
c.disk <- function(x, ...) {
|
||||
y <- NextMethod()
|
||||
y <- as.disk(y)
|
||||
attributes(y) <- attributes(x)
|
||||
y
|
||||
c.disk <- function(...) {
|
||||
as.disk(unlist(lapply(list(...), as.character)))
|
||||
}
|
||||
|
||||
#' @method unique disk
|
||||
@@ -198,6 +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(
|
||||
@@ -205,7 +217,7 @@ get_skimmers.disk <- function(column) {
|
||||
min = ~min(as.double(.), na.rm = TRUE),
|
||||
max = ~max(as.double(.), na.rm = TRUE),
|
||||
median = ~stats::median(as.double(.), na.rm = TRUE),
|
||||
n_unique = ~pm_n_distinct(., na.rm = TRUE),
|
||||
n_unique = ~length(unique(stats::na.omit(.))),
|
||||
hist = ~skimr::inline_hist(stats::na.omit(as.double(.)))
|
||||
)
|
||||
}
|
||||
|
||||
+26
-28
@@ -27,15 +27,15 @@
|
||||
#'
|
||||
#' 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 episode_days required episode length in days, can also be less than a day, see *Details*
|
||||
#' @param ... currently not used
|
||||
#' @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
|
||||
#' Dates are first sorted from old to new. The oldest date will mark the start of the first episode. After this date, the next date will be marked that is at least `episode_days` days later than the start of the first episode. From that second marked date on, the next date will be marked that is at least `episode_days` days later than the start of the second episode which will be the start of the third episode, and so on. Before the vector is being returned, the original order will be restored.
|
||||
#'
|
||||
#' The [first_isolate()] function is a wrapper around the [is_new_episode()] function, but is more efficient for data sets containing microorganism codes or names.
|
||||
#' The [first_isolate()] function is a wrapper around the [is_new_episode()] function, but is more efficient for data sets containing microorganism codes or names and allows for different isolate selection methods.
|
||||
#'
|
||||
#' The `dplyr` package is not required for these functions to work, but these functions support [variable grouping][dplyr::group_by()] and work conveniently inside `dplyr` verbs such as [`filter()`][dplyr::filter()], [`mutate()`][dplyr::mutate()] and [`summarise()`][dplyr::summarise()].
|
||||
#' The `dplyr` package is not required for these functions to work, but these functions do support [variable grouping][dplyr::group_by()] and work conveniently inside `dplyr` verbs such as [`filter()`][dplyr::filter()], [`mutate()`][dplyr::mutate()] and [`summarise()`][dplyr::summarise()].
|
||||
#' @return
|
||||
#' * [get_episode()]: a [double] vector
|
||||
#' * [is_new_episode()]: a [logical] vector
|
||||
@@ -85,10 +85,11 @@
|
||||
#' n_episodes_30 = sum(is_new_episode(date, episode_days = 30)))
|
||||
#'
|
||||
#'
|
||||
#' # grouping on patients and microorganisms leads to the same results
|
||||
#' # as first_isolate():
|
||||
#' # grouping on patients and microorganisms leads to the same
|
||||
#' # results as first_isolate() when using 'episode-based':
|
||||
#' x <- example_isolates %>%
|
||||
#' filter(first_isolate(., include_unknown = TRUE))
|
||||
#' filter_first_isolate(include_unknown = TRUE,
|
||||
#' method = "episode-based")
|
||||
#'
|
||||
#' y <- example_isolates %>%
|
||||
#' group_by(patient_id, mo) %>%
|
||||
@@ -104,11 +105,11 @@
|
||||
#' }
|
||||
#' }
|
||||
get_episode <- function(x, episode_days, ...) {
|
||||
meet_criteria(x, allow_class = c("Date", "POSIXt"))
|
||||
meet_criteria(episode_days, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
|
||||
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,
|
||||
... = ...)
|
||||
}
|
||||
@@ -116,27 +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(episode_days, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
|
||||
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, ...) {
|
||||
x <- as.double(as.POSIXct(x)) # as.POSIXct() for Date classes
|
||||
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))
|
||||
@@ -154,7 +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
|
||||
@@ -180,11 +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
|
||||
}
|
||||
|
||||
+221
-360
@@ -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)
|
||||
@@ -50,22 +54,35 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
|
||||
#' To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see *Details*.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param x data with antibiotic columns, such as `amox`, `AMX` and `AMC`
|
||||
#' @param info a logical to indicate whether progress should be printed to the console, defaults to only print while in interactive sessions
|
||||
#' @param rules a character vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expert"`, `"other"`, `"all"`, and defaults to `c("breakpoints", "expert")`. The default value can be set to another value, e.g. using `options(AMR_eucastrules = "all")`.
|
||||
#' @param info a [logical] to indicate whether progress should be printed to the console, defaults to only print while in interactive sessions
|
||||
#' @param rules a [character] vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expert")`. The default value can be set to another value, e.g. using `options(AMR_eucastrules = "all")`. If using `"custom"`, be sure to fill in argument `custom_rules` too. Custom rules can be created with [custom_eucast_rules()].
|
||||
#' @param verbose a [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.
|
||||
#' @param version_breakpoints the version number to use for the EUCAST Clinical Breakpoints guideline. Can be 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)`
|
||||
#' @param only_rsi_columns a logical to indicate whether only antibiotic columns must be detected that were transformed to class `<rsi>` (see [as.rsi()]) on beforehand (defaults to `FALSE`)
|
||||
#' @param only_rsi_columns a [logical] to indicate whether only antibiotic columns must be detected that were transformed to class `<rsi>` (see [as.rsi()]) on beforehand (defaults to `FALSE`)
|
||||
#' @param custom_rules custom rules to apply, created with [custom_eucast_rules()]
|
||||
#' @inheritParams first_isolate
|
||||
#' @details
|
||||
#' **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.
|
||||
#' **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>.
|
||||
#' 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
|
||||
#'
|
||||
#' Custom rules can be created using [custom_eucast_rules()], e.g.:
|
||||
#'
|
||||
#' ```
|
||||
#' x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
|
||||
#' AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
|
||||
#'
|
||||
#' eucast_rules(example_isolates, rules = "custom", custom_rules = x)
|
||||
#' ```
|
||||
#'
|
||||
#'
|
||||
#' ## 'Other' Rules
|
||||
#'
|
||||
@@ -80,9 +97,9 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
|
||||
#' @section Antibiotics:
|
||||
#' To define antibiotics column names, leave as it is to determine it automatically with [guess_ab_col()] or input a text (case-insensitive), or use `NULL` to skip a column (e.g. `TIC = NULL` to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
|
||||
#'
|
||||
#' The following antibiotics are used for the functions [eucast_rules()] and [mdro()]. These are shown below in the format 'name (`antimicrobial ID`, [ATC code](https://www.whocc.no/atc/structure_and_principles/))', sorted alphabetically:
|
||||
#' The following antibiotics are eligible for the functions [eucast_rules()] and [mdro()]. These are shown below in the format 'name (`antimicrobial ID`, [ATC code](https://www.whocc.no/atc/structure_and_principles/))', sorted alphabetically:
|
||||
#'
|
||||
#' `r create_ab_documentation(c("AMC", "AMK", "AMP", "AMX", "APL", "APX", "ATM", "AVB", "AVO", "AZD", "AZL", "AZM", "BAM", "BPR", "CAC", "CAT", "CAZ", "CCP", "CCV", "CCX", "CDC", "CDR", "CDZ", "CEC", "CED", "CEI", "CEM", "CEP", "CFM", "CFM1", "CFP", "CFR", "CFS", "CFZ", "CHE", "CHL", "CIC", "CID", "CIP", "CLI", "CLM", "CLO", "CLR", "CMX", "CMZ", "CND", "COL", "CPD", "CPI", "CPL", "CPM", "CPO", "CPR", "CPT", "CPX", "CRB", "CRD", "CRN", "CRO", "CSL", "CTB", "CTC", "CTF", "CTL", "CTS", "CTT", "CTX", "CTZ", "CXM", "CYC", "CZA", "CZD", "CZO", "CZP", "CZX", "DAL", "DAP", "DIC", "DIR", "DIT", "DIX", "DIZ", "DKB", "DOR", "DOX", "ENX", "EPC", "ERY", "ETP", "FEP", "FLC", "FLE", "FLR1", "FOS", "FOV", "FOX", "FOX1", "FUS", "GAT", "GEM", "GEN", "GRX", "HAP", "HET", "IPM", "ISE", "JOS", "KAN", "LEN", "LEX", "LIN", "LNZ", "LOM", "LOR", "LTM", "LVX", "MAN", "MCM", "MEC", "MEM", "MET", "MEV", "MEZ", "MFX", "MID", "MNO", "MTM", "NAC", "NAF", "NAL", "NEO", "NET", "NIT", "NOR", "NOV", "NVA", "OFX", "OLE", "ORI", "OXA", "PAZ", "PEF", "PEN", "PHE", "PHN", "PIP", "PLB", "PME", "PNM", "PRC", "PRI", "PRL", "PRP", "PRU", "PVM", "QDA", "RAM", "RFL", "RID", "RIF", "ROK", "RST", "RXT", "SAM", "SBC", "SDI", "SDM", "SIS", "SLF", "SLF1", "SLF10", "SLF11", "SLF12", "SLF13", "SLF2", "SLF3", "SLF4", "SLF5", "SLF6", "SLF7", "SLF8", "SLF9", "SLT1", "SLT2", "SLT3", "SLT4", "SLT5", "SLT6", "SMX", "SPI", "SPX", "SRX", "STR", "STR1", "SUD", "SUL", "SUT", "SXT", "SZO", "TAL", "TAZ", "TCC", "TCM", "TCY", "TEC", "TEM", "TGC", "THA", "TIC", "TIO", "TLT", "TLV", "TMP", "TMX", "TOB", "TRL", "TVA", "TZD", "TZP", "VAN"))`
|
||||
#' `r create_eucast_ab_documentation()`
|
||||
#' @aliases EUCAST
|
||||
#' @rdname eucast_rules
|
||||
#' @export
|
||||
@@ -92,6 +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)
|
||||
@@ -146,22 +164,37 @@ 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,
|
||||
...) {
|
||||
meet_criteria(x, allow_class = "data.frame")
|
||||
meet_criteria(col_mo, allow_class = "character", has_length = 1, is_in = colnames(x), allow_NULL = TRUE)
|
||||
meet_criteria(info, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(rules, allow_class = "character", has_length = c(1, 2, 3, 4), is_in = c("breakpoints", "expert", "other", "all"))
|
||||
meet_criteria(rules, allow_class = "character", has_length = c(1, 2, 3, 4, 5), is_in = c("breakpoints", "expert", "other", "all", "custom"))
|
||||
meet_criteria(verbose, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(version_breakpoints, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_BREAKPOINTS)))
|
||||
meet_criteria(version_expertrules, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_EXPERT_RULES)))
|
||||
meet_criteria(ampc_cephalosporin_resistance, allow_class = c("logical", "character", "rsi"), has_length = 1, allow_NA = TRUE, allow_NULL = TRUE)
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(custom_rules, allow_class = "custom_eucast_rules", allow_NULL = TRUE)
|
||||
|
||||
if ("custom" %in% rules & is.null(custom_rules)) {
|
||||
warning_("No custom rules were set with the `custom_rules` argument",
|
||||
call = FALSE,
|
||||
immediate = TRUE)
|
||||
rules <- rules[rules != "custom"]
|
||||
if (length(rules) == 0) {
|
||||
if (info == TRUE) {
|
||||
message_("No other rules were set, returning original data", add_fn = font_red, as_note = FALSE)
|
||||
}
|
||||
return(x)
|
||||
}
|
||||
}
|
||||
|
||||
x_deparsed <- deparse(substitute(x))
|
||||
if (length(x_deparsed) > 1 || !all(x_deparsed %like% "[a-z]+")) {
|
||||
if (length(x_deparsed) > 1 || any(x_deparsed %unlike% "[a-z]+")) {
|
||||
x_deparsed <- "your_data"
|
||||
}
|
||||
|
||||
@@ -196,8 +229,6 @@ eucast_rules <- function(x,
|
||||
if (is.null(col_mo)) {
|
||||
col_mo <- search_type_in_df(x = x, type = "mo", info = info)
|
||||
stop_if(is.null(col_mo), "`col_mo` must be set")
|
||||
} else {
|
||||
stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found")
|
||||
}
|
||||
|
||||
decimal.mark <- getOption("OutDec")
|
||||
@@ -214,7 +245,13 @@ eucast_rules <- function(x,
|
||||
cat(font_subtle(" (no changes)\n"))
|
||||
} else {
|
||||
# opening
|
||||
cat(font_grey(" ("))
|
||||
if (n_added > 0 & n_changed == 0) {
|
||||
cat(font_green(" ("))
|
||||
} else if (n_added == 0 & n_changed > 0) {
|
||||
cat(font_blue(" ("))
|
||||
} else {
|
||||
cat(font_grey(" ("))
|
||||
}
|
||||
# additions
|
||||
if (n_added > 0) {
|
||||
if (n_added == 1) {
|
||||
@@ -236,7 +273,13 @@ eucast_rules <- function(x,
|
||||
}
|
||||
}
|
||||
# closing
|
||||
cat(font_grey(")\n"))
|
||||
if (n_added > 0 & n_changed == 0) {
|
||||
cat(font_green(")\n"))
|
||||
} else if (n_added == 0 & n_changed > 0) {
|
||||
cat(font_blue(")\n"))
|
||||
} else {
|
||||
cat(font_grey(")\n"))
|
||||
}
|
||||
}
|
||||
warned <<- FALSE
|
||||
}
|
||||
@@ -263,238 +306,13 @@ eucast_rules <- function(x,
|
||||
info = info,
|
||||
only_rsi_columns = only_rsi_columns,
|
||||
...)
|
||||
|
||||
AMC <- cols_ab["AMC"]
|
||||
AMK <- cols_ab["AMK"]
|
||||
AMP <- cols_ab["AMP"]
|
||||
AMX <- cols_ab["AMX"]
|
||||
APL <- cols_ab["APL"]
|
||||
APX <- cols_ab["APX"]
|
||||
ATM <- cols_ab["ATM"]
|
||||
AVB <- cols_ab["AVB"]
|
||||
AVO <- cols_ab["AVO"]
|
||||
AZD <- cols_ab["AZD"]
|
||||
AZL <- cols_ab["AZL"]
|
||||
AZM <- cols_ab["AZM"]
|
||||
BAM <- cols_ab["BAM"]
|
||||
BPR <- cols_ab["BPR"]
|
||||
CAC <- cols_ab["CAC"]
|
||||
CAT <- cols_ab["CAT"]
|
||||
CAZ <- cols_ab["CAZ"]
|
||||
CCP <- cols_ab["CCP"]
|
||||
CCV <- cols_ab["CCV"]
|
||||
CCX <- cols_ab["CCX"]
|
||||
CDC <- cols_ab["CDC"]
|
||||
CDR <- cols_ab["CDR"]
|
||||
CDZ <- cols_ab["CDZ"]
|
||||
CEC <- cols_ab["CEC"]
|
||||
CED <- cols_ab["CED"]
|
||||
CEI <- cols_ab["CEI"]
|
||||
CEM <- cols_ab["CEM"]
|
||||
CEP <- cols_ab["CEP"]
|
||||
CFM <- cols_ab["CFM"]
|
||||
CFM1 <- cols_ab["CFM1"]
|
||||
CFP <- cols_ab["CFP"]
|
||||
CFR <- cols_ab["CFR"]
|
||||
CFS <- cols_ab["CFS"]
|
||||
CFZ <- cols_ab["CFZ"]
|
||||
CHE <- cols_ab["CHE"]
|
||||
CHL <- cols_ab["CHL"]
|
||||
CIC <- cols_ab["CIC"]
|
||||
CID <- cols_ab["CID"]
|
||||
CIP <- cols_ab["CIP"]
|
||||
CLI <- cols_ab["CLI"]
|
||||
CLM <- cols_ab["CLM"]
|
||||
CLO <- cols_ab["CLO"]
|
||||
CLR <- cols_ab["CLR"]
|
||||
CMX <- cols_ab["CMX"]
|
||||
CMZ <- cols_ab["CMZ"]
|
||||
CND <- cols_ab["CND"]
|
||||
COL <- cols_ab["COL"]
|
||||
CPD <- cols_ab["CPD"]
|
||||
CPI <- cols_ab["CPI"]
|
||||
CPL <- cols_ab["CPL"]
|
||||
CPM <- cols_ab["CPM"]
|
||||
CPO <- cols_ab["CPO"]
|
||||
CPR <- cols_ab["CPR"]
|
||||
CPT <- cols_ab["CPT"]
|
||||
CPX <- cols_ab["CPX"]
|
||||
CRB <- cols_ab["CRB"]
|
||||
CRD <- cols_ab["CRD"]
|
||||
CRN <- cols_ab["CRN"]
|
||||
CRO <- cols_ab["CRO"]
|
||||
CSL <- cols_ab["CSL"]
|
||||
CTB <- cols_ab["CTB"]
|
||||
CTC <- cols_ab["CTC"]
|
||||
CTF <- cols_ab["CTF"]
|
||||
CTL <- cols_ab["CTL"]
|
||||
CTS <- cols_ab["CTS"]
|
||||
CTT <- cols_ab["CTT"]
|
||||
CTX <- cols_ab["CTX"]
|
||||
CTZ <- cols_ab["CTZ"]
|
||||
CXM <- cols_ab["CXM"]
|
||||
CYC <- cols_ab["CYC"]
|
||||
CZA <- cols_ab["CZA"]
|
||||
CZD <- cols_ab["CZD"]
|
||||
CZO <- cols_ab["CZO"]
|
||||
CZP <- cols_ab["CZP"]
|
||||
CZX <- cols_ab["CZX"]
|
||||
DAL <- cols_ab["DAL"]
|
||||
DAP <- cols_ab["DAP"]
|
||||
DIC <- cols_ab["DIC"]
|
||||
DIR <- cols_ab["DIR"]
|
||||
DIT <- cols_ab["DIT"]
|
||||
DIX <- cols_ab["DIX"]
|
||||
DIZ <- cols_ab["DIZ"]
|
||||
DKB <- cols_ab["DKB"]
|
||||
DOR <- cols_ab["DOR"]
|
||||
DOX <- cols_ab["DOX"]
|
||||
ENX <- cols_ab["ENX"]
|
||||
EPC <- cols_ab["EPC"]
|
||||
ERY <- cols_ab["ERY"]
|
||||
ETP <- cols_ab["ETP"]
|
||||
FEP <- cols_ab["FEP"]
|
||||
FLC <- cols_ab["FLC"]
|
||||
FLE <- cols_ab["FLE"]
|
||||
FLR1 <- cols_ab["FLR1"]
|
||||
FOS <- cols_ab["FOS"]
|
||||
FOV <- cols_ab["FOV"]
|
||||
FOX <- cols_ab["FOX"]
|
||||
FOX1 <- cols_ab["FOX1"]
|
||||
FUS <- cols_ab["FUS"]
|
||||
GAT <- cols_ab["GAT"]
|
||||
GEM <- cols_ab["GEM"]
|
||||
GEN <- cols_ab["GEN"]
|
||||
GRX <- cols_ab["GRX"]
|
||||
HAP <- cols_ab["HAP"]
|
||||
HET <- cols_ab["HET"]
|
||||
IPM <- cols_ab["IPM"]
|
||||
ISE <- cols_ab["ISE"]
|
||||
JOS <- cols_ab["JOS"]
|
||||
KAN <- cols_ab["KAN"]
|
||||
LEN <- cols_ab["LEN"]
|
||||
LEX <- cols_ab["LEX"]
|
||||
LIN <- cols_ab["LIN"]
|
||||
LNZ <- cols_ab["LNZ"]
|
||||
LOM <- cols_ab["LOM"]
|
||||
LOR <- cols_ab["LOR"]
|
||||
LTM <- cols_ab["LTM"]
|
||||
LVX <- cols_ab["LVX"]
|
||||
MAN <- cols_ab["MAN"]
|
||||
MCM <- cols_ab["MCM"]
|
||||
MEC <- cols_ab["MEC"]
|
||||
MEM <- cols_ab["MEM"]
|
||||
MET <- cols_ab["MET"]
|
||||
MEV <- cols_ab["MEV"]
|
||||
MEZ <- cols_ab["MEZ"]
|
||||
MFX <- cols_ab["MFX"]
|
||||
MID <- cols_ab["MID"]
|
||||
MNO <- cols_ab["MNO"]
|
||||
MTM <- cols_ab["MTM"]
|
||||
NAC <- cols_ab["NAC"]
|
||||
NAF <- cols_ab["NAF"]
|
||||
NAL <- cols_ab["NAL"]
|
||||
NEO <- cols_ab["NEO"]
|
||||
NET <- cols_ab["NET"]
|
||||
NIT <- cols_ab["NIT"]
|
||||
NOR <- cols_ab["NOR"]
|
||||
NOV <- cols_ab["NOV"]
|
||||
NVA <- cols_ab["NVA"]
|
||||
OFX <- cols_ab["OFX"]
|
||||
OLE <- cols_ab["OLE"]
|
||||
ORI <- cols_ab["ORI"]
|
||||
OXA <- cols_ab["OXA"]
|
||||
PAZ <- cols_ab["PAZ"]
|
||||
PEF <- cols_ab["PEF"]
|
||||
PEN <- cols_ab["PEN"]
|
||||
PHE <- cols_ab["PHE"]
|
||||
PHN <- cols_ab["PHN"]
|
||||
PIP <- cols_ab["PIP"]
|
||||
PLB <- cols_ab["PLB"]
|
||||
PME <- cols_ab["PME"]
|
||||
PNM <- cols_ab["PNM"]
|
||||
PRC <- cols_ab["PRC"]
|
||||
PRI <- cols_ab["PRI"]
|
||||
PRL <- cols_ab["PRL"]
|
||||
PRP <- cols_ab["PRP"]
|
||||
PRU <- cols_ab["PRU"]
|
||||
PVM <- cols_ab["PVM"]
|
||||
QDA <- cols_ab["QDA"]
|
||||
RAM <- cols_ab["RAM"]
|
||||
RFL <- cols_ab["RFL"]
|
||||
RID <- cols_ab["RID"]
|
||||
RIF <- cols_ab["RIF"]
|
||||
ROK <- cols_ab["ROK"]
|
||||
RST <- cols_ab["RST"]
|
||||
RXT <- cols_ab["RXT"]
|
||||
SAM <- cols_ab["SAM"]
|
||||
SBC <- cols_ab["SBC"]
|
||||
SDI <- cols_ab["SDI"]
|
||||
SDM <- cols_ab["SDM"]
|
||||
SIS <- cols_ab["SIS"]
|
||||
SLF <- cols_ab["SLF"]
|
||||
SLF1 <- cols_ab["SLF1"]
|
||||
SLF10 <- cols_ab["SLF10"]
|
||||
SLF11 <- cols_ab["SLF11"]
|
||||
SLF12 <- cols_ab["SLF12"]
|
||||
SLF13 <- cols_ab["SLF13"]
|
||||
SLF2 <- cols_ab["SLF2"]
|
||||
SLF3 <- cols_ab["SLF3"]
|
||||
SLF4 <- cols_ab["SLF4"]
|
||||
SLF5 <- cols_ab["SLF5"]
|
||||
SLF6 <- cols_ab["SLF6"]
|
||||
SLF7 <- cols_ab["SLF7"]
|
||||
SLF8 <- cols_ab["SLF8"]
|
||||
SLF9 <- cols_ab["SLF9"]
|
||||
SLT1 <- cols_ab["SLT1"]
|
||||
SLT2 <- cols_ab["SLT2"]
|
||||
SLT3 <- cols_ab["SLT3"]
|
||||
SLT4 <- cols_ab["SLT4"]
|
||||
SLT5 <- cols_ab["SLT5"]
|
||||
SLT6 <- cols_ab["SLT6"]
|
||||
SMX <- cols_ab["SMX"]
|
||||
SPI <- cols_ab["SPI"]
|
||||
SPX <- cols_ab["SPX"]
|
||||
SRX <- cols_ab["SRX"]
|
||||
STR <- cols_ab["STR"]
|
||||
STR1 <- cols_ab["STR1"]
|
||||
SUD <- cols_ab["SUD"]
|
||||
SUL <- cols_ab["SUL"]
|
||||
SUT <- cols_ab["SUT"]
|
||||
SXT <- cols_ab["SXT"]
|
||||
SZO <- cols_ab["SZO"]
|
||||
TAL <- cols_ab["TAL"]
|
||||
TAZ <- cols_ab["TAZ"]
|
||||
TCC <- cols_ab["TCC"]
|
||||
TCM <- cols_ab["TCM"]
|
||||
TCY <- cols_ab["TCY"]
|
||||
TEC <- cols_ab["TEC"]
|
||||
TEM <- cols_ab["TEM"]
|
||||
TGC <- cols_ab["TGC"]
|
||||
THA <- cols_ab["THA"]
|
||||
TIC <- cols_ab["TIC"]
|
||||
TIO <- cols_ab["TIO"]
|
||||
TLT <- cols_ab["TLT"]
|
||||
TLV <- cols_ab["TLV"]
|
||||
TMP <- cols_ab["TMP"]
|
||||
TMX <- cols_ab["TMX"]
|
||||
TOB <- cols_ab["TOB"]
|
||||
TRL <- cols_ab["TRL"]
|
||||
TVA <- cols_ab["TVA"]
|
||||
TZD <- cols_ab["TZD"]
|
||||
TZP <- cols_ab["TZP"]
|
||||
VAN <- cols_ab["VAN"]
|
||||
|
||||
ab_missing <- function(ab) {
|
||||
all(ab %in% c(NULL, NA))
|
||||
}
|
||||
|
||||
if (ab_missing(AMP) & !ab_missing(AMX)) {
|
||||
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 '", font_bold(AMX), "' as input for ampicillin since many EUCAST rules depend on it.")
|
||||
message_("Using column '", cols_ab[names(cols_ab) == "AMX"], "' as input for ampicillin since many EUCAST rules depend on it.")
|
||||
}
|
||||
AMP <- AMX
|
||||
cols_ab <- c(cols_ab, c(AMP = unname(cols_ab[names(cols_ab) == "AMX"])))
|
||||
}
|
||||
|
||||
# data preparation ----
|
||||
@@ -502,62 +320,18 @@ eucast_rules <- function(x,
|
||||
message_("Preparing data...", appendLF = FALSE, as_note = FALSE)
|
||||
}
|
||||
|
||||
# nolint start
|
||||
# antibiotic classes ----
|
||||
aminoglycosides <- c(AMK, DKB, GEN, ISE, KAN, NEO, NET, RST, SIS, STR, STR1, TOB)
|
||||
aminopenicillins <- c(AMP, AMX)
|
||||
carbapenems <- c(DOR, ETP, IPM, MEM, MEV)
|
||||
cephalosporins <- c(CDZ, CCP, CAC, CEC, CFR, RID, MAN, CTZ, CZD, CZO, CDR, DIT, FEP, CAT, CFM, CMX, CMZ, DIZ, CID, CFP, CSL, CND, CTX, CTT, CTF, FOX, CPM, CPO, CPD, CPR, CRD, CFS, CPT, CAZ, CCV, CTL, CTB, CZX, BPR, CFM1, CEI, CRO, CXM, LEX, CEP, HAP, CED, LTM, LOR)
|
||||
cephalosporins_1st <- c(CAC, CFR, RID, CTZ, CZD, CZO, CRD, CTL, LEX, CEP, HAP, CED)
|
||||
cephalosporins_2nd <- c(CEC, MAN, CMZ, CID, CND, CTT, CTF, FOX, CPR, CXM, LOR)
|
||||
cephalosporins_3rd <- c(CDZ, CCP, CCX, CDR, DIT, DIX, CAT, CPI, CFM, CMX, DIZ, CFP, CSL, CTX, CTC, CTS, CHE, FOV, CFZ, CPM, CPD, CPX, CDC, CFS, CAZ, CZA, CCV, CEM, CPL, CTB, TIO, CZX, CZP, CRO, LTM)
|
||||
cephalosporins_except_CAZ <- cephalosporins[cephalosporins != ifelse(is.null(CAZ), "", CAZ)]
|
||||
fluoroquinolones <- c(CIP, ENX, FLE, GAT, GEM, GRX, LVX, LOM, MFX, NOR, OFX, PAZ, PEF, PRU, RFL, SPX, TMX, TVA)
|
||||
glycopeptides <- c(AVO, NVA, RAM, TEC, TCM, VAN) # dalba/orita/tela are in lipoglycopeptides
|
||||
lincosamides <- c(CLI, LIN, PRL)
|
||||
lipoglycopeptides <- c(DAL, ORI, TLV)
|
||||
macrolides <- c(AZM, CLR, DIR, ERY, FLR1, JOS, MID, MCM, OLE, ROK, RXT, SPI, TLT, TRL)
|
||||
oxazolidinones <- c(CYC, LNZ, THA, TZD)
|
||||
polymyxins <- c(PLB, COL)
|
||||
streptogramins <- c(QDA, PRI)
|
||||
tetracyclines <- c(DOX, MNO, TCY) # since EUCAST v3.1 tigecycline (TGC) is set apart
|
||||
ureidopenicillins <- c(PIP, TZP, AZL, MEZ)
|
||||
all_betalactams <- c(aminopenicillins, cephalosporins, carbapenems, ureidopenicillins, AMC, OXA, FLC, PEN)
|
||||
# nolint end
|
||||
|
||||
# Some helper functions ---------------------------------------------------
|
||||
get_antibiotic_columns <- function(x, df) {
|
||||
x <- trimws(unlist(strsplit(x, ",", fixed = TRUE)))
|
||||
y <- character(0)
|
||||
for (i in seq_len(length(x))) {
|
||||
if (is.function(get(x[i]))) {
|
||||
stop("Column ", x[i], " is also a function. Please create an issue on github.com/msberends/AMR/issues.")
|
||||
}
|
||||
y <- c(y, tryCatch(get(x[i]), error = function(e) ""))
|
||||
}
|
||||
y[y != "" & y %in% colnames(df)]
|
||||
}
|
||||
markup_italics_where_needed <- function(x) {
|
||||
# returns names found in family, genus or species as italics
|
||||
if (!has_colour()) {
|
||||
return(x)
|
||||
}
|
||||
x <- unlist(strsplit(x, " "))
|
||||
ind <- gsub("[)(:]", "", x) %in% c(MO_lookup[which(MO_lookup$rank %in% c("family", "genus")), ]$fullname,
|
||||
MO_lookup[which(MO_lookup$rank == "species"), ]$species)
|
||||
x[ind] <- font_italic(x[ind], collapse = NULL)
|
||||
paste(x, collapse = " ")
|
||||
}
|
||||
get_antibiotic_names <- function(x) {
|
||||
x <- x %pm>%
|
||||
strsplit(",") %pm>%
|
||||
unlist() %pm>%
|
||||
trimws() %pm>%
|
||||
vapply(FUN.VALUE = character(1), function(x) if (x %in% antibiotics$ab) ab_name(x, language = NULL, tolower = TRUE) else x) %pm>%
|
||||
vapply(FUN.VALUE = character(1), function(x) if (x %in% antibiotics$ab) ab_name(x, language = NULL, tolower = TRUE, fast_mode = TRUE) else x) %pm>%
|
||||
sort() %pm>%
|
||||
paste(collapse = ", ")
|
||||
x <- gsub("_", " ", x, fixed = TRUE)
|
||||
x <- gsub("except CAZ", paste("except", ab_name("CAZ", language = NULL, tolower = TRUE)), x, fixed = TRUE)
|
||||
x <- gsub("except TGC", paste("except", ab_name("TGC", language = NULL, tolower = TRUE)), x, fixed = TRUE)
|
||||
x <- gsub("cephalosporins (1st|2nd|3rd|4th|5th)", "cephalosporins (\\1 gen.)", x)
|
||||
x
|
||||
}
|
||||
@@ -633,10 +407,13 @@ eucast_rules <- function(x,
|
||||
pm_distinct(`.rowid`, .keep_all = TRUE) %pm>%
|
||||
as.data.frame(stringsAsFactors = FALSE)
|
||||
x[, col_mo] <- as.mo(as.character(x[, col_mo, drop = TRUE]))
|
||||
x <- x %pm>%
|
||||
left_join_microorganisms(by = col_mo, suffix = c("_oldcols", ""))
|
||||
# rename col_mo to prevent interference with joined columns
|
||||
colnames(x)[colnames(x) == col_mo] <- ".col_mo"
|
||||
col_mo <- ".col_mo"
|
||||
# join to microorganisms data set
|
||||
x <- left_join_microorganisms(x, by = col_mo, suffix = c("_oldcols", ""))
|
||||
x$gramstain <- mo_gramstain(x[, col_mo, drop = TRUE], language = NULL)
|
||||
x$genus_species <- paste(x$genus, x$species)
|
||||
x$genus_species <- trimws(paste(x$genus, x$species))
|
||||
if (info == TRUE & NROW(x) > 10000) {
|
||||
message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
|
||||
}
|
||||
@@ -662,33 +439,47 @@ eucast_rules <- function(x,
|
||||
font_red(paste0("v", utils::packageDescription("AMR")$Version, ", ",
|
||||
format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y"))), "), see ?eucast_rules\n"))))
|
||||
}
|
||||
|
||||
ab_enzyme <- subset(antibiotics, name %like% "/")[, c("ab", "name")]
|
||||
ab_enzyme$base_name <- gsub("^([a-zA-Z0-9]+).*", "\\1", ab_enzyme$name)
|
||||
ab_enzyme$base_ab <- as.ab(ab_enzyme$base_name)
|
||||
colnames(ab_enzyme) <- c("enzyme_ab", "enzyme_name")
|
||||
ab_enzyme$base_name <- gsub("^([a-zA-Z0-9]+).*", "\\1", ab_enzyme$enzyme_name)
|
||||
ab_enzyme$base_ab <- antibiotics[match(ab_enzyme$base_name, antibiotics$name), "ab", drop = TRUE]
|
||||
ab_enzyme <- subset(ab_enzyme, !is.na(base_ab))
|
||||
# make ampicillin and amoxicillin interchangable
|
||||
ampi <- subset(ab_enzyme, base_ab == "AMX")
|
||||
ampi$base_ab <- "AMP"
|
||||
ampi$base_name <- ab_name("AMP", language = NULL)
|
||||
amox <- subset(ab_enzyme, base_ab == "AMP")
|
||||
amox$base_ab <- "AMX"
|
||||
amox$base_name <- ab_name("AMX", language = NULL)
|
||||
# merge and sort
|
||||
ab_enzyme <- rbind(ab_enzyme, ampi, amox)
|
||||
ab_enzyme <- ab_enzyme[order(ab_enzyme$enzyme_name), ]
|
||||
|
||||
for (i in seq_len(nrow(ab_enzyme))) {
|
||||
if (all(c(ab_enzyme[i, ]$ab, ab_enzyme[i, ]$base_ab) %in% names(cols_ab), na.rm = TRUE)) {
|
||||
ab_name_base <- ab_name(cols_ab[ab_enzyme[i, ]$base_ab], language = NULL, tolower = TRUE)
|
||||
ab_name_enzyme <- ab_name(cols_ab[ab_enzyme[i, ]$ab], language = NULL, tolower = TRUE)
|
||||
# check if both base and base + enzyme inhibitor are part of the data set
|
||||
if (all(c(ab_enzyme$base_ab[i], ab_enzyme$enzyme_ab[i]) %in% names(cols_ab), na.rm = TRUE)) {
|
||||
col_base <- unname(cols_ab[ab_enzyme$base_ab[i]])
|
||||
col_enzyme <- unname(cols_ab[ab_enzyme$enzyme_ab[i]])
|
||||
|
||||
# Set base to R where base + enzyme inhibitor is R ----
|
||||
rule_current <- paste0("Set ", ab_name_base, " (", cols_ab[ab_enzyme[i, ]$base_ab], ") = R where ",
|
||||
ab_name_enzyme, " (", cols_ab[ab_enzyme[i, ]$ab], ") = R")
|
||||
rule_current <- paste0(ab_enzyme$base_name[i], " ('", font_bold(col_base), "') = R if ",
|
||||
tolower(ab_enzyme$enzyme_name[i]), " ('", font_bold(col_enzyme), "') = R")
|
||||
if (info == TRUE) {
|
||||
cat(word_wrap(rule_current))
|
||||
cat("\n")
|
||||
cat(word_wrap(rule_current,
|
||||
width = getOption("width") - 30,
|
||||
extra_indent = 6))
|
||||
}
|
||||
run_changes <- edit_rsi(x = x,
|
||||
col_mo = col_mo,
|
||||
to = "R",
|
||||
rule = c(rule_current, "Other rules", "",
|
||||
paste0("Non-EUCAST: AMR package v", utils::packageDescription("AMR")$Version)),
|
||||
rows = which(as.rsi_no_warning(x[, cols_ab[ab_enzyme[i, ]$ab]]) == "R"),
|
||||
cols = cols_ab[ab_enzyme[i, ]$base_ab],
|
||||
rows = which(as.rsi_no_warning(x[, col_enzyme, drop = TRUE]) == "R"),
|
||||
cols = col_base,
|
||||
last_verbose_info = verbose_info,
|
||||
original_data = x.bak,
|
||||
warned = warned,
|
||||
info = info)
|
||||
info = info,
|
||||
verbose = verbose)
|
||||
n_added <- n_added + run_changes$added
|
||||
n_changed <- n_changed + run_changes$changed
|
||||
verbose_info <- run_changes$verbose_info
|
||||
@@ -704,23 +495,25 @@ eucast_rules <- function(x,
|
||||
}
|
||||
|
||||
# Set base + enzyme inhibitor to S where base is S ----
|
||||
rule_current <- paste0("Set ", ab_name_enzyme, " (", cols_ab[ab_enzyme[i, ]$ab], ") = S where ",
|
||||
ab_name_base, " (", cols_ab[ab_enzyme[i, ]$base_ab], ") = S")
|
||||
rule_current <- paste0(ab_enzyme$enzyme_name[i], " ('", font_bold(col_enzyme), "') = S if ",
|
||||
tolower(ab_enzyme$base_name[i]), " ('", font_bold(col_base), "') = S")
|
||||
|
||||
if (info == TRUE) {
|
||||
cat(word_wrap(rule_current))
|
||||
cat("\n")
|
||||
cat(word_wrap(rule_current,
|
||||
width = getOption("width") - 30,
|
||||
extra_indent = 6))
|
||||
}
|
||||
run_changes <- edit_rsi(x = x,
|
||||
col_mo = col_mo,
|
||||
to = "S",
|
||||
rule = c(rule_current, "Other rules", "",
|
||||
paste0("Non-EUCAST: AMR package v", utils::packageDescription("AMR")$Version)),
|
||||
rows = which(as.rsi_no_warning(x[, cols_ab[ab_enzyme[i, ]$base_ab]]) == "S"),
|
||||
cols = cols_ab[ab_enzyme[i, ]$ab],
|
||||
rows = which(as.rsi_no_warning(x[, col_base, drop = TRUE]) == "S"),
|
||||
cols = col_enzyme,
|
||||
last_verbose_info = verbose_info,
|
||||
original_data = x.bak,
|
||||
warned = warned,
|
||||
info = info)
|
||||
info = info,
|
||||
verbose = verbose)
|
||||
n_added <- n_added + run_changes$added
|
||||
n_changed <- n_changed + run_changes$changed
|
||||
verbose_info <- run_changes$verbose_info
|
||||
@@ -740,36 +533,44 @@ eucast_rules <- function(x,
|
||||
} else {
|
||||
if (info == TRUE) {
|
||||
cat("\n")
|
||||
message_("Skipping inheritance rules defined by this package, such as setting trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R. Use `eucast_rules(..., rules = \"all\")` to also apply those rules.")
|
||||
message_("Skipping inheritance rules defined by this AMR package, such as setting trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R. Add \"other\" or \"all\" to the `rules` argument to apply those rules.")
|
||||
}
|
||||
}
|
||||
|
||||
if (!any(c("all", "custom") %in% rules) & !is.null(custom_rules)) {
|
||||
if (info == TRUE) {
|
||||
message_("Skipping custom EUCAST rules, since the `rules` argument does not contain \"custom\".")
|
||||
}
|
||||
custom_rules <- NULL
|
||||
}
|
||||
|
||||
# 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 ----
|
||||
if (any(c("all", "breakpoints") %in% rules)) {
|
||||
eucast_rules_df <- subset(eucast_rules_df,
|
||||
!reference.rule_group %like% "breakpoint" |
|
||||
reference.rule_group %unlike% "breakpoint" |
|
||||
(reference.rule_group %like% "breakpoint" & reference.version == version_breakpoints))
|
||||
}
|
||||
if (any(c("all", "expert") %in% rules)) {
|
||||
eucast_rules_df <- subset(eucast_rules_df,
|
||||
!reference.rule_group %like% "expert" |
|
||||
reference.rule_group %unlike% "expert" |
|
||||
(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,
|
||||
!reference.rule %like% "ampc")
|
||||
reference.rule %unlike% "ampc")
|
||||
} else {
|
||||
if (isTRUE(ampc_cephalosporin_resistance)) {
|
||||
ampc_cephalosporin_resistance <- "R"
|
||||
@@ -777,6 +578,7 @@ eucast_rules <- function(x,
|
||||
eucast_rules_df[which(eucast_rules_df$reference.rule %like% "ampc"), "to_value"] <- as.character(ampc_cephalosporin_resistance)
|
||||
}
|
||||
|
||||
# Go over all rules and apply them ----
|
||||
for (i in seq_len(nrow(eucast_rules_df))) {
|
||||
|
||||
rule_previous <- eucast_rules_df[max(1, i - 1), "reference.rule", drop = TRUE]
|
||||
@@ -784,6 +586,14 @@ eucast_rules <- function(x,
|
||||
rule_next <- eucast_rules_df[min(nrow(eucast_rules_df), i + 1), "reference.rule", drop = TRUE]
|
||||
rule_group_previous <- eucast_rules_df[max(1, i - 1), "reference.rule_group", drop = TRUE]
|
||||
rule_group_current <- eucast_rules_df[i, "reference.rule_group", drop = TRUE]
|
||||
# don't apply rules if user doesn't want to apply them
|
||||
if (rule_group_current %like% "breakpoint" & !any(c("all", "breakpoints") %in% rules)) {
|
||||
next
|
||||
}
|
||||
if (rule_group_current %like% "expert" & !any(c("all", "expert") %in% rules)) {
|
||||
next
|
||||
}
|
||||
|
||||
if (isFALSE(info) | isFALSE(verbose)) {
|
||||
rule_text <- ""
|
||||
} else {
|
||||
@@ -804,17 +614,9 @@ eucast_rules <- function(x,
|
||||
rule_next <- ""
|
||||
}
|
||||
|
||||
# don't apply rules if user doesn't want to apply them
|
||||
if (rule_group_current %like% "breakpoint" & !any(c("all", "breakpoints") %in% rules)) {
|
||||
next
|
||||
}
|
||||
if (rule_group_current %like% "expert" & !any(c("all", "expert") %in% rules)) {
|
||||
next
|
||||
}
|
||||
|
||||
if (info == TRUE) {
|
||||
# Print EUCAST intro ------------------------------------------------------
|
||||
if (!rule_group_current %like% "other" & eucast_notification_shown == FALSE) {
|
||||
if (rule_group_current %unlike% "other" & eucast_notification_shown == FALSE) {
|
||||
cat(
|
||||
paste0("\n", font_grey(strrep("-", 0.95 * options()$width)), "\n",
|
||||
word_wrap("Rules by the ", font_bold("European Committee on Antimicrobial Susceptibility Testing (EUCAST)")), "\n",
|
||||
@@ -843,9 +645,10 @@ eucast_rules <- function(x,
|
||||
# Print rule -------------------------------------------------------------
|
||||
if (rule_current != rule_previous) {
|
||||
# is new rule within group, print its name
|
||||
cat(markup_italics_where_needed(word_wrap(rule_current,
|
||||
width = getOption("width") - 30,
|
||||
extra_indent = 6)))
|
||||
cat(italicise_taxonomy(word_wrap(rule_current,
|
||||
width = getOption("width") - 30,
|
||||
extra_indent = 6),
|
||||
type = "ansi"))
|
||||
warned <- FALSE
|
||||
}
|
||||
}
|
||||
@@ -899,26 +702,26 @@ eucast_rules <- function(x,
|
||||
source_value <- trimws(unlist(strsplit(eucast_rules_df[i, "have_these_values", drop = TRUE], ",", fixed = TRUE)))
|
||||
target_antibiotics <- eucast_rules_df[i, "then_change_these_antibiotics", drop = TRUE]
|
||||
target_value <- eucast_rules_df[i, "to_value", drop = TRUE]
|
||||
|
||||
|
||||
if (is.na(source_antibiotics)) {
|
||||
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, x)
|
||||
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))
|
||||
}
|
||||
if (length(source_antibiotics) == 0) {
|
||||
rows <- integer(0)
|
||||
} else if (length(source_antibiotics) == 1) {
|
||||
rows <- tryCatch(which(x[, if_mo_property, drop = TRUE] %like% mo_value
|
||||
& as.rsi_no_warning(x[, source_antibiotics[1L]]) == source_value[1L]),
|
||||
error = function(e) integer(0))
|
||||
rows <- tryCatch(which(x[, if_mo_property, drop = TRUE] %like% mo_value
|
||||
& as.rsi_no_warning(x[, source_antibiotics[1L]]) == source_value[1L]),
|
||||
error = function(e) integer(0))
|
||||
} else if (length(source_antibiotics) == 2) {
|
||||
rows <- tryCatch(which(x[, if_mo_property, drop = TRUE] %like% mo_value
|
||||
& as.rsi_no_warning(x[, source_antibiotics[1L]]) == source_value[1L]
|
||||
& as.rsi_no_warning(x[, source_antibiotics[2L]]) == source_value[2L]),
|
||||
error = function(e) integer(0))
|
||||
rows <- tryCatch(which(x[, if_mo_property, drop = TRUE] %like% mo_value
|
||||
& as.rsi_no_warning(x[, source_antibiotics[1L]]) == source_value[1L]
|
||||
& as.rsi_no_warning(x[, source_antibiotics[2L]]) == source_value[2L]),
|
||||
error = function(e) integer(0))
|
||||
# nolint start
|
||||
# } else if (length(source_antibiotics) == 3) {
|
||||
# rows <- tryCatch(which(x[, if_mo_property, drop = TRUE] %like% mo_value
|
||||
@@ -932,12 +735,11 @@ eucast_rules <- function(x,
|
||||
}
|
||||
}
|
||||
|
||||
cols <- get_antibiotic_columns(target_antibiotics, x)
|
||||
cols <- get_ab_from_namespace(target_antibiotics, cols_ab)
|
||||
|
||||
# Apply rule on data ------------------------------------------------------
|
||||
# this will return the unique number of changes
|
||||
run_changes <- edit_rsi(x = x,
|
||||
col_mo = col_mo,
|
||||
to = target_value,
|
||||
rule = c(rule_text, rule_group_current, rule_current,
|
||||
ifelse(rule_group_current %like% "breakpoint",
|
||||
@@ -948,7 +750,8 @@ eucast_rules <- function(x,
|
||||
last_verbose_info = verbose_info,
|
||||
original_data = x.bak,
|
||||
warned = warned,
|
||||
info = info)
|
||||
info = info,
|
||||
verbose = verbose)
|
||||
n_added <- n_added + run_changes$added
|
||||
n_changed <- n_changed + run_changes$changed
|
||||
verbose_info <- run_changes$verbose_info
|
||||
@@ -962,6 +765,61 @@ eucast_rules <- function(x,
|
||||
n_added <- 0
|
||||
n_changed <- 0
|
||||
}
|
||||
} # end of going over all rules
|
||||
|
||||
# Apply custom rules ----
|
||||
if (!is.null(custom_rules)) {
|
||||
if (info == TRUE) {
|
||||
cat("\n")
|
||||
cat(font_bold("Custom EUCAST rules, set by user"), "\n")
|
||||
}
|
||||
for (i in seq_len(length(custom_rules))) {
|
||||
rule <- custom_rules[[i]]
|
||||
rows <- which(eval(parse(text = rule$query), envir = x))
|
||||
cols <- as.character(rule$result_group)
|
||||
cols <- c(cols[cols %in% colnames(x)], # direct column names
|
||||
unname(cols_ab[names(cols_ab) %in% cols])) # based on previous cols_ab finding
|
||||
cols <- unique(cols)
|
||||
target_value <- as.character(rule$result_value)
|
||||
rule_text <- paste0("report as '", target_value, "' when ",
|
||||
format_custom_query_rule(rule$query, colours = FALSE), ": ",
|
||||
get_antibiotic_names(cols))
|
||||
if (info == TRUE) {
|
||||
# print rule
|
||||
cat(italicise_taxonomy(word_wrap(format_custom_query_rule(rule$query, colours = FALSE),
|
||||
width = getOption("width") - 30,
|
||||
extra_indent = 6),
|
||||
type = "ansi"))
|
||||
warned <- FALSE
|
||||
}
|
||||
run_changes <- edit_rsi(x = x,
|
||||
to = target_value,
|
||||
rule = c(rule_text,
|
||||
"Custom EUCAST rules",
|
||||
paste0("Custom EUCAST rule ", i),
|
||||
paste0("Object '", deparse(substitute(custom_rules)),
|
||||
"' consisting of ", length(custom_rules), " custom rules")),
|
||||
rows = rows,
|
||||
cols = cols,
|
||||
last_verbose_info = verbose_info,
|
||||
original_data = x.bak,
|
||||
warned = warned,
|
||||
info = info,
|
||||
verbose = verbose)
|
||||
n_added <- n_added + run_changes$added
|
||||
n_changed <- n_changed + run_changes$changed
|
||||
verbose_info <- run_changes$verbose_info
|
||||
x <- run_changes$output
|
||||
warn_lacking_rsi_class <- c(warn_lacking_rsi_class, run_changes$rsi_warn)
|
||||
# Print number of new changes ---------------------------------------------
|
||||
if (info == TRUE & rule_next != rule_current) {
|
||||
# print only on last one of rules in this group
|
||||
txt_ok(n_added = n_added, n_changed = n_changed, warned = warned)
|
||||
# and reset counters
|
||||
n_added <- 0
|
||||
n_changed <- 0
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
# Print overview ----------------------------------------------------------
|
||||
@@ -1053,13 +911,15 @@ eucast_rules <- function(x,
|
||||
|
||||
if (length(warn_lacking_rsi_class) > 0) {
|
||||
warn_lacking_rsi_class <- unique(warn_lacking_rsi_class)
|
||||
# take order from original data set
|
||||
warn_lacking_rsi_class <- warn_lacking_rsi_class[order(colnames(x.bak))]
|
||||
warn_lacking_rsi_class <- warn_lacking_rsi_class[!is.na(warn_lacking_rsi_class)]
|
||||
warning_("Not all columns with antimicrobial results are of class <rsi>. Transform them on beforehand, with e.g.:\n",
|
||||
" ", x_deparsed, " %>% mutate_if(is.rsi.eligible, as.rsi)\n",
|
||||
" ", x_deparsed, " %>% mutate(across((is.rsi.eligible), as.rsi))\n",
|
||||
" ", x_deparsed, " %>% as.rsi(", ifelse(length(warn_lacking_rsi_class) == 1,
|
||||
" - ", x_deparsed, " %>% as.rsi(", ifelse(length(warn_lacking_rsi_class) == 1,
|
||||
warn_lacking_rsi_class,
|
||||
paste0(warn_lacking_rsi_class[1], ":", warn_lacking_rsi_class[length(warn_lacking_rsi_class)])),
|
||||
")",
|
||||
paste0(warn_lacking_rsi_class[1], ":", warn_lacking_rsi_class[length(warn_lacking_rsi_class)])), ")\n",
|
||||
" - ", x_deparsed, " %>% mutate_if(is.rsi.eligible, as.rsi)\n",
|
||||
" - ", x_deparsed, " %>% mutate(across(where(is.rsi.eligible), as.rsi))",
|
||||
call = FALSE)
|
||||
}
|
||||
|
||||
@@ -1080,16 +940,16 @@ eucast_rules <- function(x,
|
||||
}
|
||||
|
||||
# helper function for editing the table ----
|
||||
edit_rsi <- function(x,
|
||||
col_mo,
|
||||
to,
|
||||
rule,
|
||||
edit_rsi <- function(x,
|
||||
to,
|
||||
rule,
|
||||
rows,
|
||||
cols,
|
||||
last_verbose_info,
|
||||
last_verbose_info,
|
||||
original_data,
|
||||
warned,
|
||||
info) {
|
||||
info,
|
||||
verbose) {
|
||||
cols <- unique(cols[!is.na(cols) & !is.null(cols)])
|
||||
|
||||
# for Verbose Mode, keep track of all changes and return them
|
||||
@@ -1104,7 +964,7 @@ edit_rsi <- function(x,
|
||||
}
|
||||
txt_warning <- function() {
|
||||
if (warned == FALSE) {
|
||||
if (info == TRUE) cat("", font_yellow_bg(font_black(" WARNING ")))
|
||||
if (info == TRUE) cat(" ", font_rsi_I_bg(" WARNING "), sep = "")
|
||||
}
|
||||
warned <<- TRUE
|
||||
}
|
||||
@@ -1125,13 +985,15 @@ edit_rsi <- function(x,
|
||||
TRUE
|
||||
})
|
||||
suppressWarnings(new_edits[rows, cols] <<- to)
|
||||
warning_('Value "', to, '" added to the factor levels of column(s) `', paste(cols, collapse = "`, `"), "` because this value was not an existing factor level. A better way is to use as.rsi() on beforehand on antimicrobial columns to guarantee the right structure.", call = FALSE)
|
||||
warning_("Value \"", to, "\" added to the factor levels of column", ifelse(length(cols) == 1, "", "s"),
|
||||
" ", vector_and(cols, quotes = "`", sort = FALSE),
|
||||
" because this value was not an existing factor level.",
|
||||
call = FALSE)
|
||||
txt_warning()
|
||||
warned <- FALSE
|
||||
} else {
|
||||
warning_(w$message, call = FALSE)
|
||||
txt_warning()
|
||||
cat("\n") # txt_warning() does not append a "\n" on itself
|
||||
}
|
||||
},
|
||||
error = function(e) {
|
||||
@@ -1146,7 +1008,7 @@ edit_rsi <- function(x,
|
||||
)
|
||||
|
||||
track_changes$output <- new_edits
|
||||
if (isTRUE(info) && !isTRUE(all.equal(x, track_changes$output))) {
|
||||
if ((info == TRUE | verbose == TRUE) && !isTRUE(all.equal(x, track_changes$output))) {
|
||||
get_original_rows <- function(rowids) {
|
||||
as.integer(rownames(original_data[which(original_data$.rowid %in% rowids), , drop = FALSE]))
|
||||
}
|
||||
@@ -1197,7 +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)
|
||||
|
||||
@@ -1,432 +0,0 @@
|
||||
# ==================================================================== #
|
||||
# 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/ #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Filter Isolates on Result in Antimicrobial Class
|
||||
#'
|
||||
#' Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside, or to filter on carbapenem-resistant isolates without the need to specify the drugs.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param x a data set
|
||||
#' @param ab_class an antimicrobial class, like `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value.
|
||||
#' @param result an antibiotic result: S, I or R (or a combination of more of them)
|
||||
#' @param scope the scope to check which variables to check, can be `"any"` (default) or `"all"`
|
||||
#' @param only_rsi_columns a logical to indicate whether only columns must be included that were transformed to class `<rsi>` (see [as.rsi()]) on beforehand (defaults to `FALSE`)
|
||||
#' @param ... arguments passed on to [filter_ab_class()]
|
||||
#' @details All columns of `x` will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.). This means that a filter function like e.g. [filter_aminoglycosides()] will include column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
|
||||
#' @rdname filter_ab_class
|
||||
#' @seealso [antibiotic_class_selectors()] for the `select()` equivalent.
|
||||
#' @export
|
||||
#' @examples
|
||||
#' filter_aminoglycosides(example_isolates)
|
||||
#'
|
||||
#' \donttest{
|
||||
#' if (require("dplyr")) {
|
||||
#'
|
||||
#' # filter on isolates that have any result for any aminoglycoside
|
||||
#' example_isolates %>% filter_aminoglycosides()
|
||||
#' example_isolates %>% filter_ab_class("aminoglycoside")
|
||||
#'
|
||||
#' # this is essentially the same as (but without determination of column names):
|
||||
#' example_isolates %>%
|
||||
#' filter_at(.vars = vars(c("GEN", "TOB", "AMK", "KAN")),
|
||||
#' .vars_predicate = any_vars(. %in% c("S", "I", "R")))
|
||||
#'
|
||||
#'
|
||||
#' # filter on isolates that show resistance to ANY aminoglycoside
|
||||
#' example_isolates %>% filter_aminoglycosides("R", "any")
|
||||
#'
|
||||
#' # filter on isolates that show resistance to ALL aminoglycosides
|
||||
#' example_isolates %>% filter_aminoglycosides("R", "all")
|
||||
#'
|
||||
#' # filter on isolates that show resistance to
|
||||
#' # any aminoglycoside and any fluoroquinolone
|
||||
#' example_isolates %>%
|
||||
#' filter_aminoglycosides("R") %>%
|
||||
#' filter_fluoroquinolones("R")
|
||||
#'
|
||||
#' # filter on isolates that show resistance to
|
||||
#' # all aminoglycosides and all fluoroquinolones
|
||||
#' example_isolates %>%
|
||||
#' filter_aminoglycosides("R", "all") %>%
|
||||
#' filter_fluoroquinolones("R", "all")
|
||||
#'
|
||||
#' # 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 %>% filter_carbapenems("R", "all")
|
||||
#' example_isolates %>% filter(across(carbapenems(), ~. == "R"))
|
||||
#' example_isolates %>% filter(across(carbapenems(), function(x) x == "R"))
|
||||
#' }
|
||||
#' }
|
||||
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
|
||||
}
|
||||
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)
|
||||
meet_criteria(result, allow_class = "character", has_length = c(1, 2, 3), 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)
|
||||
|
||||
check_dataset_integrity()
|
||||
|
||||
# save to return later
|
||||
x_class <- class(x)
|
||||
x.bak <- x
|
||||
x <- as.data.frame(x, stringsAsFactors = FALSE)
|
||||
|
||||
if (is.null(result)) {
|
||||
result <- c("S", "I", "R")
|
||||
}
|
||||
# make result = "SI" works too:
|
||||
result <- unlist(strsplit(result, ""))
|
||||
|
||||
stop_ifnot(all(result %in% c("S", "I", "R")), "`result` must be one or more of: 'S', 'I', 'R'")
|
||||
stop_ifnot(all(scope %in% c("any", "all")), "`scope` must be one of: 'any', 'all'")
|
||||
|
||||
# get all columns in data with names that resemble antibiotics
|
||||
ab_in_data <- get_column_abx(x, info = FALSE, only_rsi_columns = only_rsi_columns)
|
||||
if (length(ab_in_data) == 0) {
|
||||
message_("No columns with class <rsi> found (see ?as.rsi), data left unchanged.")
|
||||
return(x.bak)
|
||||
}
|
||||
# get reference data
|
||||
ab_class.bak <- ab_class
|
||||
ab_class <- gsub("[^a-zA-Z0-9]+", ".*", ab_class)
|
||||
ab_class <- gsub("(ph|f)", "(ph|f)", ab_class)
|
||||
ab_class <- gsub("(t|th)", "(t|th)", ab_class)
|
||||
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 == "") {
|
||||
message_("Unknown antimicrobial class '", ab_class.bak, "', data left unchanged.")
|
||||
return(x.bak)
|
||||
}
|
||||
# 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 (length(agents) == 0) {
|
||||
message_("No antimicrobial agents of class ", ab_group,
|
||||
" found (such as ", find_ab_names(ab_class, 2),
|
||||
")",
|
||||
ifelse(only_rsi_columns == TRUE, " with class <rsi>,", ","),
|
||||
" data left unchanged.")
|
||||
return(x.bak)
|
||||
}
|
||||
|
||||
if (scope == "any") {
|
||||
scope_txt <- " or "
|
||||
scope_fn <- any
|
||||
} else {
|
||||
scope_txt <- " and "
|
||||
scope_fn <- all
|
||||
}
|
||||
if (length(agents) > 1) {
|
||||
operator <- " are"
|
||||
scope <- paste("values in", scope, "of columns ")
|
||||
} else {
|
||||
operator <- " is"
|
||||
scope <- "value in column "
|
||||
}
|
||||
if (length(result) > 1) {
|
||||
operator <- paste(operator, "either")
|
||||
}
|
||||
|
||||
# sort columns on official name
|
||||
agents <- agents[order(ab_name(names(agents), language = NULL))]
|
||||
|
||||
message_("Filtering on ", ab_group, ": ", scope,
|
||||
paste(paste0("`", font_bold(agents, collapse = NULL),
|
||||
"` (", ab_name(names(agents), tolower = TRUE, language = NULL), ")"),
|
||||
collapse = scope_txt),
|
||||
operator, " ", vector_or(result, quotes = TRUE),
|
||||
as_note = FALSE,
|
||||
extra_indent = 6)
|
||||
x_transposed <- as.list(as.data.frame(t(x[, agents, drop = FALSE]), stringsAsFactors = FALSE))
|
||||
filtered <- vapply(FUN.VALUE = logical(1), x_transposed, function(y) scope_fn(y %in% result, na.rm = TRUE))
|
||||
x <- x[which(filtered), , drop = FALSE]
|
||||
class(x) <- x_class
|
||||
x
|
||||
}
|
||||
|
||||
#' @rdname filter_ab_class
|
||||
#' @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,
|
||||
...)
|
||||
}
|
||||
|
||||
#' @rdname filter_ab_class
|
||||
#' @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,
|
||||
...)
|
||||
}
|
||||
|
||||
#' @rdname filter_ab_class
|
||||
#' @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,
|
||||
...)
|
||||
}
|
||||
|
||||
#' @rdname filter_ab_class
|
||||
#' @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,
|
||||
...)
|
||||
}
|
||||
|
||||
#' @rdname filter_ab_class
|
||||
#' @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,
|
||||
...)
|
||||
}
|
||||
|
||||
#' @rdname filter_ab_class
|
||||
#' @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,
|
||||
...)
|
||||
}
|
||||
|
||||
#' @rdname filter_ab_class
|
||||
#' @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,
|
||||
...)
|
||||
}
|
||||
|
||||
#' @rdname filter_ab_class
|
||||
#' @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,
|
||||
...)
|
||||
}
|
||||
|
||||
#' @rdname filter_ab_class
|
||||
#' @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,
|
||||
...)
|
||||
}
|
||||
|
||||
#' @rdname filter_ab_class
|
||||
#' @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,
|
||||
...)
|
||||
}
|
||||
|
||||
#' @rdname filter_ab_class
|
||||
#' @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,
|
||||
...)
|
||||
}
|
||||
|
||||
#' @rdname filter_ab_class
|
||||
#' @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,
|
||||
...)
|
||||
}
|
||||
|
||||
#' @rdname filter_ab_class
|
||||
#' @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,
|
||||
...)
|
||||
}
|
||||
|
||||
#' @rdname filter_ab_class
|
||||
#' @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,
|
||||
...)
|
||||
}
|
||||
|
||||
find_ab_group <- function(ab_class) {
|
||||
ab_class <- gsub("[^a-zA-Z0-9]", ".*", ab_class)
|
||||
ifelse(ab_class %in% c("aminoglycoside",
|
||||
"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_names <- function(ab_group, n = 3) {
|
||||
ab_group <- gsub("[^a-zA-Z0-9]", ".*", ab_group)
|
||||
drugs <- antibiotics[which(antibiotics$group %like% ab_group & !antibiotics$ab %like% "[0-9]$"), ]$name
|
||||
paste0(sort(ab_name(sample(drugs, size = min(n, length(drugs)), replace = FALSE),
|
||||
tolower = TRUE, language = NULL)),
|
||||
collapse = ", ")
|
||||
}
|
||||
+239
-170
@@ -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. 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
|
||||
@@ -34,78 +34,105 @@
|
||||
#' @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_keyantibiotics column name of the key antibiotics to determine first (weighted) isolates, see [key_antibiotics()]. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' (case insensitive). Use `col_keyantibiotics = FALSE` to prevent this.
|
||||
#' @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 character vector with test codes that should be excluded (case-insensitive)
|
||||
#' @param icu_exclude logical to indicate whether ICU isolates should be excluded (rows with value `TRUE` in the column set with `col_icu`)
|
||||
#' @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`)
|
||||
#' @param specimen_group value in the column set with `col_specimen` to filter on
|
||||
#' @param type type to determine weighed isolates; can be `"keyantibiotics"` or `"points"`, see *Details*
|
||||
#' @param ignore_I logical to indicate whether antibiotic interpretations with `"I"` will be ignored when `type = "keyantibiotics"`, see *Details*
|
||||
#' @param points_threshold points until the comparison of key antibiotics will lead to inclusion of an isolate when `type = "points"`, see *Details*
|
||||
#' @param info print progress
|
||||
#' @param include_unknown logical to indicate whether 'unknown' microorganisms should be included too, i.e. microbial code `"UNKNOWN"`, which defaults to `FALSE`. For WHONET users, this means that all records with organism code `"con"` (*contamination*) will be excluded at default. Isolates with a microbial ID of `NA` will always be excluded as first isolate.
|
||||
#' @param include_untested_rsi logical to indicate whether also rows without antibiotic results are still eligible for becoming a first isolate. Use `include_untested_rsi = FALSE` to always return `FALSE` for such rows. This checks the data set for columns of class `<rsi>` and consequently requires transforming columns with antibiotic results using [as.rsi()] first.
|
||||
#' @param ... arguments passed on to [first_isolate()] when using [filter_first_isolate()], or arguments passed on to [key_antibiotics()] when using [filter_first_weighted_isolate()]
|
||||
#' @param type type to determine weighed isolates; can be `"keyantimicrobials"` or `"points"`, see *Details*
|
||||
#' @param method the method to apply, either `"phenotype-based"`, `"episode-based"`, `"patient-based"` or `"isolate-based"` (can be abbreviated), see *Details*. The default is `"phenotype-based"` if antimicrobial test results are present in the data, and `"episode-based"` otherwise.
|
||||
#' @param ignore_I [logical] to indicate whether antibiotic interpretations with `"I"` will be ignored when `type = "keyantimicrobials"`, see *Details*
|
||||
#' @param points_threshold minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when `type = "points"`, see *Details*
|
||||
#' @param info a [logical] to indicate info should be printed, defaults to `TRUE` only in interactive mode
|
||||
#' @param include_unknown a [logical] to indicate whether 'unknown' microorganisms should be included too, i.e. microbial code `"UNKNOWN"`, which defaults to `FALSE`. For WHONET users, this means that all records with organism code `"con"` (*contamination*) will be excluded at default. Isolates with a microbial ID of `NA` will always be excluded as first isolate.
|
||||
#' @param include_untested_rsi a [logical] to indicate whether also rows without antibiotic results are still eligible for becoming a first isolate. Use `include_untested_rsi = FALSE` to always return `FALSE` for such rows. This checks the data set for columns of class `<rsi>` and consequently requires transforming columns with antibiotic results using [as.rsi()] first.
|
||||
#' @param ... arguments passed on to [first_isolate()] when using [filter_first_isolate()], otherwise arguments passed on to [key_antimicrobials()] (such as `universal`, `gram_negative`, `gram_positive`)
|
||||
#' @details
|
||||
#' These functions are context-aware. This means that then the `x` argument can be left blank, see *Examples*.
|
||||
#' To conduct epidemiological analyses on antimicrobial resistance data, only so-called first isolates should be included to prevent overestimation and underestimation of antimicrobial resistance. Different methods can be used to do so, see below.
|
||||
#'
|
||||
#' These functions are context-aware. This means that the `x` argument can be left blank if used inside a [data.frame] call, see *Examples*.
|
||||
#'
|
||||
#' The [first_isolate()] function is a wrapper around the [is_new_episode()] function, but more efficient for data sets containing microorganism codes or names.
|
||||
#'
|
||||
#' All isolates with a microbial ID of `NA` will be excluded as first isolate.
|
||||
#'
|
||||
#' ## Why this is so Important
|
||||
#' To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode [(Hindler *et al.* 2007)](https://pubmed.ncbi.nlm.nih.gov/17304462/). If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all *S. aureus* isolates would be overestimated, because you included this MRSA more than once. It would be [selection bias](https://en.wikipedia.org/wiki/Selection_bias).
|
||||
#'
|
||||
#' ## `filter_*()` Shortcuts
|
||||
#'
|
||||
#' The functions [filter_first_isolate()] and [filter_first_weighted_isolate()] are helper functions to quickly filter on first isolates.
|
||||
#' ## Different methods
|
||||
#'
|
||||
#' The function [filter_first_isolate()] is essentially equal to either:
|
||||
#' According to Hindler *et al.* (2007, \doi{10.1086/511864}), there are different methods (algorithms) to select first isolates with increasing reliability: isolate-based, patient-based, episode-based and phenotype-based. All methods select on a combination of the taxonomic genus and species (not subspecies).
|
||||
#'
|
||||
#' ```
|
||||
#' x[first_isolate(x, ...), ]
|
||||
#'
|
||||
#' x %>% filter(first_isolate(...))
|
||||
#' ```
|
||||
#' All mentioned methods are covered in the [first_isolate()] function:
|
||||
#'
|
||||
#' The function [filter_first_weighted_isolate()] is essentially equal to:
|
||||
#'
|
||||
#' ```
|
||||
#' x %>%
|
||||
#' mutate(keyab = key_antibiotics(.)) %>%
|
||||
#' mutate(only_weighted_firsts = first_isolate(x,
|
||||
#' col_keyantibiotics = "keyab", ...)) %>%
|
||||
#' filter(only_weighted_firsts == TRUE) %>%
|
||||
#' select(-only_weighted_firsts, -keyab)
|
||||
#' ```
|
||||
#' @section Key Antibiotics:
|
||||
#' There are two ways to determine whether isolates can be included as first weighted isolates which will give generally the same results:
|
||||
#'
|
||||
#' 1. Using `type = "keyantibiotics"` and argument `ignore_I`
|
||||
#' | **Method** | **Function to apply** |
|
||||
#' |--------------------------------------------------|-------------------------------------------------------|
|
||||
#' | **Isolate-based** | `first_isolate(x, method = "isolate-based")` |
|
||||
#' | *(= all isolates)* | |
|
||||
#' | | |
|
||||
#' | | |
|
||||
#' | **Patient-based** | `first_isolate(x, method = "patient-based")` |
|
||||
#' | *(= first isolate per patient)* | |
|
||||
#' | | |
|
||||
#' | | |
|
||||
#' | **Episode-based** | `first_isolate(x, method = "episode-based")`, or: |
|
||||
#' | *(= first isolate per episode)* | |
|
||||
#' | - 7-Day interval from initial isolate | - `first_isolate(x, method = "e", episode_days = 7)` |
|
||||
#' | - 30-Day interval from initial isolate | - `first_isolate(x, method = "e", episode_days = 30)` |
|
||||
#' | | |
|
||||
#' | | |
|
||||
#' | **Phenotype-based** | `first_isolate(x, method = "phenotype-based")`, or: |
|
||||
#' | *(= first isolate per phenotype)* | |
|
||||
#' | - Major difference in any antimicrobial result | - `first_isolate(x, type = "points")` |
|
||||
#' | - Any difference in key antimicrobial results | - `first_isolate(x, type = "keyantimicrobials")` |
|
||||
#'
|
||||
#' Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With `ignore_I = FALSE`, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. Read more about this in the [key_antibiotics()] function.
|
||||
#' ### Isolate-based
|
||||
#'
|
||||
#' This method does not require any selection, as all isolates should be included. It does, however, respect all arguments set in the [first_isolate()] function. For example, the default setting for `include_unknown` (`FALSE`) will omit selection of rows without a microbial ID.
|
||||
#'
|
||||
#' ### Patient-based
|
||||
#'
|
||||
#' To include every genus-species combination per patient once, set the `episode_days` to `Inf`. Although often inappropriate, this method makes sure that no duplicate isolates are selected from the same patient. In a large longitudinal data set, this could mean that isolates are *excluded* that were found years after the initial isolate.
|
||||
#'
|
||||
#' ### Episode-based
|
||||
#'
|
||||
#' To include every genus-species combination per patient episode once, set the `episode_days` to a sensible number of days. Depending on the type of analysis, this could be 14, 30, 60 or 365. Short episodes are common for analysing specific hospital or ward data, long episodes are common for analysing regional and national data.
|
||||
#'
|
||||
#' This is the most common method to correct for duplicate isolates. Patients are categorised into episodes based on their ID and dates (e.g., the date of specimen receipt or laboratory result). While this is a common method, it does not take into account antimicrobial test results. This means that e.g. a methicillin-resistant *Staphylococcus aureus* (MRSA) isolate cannot be differentiated from a wildtype *Staphylococcus aureus* isolate.
|
||||
#'
|
||||
#' ### Phenotype-based
|
||||
#'
|
||||
#' 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` (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.
|
||||
#'
|
||||
#' 2. Using `type = "points"` and argument `points_threshold`
|
||||
#' 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.
|
||||
#'
|
||||
#' A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds `points_threshold`, which defaults to `2`, an isolate will be (re)selected as a first weighted isolate.
|
||||
#'
|
||||
#' 2. Using `type = "keyantimicrobials"` and argument `ignore_I`
|
||||
#'
|
||||
#' This method only weighs specific antimicrobial agents, called *key antimicrobials*. Any difference from S to R (or vice versa) in these key antimicrobials will select an isolate as a first weighted isolate. With `ignore_I = FALSE`, also differences from I to S or R (or vice versa) will lead to this.
|
||||
#'
|
||||
#' Key antimicrobials are internally selected using the [key_antimicrobials()] function, but can also be added manually as a variable to the data and set in the `col_keyantimicrobials` argument. Another option is to pass the output of the [key_antimicrobials()] function directly to the `col_keyantimicrobials` argument.
|
||||
#'
|
||||
#'
|
||||
#' The default method is phenotype-based (using `type = "points"`) and episode-based (using `episode_days = 365`). This makes sure that every genus-species combination is selected per patient once per year, while taking into account all antimicrobial test results. If no antimicrobial test results are available in the data set, only the episode-based method is applied at default.
|
||||
#' @rdname first_isolate
|
||||
#' @seealso [key_antibiotics()]
|
||||
#' @seealso [key_antimicrobials()]
|
||||
#' @export
|
||||
#' @return A [`logical`] vector
|
||||
#' @source Methodology of this function is strictly based on:
|
||||
#'
|
||||
#' **M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition**, 2014, *Clinical and Laboratory Standards Institute (CLSI)*. <https://clsi.org/standards/products/microbiology/documents/m39/>.
|
||||
#' - **M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition**, 2014, *Clinical and Laboratory Standards Institute (CLSI)*. <https://clsi.org/standards/products/microbiology/documents/m39/>.
|
||||
#'
|
||||
#' - Hindler JF and Stelling J (2007). **Analysis and Presentation of Cumulative Antibiograms: A New Consensus Guideline from the Clinical and Laboratory Standards Institute.** Clinical Infectious Diseases, 44(6), 867–873. \doi{10.1086/511864}
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
#' @examples
|
||||
#' # `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()), ]
|
||||
#'
|
||||
@@ -114,11 +141,9 @@
|
||||
#' example_isolates %>%
|
||||
#' filter(first_isolate())
|
||||
#'
|
||||
#' # short-hand versions:
|
||||
#' # short-hand version:
|
||||
#' example_isolates %>%
|
||||
#' filter_first_isolate()
|
||||
#' example_isolates %>%
|
||||
#' filter_first_weighted_isolate()
|
||||
#'
|
||||
#' # grouped determination of first isolates (also prints group names):
|
||||
#' example_isolates %>%
|
||||
@@ -132,14 +157,14 @@
|
||||
#' resistance = resistance(GEN)) # gentamicin resistance
|
||||
#'
|
||||
#' B <- example_isolates %>%
|
||||
#' filter_first_weighted_isolate() %>% # the 1st isolate filter
|
||||
#' filter_first_isolate() %>% # the 1st isolate filter
|
||||
#' group_by(hospital_id) %>%
|
||||
#' summarise(count = n_rsi(GEN), # gentamicin availability
|
||||
#' resistance = resistance(GEN)) # gentamicin resistance
|
||||
#'
|
||||
#' # Have a look at A and B.
|
||||
#' # B is more reliable because every isolate is counted only once.
|
||||
#' # Gentamicin resistance in hospital D appears to be 3.7% higher than
|
||||
#' # Gentamicin resistance in hospital D appears to be 4.2% higher than
|
||||
#' # when you (erroneously) would have used all isolates for analysis.
|
||||
#' }
|
||||
#' }
|
||||
@@ -150,18 +175,32 @@ first_isolate <- function(x = NULL,
|
||||
col_testcode = NULL,
|
||||
col_specimen = NULL,
|
||||
col_icu = NULL,
|
||||
col_keyantibiotics = NULL,
|
||||
col_keyantimicrobials = NULL,
|
||||
episode_days = 365,
|
||||
testcodes_exclude = NULL,
|
||||
icu_exclude = FALSE,
|
||||
specimen_group = NULL,
|
||||
type = "keyantibiotics",
|
||||
type = "points",
|
||||
method = c("phenotype-based", "episode-based", "patient-based", "isolate-based"),
|
||||
ignore_I = TRUE,
|
||||
points_threshold = 2,
|
||||
info = interactive(),
|
||||
include_unknown = FALSE,
|
||||
include_untested_rsi = TRUE,
|
||||
...) {
|
||||
|
||||
dots <- unlist(list(...))
|
||||
if (length(dots) != 0) {
|
||||
# backwards compatibility with old arguments
|
||||
dots.names <- names(dots)
|
||||
if ("filter_specimen" %in% dots.names) {
|
||||
specimen_group <- dots[which(dots.names == "filter_specimen")]
|
||||
}
|
||||
if ("col_keyantibiotics" %in% dots.names) {
|
||||
col_keyantimicrobials <- dots[which(dots.names == "col_keyantibiotics")]
|
||||
}
|
||||
}
|
||||
|
||||
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)
|
||||
@@ -177,15 +216,29 @@ first_isolate <- function(x = NULL,
|
||||
}
|
||||
meet_criteria(col_specimen, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
|
||||
meet_criteria(col_icu, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
|
||||
if (isFALSE(col_keyantibiotics)) {
|
||||
col_keyantibiotics <- NULL
|
||||
# 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"))
|
||||
# key antimicrobials
|
||||
if (length(col_keyantimicrobials) > 1) {
|
||||
meet_criteria(col_keyantimicrobials, allow_class = "character", has_length = nrow(x))
|
||||
x$keyabcol <- col_keyantimicrobials
|
||||
col_keyantimicrobials <- "keyabcol"
|
||||
} else {
|
||||
if (isFALSE(col_keyantimicrobials)) {
|
||||
col_keyantimicrobials <- NULL
|
||||
# method cannot be phenotype-based anymore
|
||||
if (method == "phenotype-based") {
|
||||
method <- "episode-based"
|
||||
}
|
||||
}
|
||||
meet_criteria(col_keyantimicrobials, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
|
||||
}
|
||||
meet_criteria(col_keyantibiotics, 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 = TRUE)
|
||||
meet_criteria(episode_days, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = FALSE)
|
||||
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)
|
||||
@@ -195,28 +248,66 @@ first_isolate <- function(x = NULL,
|
||||
# remove data.table, grouping from tibbles, etc.
|
||||
x <- as.data.frame(x, stringsAsFactors = FALSE)
|
||||
|
||||
dots <- unlist(list(...))
|
||||
if (length(dots) != 0) {
|
||||
# backwards compatibility with old arguments
|
||||
dots.names <- names(dots)
|
||||
if ("filter_specimen" %in% dots.names) {
|
||||
specimen_group <- dots[which(dots.names == "filter_specimen")]
|
||||
}
|
||||
if ("tbl" %in% dots.names) {
|
||||
x <- dots[which(dots.names == "tbl")]
|
||||
}
|
||||
any_col_contains_rsi <- any(vapply(FUN.VALUE = logical(1),
|
||||
X = x,
|
||||
# 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 ",
|
||||
ifelse(method %in% c("episode-based", "phenotype-based"),
|
||||
ifelse(is.infinite(episode_days),
|
||||
"without a specified episode length",
|
||||
paste("using an episode length of", episode_days, "days")),
|
||||
"")),
|
||||
as_note = FALSE,
|
||||
add_fn = font_black)
|
||||
}
|
||||
|
||||
# try to find columns based on type
|
||||
# -- mo
|
||||
if (is.null(col_mo)) {
|
||||
col_mo <- search_type_in_df(x = x, type = "mo")
|
||||
col_mo <- search_type_in_df(x = x, type = "mo", info = info)
|
||||
stop_if(is.null(col_mo), "`col_mo` must be set")
|
||||
}
|
||||
|
||||
# methods ----
|
||||
if (method == "isolate-based") {
|
||||
episode_days <- Inf
|
||||
col_keyantimicrobials <- NULL
|
||||
x$dummy_dates <- Sys.Date()
|
||||
col_date <- "dummy_dates"
|
||||
x$dummy_patients <- paste("dummy", seq_len(nrow(x))) # all 'patients' must be unique
|
||||
col_patient_id <- "dummy_patients"
|
||||
} else if (method == "patient-based") {
|
||||
episode_days <- Inf
|
||||
col_keyantimicrobials <- NULL
|
||||
} else if (method == "episode-based") {
|
||||
col_keyantimicrobials <- NULL
|
||||
} else if (method == "phenotype-based") {
|
||||
if (missing(type) & !is.null(col_keyantimicrobials)) {
|
||||
# type = "points" is default, but not set explicitly, while col_keyantimicrobials is
|
||||
type <- "keyantimicrobials"
|
||||
}
|
||||
if (type == "points") {
|
||||
x$keyantimicrobials <- all_antimicrobials(x, only_rsi_columns = FALSE)
|
||||
col_keyantimicrobials <- "keyantimicrobials"
|
||||
} else if (type == "keyantimicrobials" & is.null(col_keyantimicrobials)) {
|
||||
col_keyantimicrobials <- search_type_in_df(x = x, type = "keyantimicrobials", info = info)
|
||||
if (is.null(col_keyantimicrobials)) {
|
||||
# still not found as a column, create it ourselves
|
||||
x$keyantimicrobials <- key_antimicrobials(x, only_rsi_columns = FALSE, col_mo = col_mo, ...)
|
||||
col_keyantimicrobials <- "keyantimicrobials"
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
# -- date
|
||||
if (is.null(col_date)) {
|
||||
col_date <- search_type_in_df(x = x, type = "date")
|
||||
col_date <- search_type_in_df(x = x, type = "date", info = info)
|
||||
stop_if(is.null(col_date), "`col_date` must be set")
|
||||
}
|
||||
|
||||
@@ -228,19 +319,14 @@ first_isolate <- function(x = NULL,
|
||||
col_patient_id <- "patient_id"
|
||||
message_("Using combined columns '", font_bold("First name"), "', '", font_bold("Last name"), "' and '", font_bold("Sex"), "' as input for `col_patient_id`")
|
||||
} else {
|
||||
col_patient_id <- search_type_in_df(x = x, type = "patient_id")
|
||||
col_patient_id <- search_type_in_df(x = x, type = "patient_id", info = info)
|
||||
}
|
||||
stop_if(is.null(col_patient_id), "`col_patient_id` must be set")
|
||||
}
|
||||
|
||||
# -- key antibiotics
|
||||
if (is.null(col_keyantibiotics)) {
|
||||
col_keyantibiotics <- search_type_in_df(x = x, type = "keyantibiotics")
|
||||
}
|
||||
|
||||
# -- specimen
|
||||
if (is.null(col_specimen) & !is.null(specimen_group)) {
|
||||
col_specimen <- search_type_in_df(x = x, type = "specimen")
|
||||
col_specimen <- search_type_in_df(x = x, type = "specimen", info = info)
|
||||
}
|
||||
|
||||
# check if columns exist
|
||||
@@ -256,7 +342,7 @@ first_isolate <- function(x = NULL,
|
||||
check_columns_existance(col_mo)
|
||||
check_columns_existance(col_testcode)
|
||||
check_columns_existance(col_icu)
|
||||
check_columns_existance(col_keyantibiotics)
|
||||
check_columns_existance(col_keyantimicrobials)
|
||||
|
||||
# convert dates to Date
|
||||
dates <- as.Date(x[, col_date, drop = TRUE])
|
||||
@@ -274,8 +360,8 @@ first_isolate <- function(x = NULL,
|
||||
testcodes_exclude <- NULL
|
||||
}
|
||||
# remove testcodes
|
||||
if (!is.null(testcodes_exclude) & info == TRUE) {
|
||||
message_("[Criterion] Exclude test codes: ", toString(paste0("'", testcodes_exclude, "'")),
|
||||
if (!is.null(testcodes_exclude) & info == TRUE & message_not_thrown_before("first_isolate.excludingtestcodes")) {
|
||||
message_("Excluding test codes: ", vector_and(testcodes_exclude, quotes = TRUE),
|
||||
add_fn = font_black,
|
||||
as_note = FALSE)
|
||||
}
|
||||
@@ -287,14 +373,14 @@ first_isolate <- function(x = NULL,
|
||||
# filter on specimen group and keyantibiotics when they are filled in
|
||||
if (!is.null(specimen_group)) {
|
||||
check_columns_existance(col_specimen, x)
|
||||
if (info == TRUE) {
|
||||
message_("[Criterion] Exclude other than specimen group '", specimen_group, "'",
|
||||
if (info == TRUE & message_not_thrown_before("first_isolate.excludingspecimen")) {
|
||||
message_("Excluding other than specimen group '", specimen_group, "'",
|
||||
add_fn = font_black,
|
||||
as_note = FALSE)
|
||||
}
|
||||
}
|
||||
if (!is.null(col_keyantibiotics)) {
|
||||
x$newvar_key_ab <- x[, col_keyantibiotics, drop = TRUE]
|
||||
if (!is.null(col_keyantimicrobials)) {
|
||||
x$newvar_key_ab <- x[, col_keyantimicrobials, drop = TRUE]
|
||||
}
|
||||
|
||||
if (is.null(testcodes_exclude)) {
|
||||
@@ -335,7 +421,7 @@ first_isolate <- function(x = NULL,
|
||||
}
|
||||
if (row.start == row.end) {
|
||||
if (info == TRUE) {
|
||||
message_("=> Found ", font_bold("1 isolate"), ", as the data only contained 1 row",
|
||||
message_("=> Found ", font_bold("1 first isolate"), ", as the data only contained 1 row",
|
||||
add_fn = font_black,
|
||||
as_note = FALSE)
|
||||
}
|
||||
@@ -343,8 +429,8 @@ first_isolate <- function(x = NULL,
|
||||
}
|
||||
if (length(c(row.start:row.end)) == pm_n_distinct(x[c(row.start:row.end), col_mo, drop = TRUE])) {
|
||||
if (info == TRUE) {
|
||||
message_("=> Found ", font_bold(paste(length(c(row.start:row.end)), "isolates")),
|
||||
", as all isolates were different microorganisms",
|
||||
message_("=> Found ", font_bold(paste(length(c(row.start:row.end)), "first isolates")),
|
||||
", as all isolates were different microbial species",
|
||||
add_fn = font_black,
|
||||
as_note = FALSE)
|
||||
}
|
||||
@@ -358,55 +444,54 @@ first_isolate <- function(x = NULL,
|
||||
!is.na(x$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$more_than_episode_ago <- unlist(lapply(unique(x$episode_group),
|
||||
function(g,
|
||||
df = x,
|
||||
days = episode_days) {
|
||||
is_new_episode(x = df[which(df$episode_group == g), ]$newvar_date,
|
||||
episode_days = days)
|
||||
}))
|
||||
|
||||
weighted.notice <- ""
|
||||
if (!is.null(col_keyantibiotics)) {
|
||||
weighted.notice <- "weighted "
|
||||
if (info == TRUE) {
|
||||
if (type == "keyantibiotics") {
|
||||
message_("[Criterion] Base inclusion on key antibiotics, ",
|
||||
if (!is.null(col_keyantimicrobials)) {
|
||||
if (info == TRUE & message_not_thrown_before("first_isolate.type")) {
|
||||
if (type == "keyantimicrobials") {
|
||||
message_("Basing inclusion on key antimicrobials, ",
|
||||
ifelse(ignore_I == FALSE, "not ", ""),
|
||||
"ignoring I",
|
||||
add_fn = font_black,
|
||||
as_note = FALSE)
|
||||
}
|
||||
if (type == "points") {
|
||||
message_("[Criterion] Base inclusion on key antibiotics, using points threshold of "
|
||||
, points_threshold,
|
||||
message_("Basing inclusion on all antimicrobial results, using a points threshold of ",
|
||||
points_threshold,
|
||||
add_fn = font_black,
|
||||
as_note = FALSE)
|
||||
}
|
||||
}
|
||||
type_param <- type
|
||||
|
||||
x$other_key_ab <- !key_antibiotics_equal(y = x$newvar_key_ab,
|
||||
z = pm_lag(x$newvar_key_ab),
|
||||
type = type_param,
|
||||
ignore_I = ignore_I,
|
||||
points_threshold = points_threshold,
|
||||
info = info)
|
||||
}
|
||||
|
||||
x$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$newvar_key_ab),
|
||||
type = type,
|
||||
ignore_I = ignore_I,
|
||||
points_threshold = points_threshold)
|
||||
x$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 != "" &
|
||||
@@ -423,12 +508,12 @@ first_isolate <- function(x = NULL,
|
||||
}
|
||||
if (!is.null(col_icu)) {
|
||||
if (icu_exclude == TRUE) {
|
||||
message_("[Criterion] Exclude isolates from ICU.",
|
||||
message_("Excluding isolates from ICU.",
|
||||
add_fn = font_black,
|
||||
as_note = FALSE)
|
||||
x[which(as.logical(x[, col_icu, drop = TRUE])), "newvar_first_isolate"] <- FALSE
|
||||
} else {
|
||||
message_("[Criterion] Include isolates from ICU.",
|
||||
message_("Including isolates from ICU.",
|
||||
add_fn = font_black,
|
||||
as_note = FALSE)
|
||||
}
|
||||
@@ -453,7 +538,9 @@ first_isolate <- function(x = NULL,
|
||||
paste0('"', x, '"')
|
||||
}
|
||||
})
|
||||
cat("\nGroup: ", paste0(names(group), " = ", group, collapse = ", "), "\n", sep = "")
|
||||
message_("\nGroup: ", paste0(names(group), " = ", group, collapse = ", "), "\n",
|
||||
as_note = FALSE,
|
||||
add_fn = font_red)
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -484,31 +571,31 @@ 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) {
|
||||
n_found <- sum(x$newvar_first_isolate, na.rm = TRUE)
|
||||
p_found_total <- percentage(n_found / nrow(x[which(!is.na(x$newvar_mo)), , drop = FALSE]), digits = 1)
|
||||
p_found_scope <- percentage(n_found / scope.size, digits = 1)
|
||||
if (!p_found_total %like% "[.]") {
|
||||
if (p_found_total %unlike% "[.]") {
|
||||
p_found_total <- gsub("%", ".0%", p_found_total, fixed = TRUE)
|
||||
}
|
||||
if (!p_found_scope %like% "[.]") {
|
||||
if (p_found_scope %unlike% "[.]") {
|
||||
p_found_scope <- gsub("%", ".0%", p_found_scope, fixed = TRUE)
|
||||
}
|
||||
# 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")),
|
||||
" (", 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")),
|
||||
" (", 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
|
||||
@@ -521,6 +608,8 @@ filter_first_isolate <- function(x = NULL,
|
||||
col_date = NULL,
|
||||
col_patient_id = NULL,
|
||||
col_mo = NULL,
|
||||
episode_days = 365,
|
||||
method = c("phenotype-based", "episode-based", "patient-based", "isolate-based"),
|
||||
...) {
|
||||
if (is_null_or_grouped_tbl(x)) {
|
||||
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
|
||||
@@ -531,47 +620,27 @@ filter_first_isolate <- function(x = NULL,
|
||||
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))
|
||||
|
||||
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"))
|
||||
|
||||
subset(x, first_isolate(x = x,
|
||||
col_date = col_date,
|
||||
col_patient_id = col_patient_id,
|
||||
col_mo = col_mo,
|
||||
episode_days = episode_days,
|
||||
method = method,
|
||||
...))
|
||||
}
|
||||
|
||||
#' @rdname first_isolate
|
||||
#' @export
|
||||
filter_first_weighted_isolate <- function(x = NULL,
|
||||
col_date = NULL,
|
||||
col_patient_id = NULL,
|
||||
col_mo = NULL,
|
||||
col_keyantibiotics = NULL,
|
||||
...) {
|
||||
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)
|
||||
coerce_method <- function(method) {
|
||||
if (is.null(method)) {
|
||||
return(method)
|
||||
}
|
||||
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))
|
||||
meet_criteria(col_keyantibiotics, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
|
||||
|
||||
y <- x
|
||||
if (is.null(col_keyantibiotics)) {
|
||||
# first try to look for it
|
||||
col_keyantibiotics <- search_type_in_df(x = x, type = "keyantibiotics")
|
||||
# still NULL? Then create it since we are calling filter_first_WEIGHTED_isolate()
|
||||
if (is.null(col_keyantibiotics)) {
|
||||
y$keyab <- suppressMessages(key_antibiotics(x,
|
||||
col_mo = col_mo,
|
||||
...))
|
||||
col_keyantibiotics <- "keyab"
|
||||
}
|
||||
}
|
||||
|
||||
subset(x, first_isolate(x = y,
|
||||
col_date = col_date,
|
||||
col_patient_id = col_patient_id))
|
||||
method <- tolower(as.character(method[1L]))
|
||||
method[method %like% "^(p$|pheno)"] <- "phenotype-based"
|
||||
method[method %like% "^(e$|episode)"] <- "episode-based"
|
||||
method[method %like% "^pat"] <- "patient-based"
|
||||
method[method %like% "^(i$|iso)"] <- "isolate-based"
|
||||
method
|
||||
}
|
||||
|
||||
+2
-2
@@ -28,9 +28,9 @@
|
||||
#' [g.test()] performs chi-squared contingency table tests and goodness-of-fit tests, just like [chisq.test()] but is more reliable (1). A *G*-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a ***G*-test of goodness-of-fit**), or to see whether the proportions of one variable are different for different values of the other variable (called a ***G*-test of independence**).
|
||||
#' @inheritSection lifecycle Questioning Lifecycle
|
||||
#' @inherit stats::chisq.test params return
|
||||
#' @details If `x` is a matrix with one row or column, or if `x` is a vector and `y` is not given, then a *goodness-of-fit test* is performed (`x` is treated as a one-dimensional contingency table). The entries of `x` must be non-negative integers. In this case, the hypothesis tested is whether the population probabilities equal those in `p`, or are all equal if `p` is not given.
|
||||
#' @details If `x` is a [matrix] with one row or column, or if `x` is a vector and `y` is not given, then a *goodness-of-fit test* is performed (`x` is treated as a one-dimensional contingency table). The entries of `x` must be non-negative integers. In this case, the hypothesis tested is whether the population probabilities equal those in `p`, or are all equal if `p` is not given.
|
||||
#'
|
||||
#' If `x` is a matrix with at least two rows and columns, it is taken as a two-dimensional contingency table: the entries of `x` must be non-negative integers. Otherwise, `x` and `y` must be vectors or factors of the same length; cases with missing values are removed, the objects are coerced to factors, and the contingency table is computed from these. Then Pearson's chi-squared test is performed of the null hypothesis that the joint distribution of the cell counts in a 2-dimensional contingency table is the product of the row and column marginals.
|
||||
#' If `x` is a [matrix] with at least two rows and columns, it is taken as a two-dimensional contingency table: the entries of `x` must be non-negative integers. Otherwise, `x` and `y` must be vectors or factors of the same length; cases with missing values are removed, the objects are coerced to factors, and the contingency table is computed from these. Then Pearson's chi-squared test is performed of the null hypothesis that the joint distribution of the cell counts in a 2-dimensional contingency table is the product of the row and column marginals.
|
||||
#'
|
||||
#' The p-value is computed from the asymptotic chi-squared distribution of the test statistic.
|
||||
#'
|
||||
|
||||
+6
-4
@@ -33,21 +33,21 @@
|
||||
#' @param labels_textsize the size of the text used for the labels
|
||||
#' @param labels_text_placement adjustment factor the placement of the variable names (`>=1` means further away from the arrow head)
|
||||
#' @param groups an optional vector of groups for the labels, with the same length as `labels`. If set, the points and labels will be coloured according to these groups. When using the [pca()] function as input for `x`, this will be determined automatically based on the attribute `non_numeric_cols`, see [pca()].
|
||||
#' @param ellipse a logical to indicate whether a normal data ellipse should be drawn for each group (set with `groups`)
|
||||
#' @param ellipse a [logical] to indicate whether a normal data ellipse should be drawn for each group (set with `groups`)
|
||||
#' @param ellipse_prob statistical size of the ellipse in normal probability
|
||||
#' @param ellipse_size the size of the ellipse line
|
||||
#' @param ellipse_alpha the alpha (transparency) of the ellipse line
|
||||
#' @param points_size the size of the points
|
||||
#' @param points_alpha the alpha (transparency) of the points
|
||||
#' @param arrows a logical to indicate whether arrows should be drawn
|
||||
#' @param arrows a [logical] to indicate whether arrows should be drawn
|
||||
#' @param arrows_textsize the size of the text for variable names
|
||||
#' @param arrows_colour the colour of the arrow and their text
|
||||
#' @param arrows_size the size (thickness) of the arrow lines
|
||||
#' @param arrows_textsize the size of the text at the end of the arrows
|
||||
#' @param arrows_textangled a logical whether the text at the end of the arrows should be angled
|
||||
#' @param arrows_textangled a [logical] whether the text at the end of the arrows should be angled
|
||||
#' @param arrows_alpha the alpha (transparency) of the arrows and their text
|
||||
#' @param base_textsize the text size for all plot elements except the labels and arrows
|
||||
#' @param ... Arguments passed on to functions
|
||||
#' @param ... arguments passed on to functions
|
||||
#' @source The [ggplot_pca()] function is based on the `ggbiplot()` function from the `ggbiplot` package by Vince Vu, as found on GitHub: <https://github.com/vqv/ggbiplot> (retrieved: 2 March 2020, their latest commit: [`7325e88`](https://github.com/vqv/ggbiplot/commit/7325e880485bea4c07465a0304c470608fffb5d9); 12 February 2015).
|
||||
#'
|
||||
#' As per their GPL-2 licence that demands documentation of code changes, the changes made based on the source code were:
|
||||
@@ -65,6 +65,7 @@
|
||||
#' # See ?example_isolates.
|
||||
#'
|
||||
#' # See ?pca for more info about Principal Component Analysis (PCA).
|
||||
#' \donttest{
|
||||
#' if (require("dplyr")) {
|
||||
#' pca_model <- example_isolates %>%
|
||||
#' filter(mo_genus(mo) == "Staphylococcus") %>%
|
||||
@@ -84,6 +85,7 @@
|
||||
#' labs(title = "Title here")
|
||||
#' }
|
||||
#' }
|
||||
#' }
|
||||
ggplot_pca <- function(x,
|
||||
choices = 1:2,
|
||||
scale = 1,
|
||||
|
||||
+44
-39
@@ -31,8 +31,8 @@
|
||||
#' @param position position adjustment of bars, either `"fill"`, `"stack"` or `"dodge"`
|
||||
#' @param x variable to show on x axis, either `"antibiotic"` (default) or `"interpretation"` or a grouping variable
|
||||
#' @param fill variable to categorise using the plots legend, either `"antibiotic"` (default) or `"interpretation"` or a grouping variable
|
||||
#' @param breaks numeric vector of positions
|
||||
#' @param limits numeric vector of length two providing limits of the scale, use `NA` to refer to the existing minimum or maximum
|
||||
#' @param breaks a [numeric] vector of positions
|
||||
#' @param limits a [numeric] vector of length two providing limits of the scale, use `NA` to refer to the existing minimum or maximum
|
||||
#' @param facet variable to split plots by, either `"interpretation"` (default) or `"antibiotic"` or a grouping variable
|
||||
#' @inheritParams proportion
|
||||
#' @param nrow (when using `facet`) number of rows
|
||||
@@ -67,6 +67,7 @@
|
||||
#' @export
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
#' @examples
|
||||
#' \donttest{
|
||||
#' if (require("ggplot2") & require("dplyr")) {
|
||||
#'
|
||||
#' # get antimicrobial results for drugs against a UTI:
|
||||
@@ -114,36 +115,36 @@
|
||||
#' ggplot() +
|
||||
#' geom_col(aes(x = x, y = y, fill = z)) +
|
||||
#' scale_rsi_colours(Value4 = "S", Value5 = "I", Value6 = "R")
|
||||
#'
|
||||
#' # resistance of ciprofloxacine per age group
|
||||
#' example_isolates %>%
|
||||
#' mutate(first_isolate = first_isolate()) %>%
|
||||
#' filter(first_isolate == TRUE,
|
||||
#' 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) %>%
|
||||
#' ggplot_rsi(x = "age_group")
|
||||
#'
|
||||
#' # a shorter version which also adjusts data label colours:
|
||||
#' example_isolates %>%
|
||||
#' select(AMX, NIT, FOS, TMP, CIP) %>%
|
||||
#' ggplot_rsi(colours = FALSE)
|
||||
#'
|
||||
#'
|
||||
#' # 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",
|
||||
#' facet = "antibiotic",
|
||||
#' nrow = 1,
|
||||
#' title = "AMR of Anti-UTI Drugs Per Hospital",
|
||||
#' x.title = "Hospital",
|
||||
#' datalabels = FALSE)
|
||||
#' }
|
||||
#'
|
||||
#' \donttest{
|
||||
#' # resistance of ciprofloxacine per age group
|
||||
#' example_isolates %>%
|
||||
#' mutate(first_isolate = first_isolate(.)) %>%
|
||||
#' filter(first_isolate == TRUE,
|
||||
#' 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) %>%
|
||||
#' ggplot_rsi(x = "age_group")
|
||||
#'
|
||||
#' # a shorter version which also adjusts data label colours:
|
||||
#' example_isolates %>%
|
||||
#' select(AMX, NIT, FOS, TMP, CIP) %>%
|
||||
#' ggplot_rsi(colours = FALSE)
|
||||
#'
|
||||
#'
|
||||
#' # it also supports groups (don't forget to use the group var on `x` or `facet`):
|
||||
#' example_isolates %>%
|
||||
#' select(hospital_id, AMX, NIT, FOS, TMP, CIP) %>%
|
||||
#' group_by(hospital_id) %>%
|
||||
#' ggplot_rsi(x = "hospital_id",
|
||||
#' facet = "antibiotic",
|
||||
#' nrow = 1,
|
||||
#' title = "AMR of Anti-UTI Drugs Per Hospital",
|
||||
#' x.title = "Hospital",
|
||||
#' datalabels = FALSE)
|
||||
#' }
|
||||
ggplot_rsi <- function(data,
|
||||
position = NULL,
|
||||
@@ -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
|
||||
|
||||
+8
-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)",
|
||||
@@ -52,20 +56,22 @@ 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",
|
||||
"ab",
|
||||
"ab_txt",
|
||||
"affect_ab_name",
|
||||
"affect_mo_name",
|
||||
"angle",
|
||||
"antibiotic",
|
||||
"antibiotics",
|
||||
"atc_group1",
|
||||
"atc_group2",
|
||||
"base_ab",
|
||||
"code",
|
||||
"cols",
|
||||
"count",
|
||||
|
||||
+109
-30
@@ -29,8 +29,8 @@
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param x a [data.frame]
|
||||
#' @param search_string a text to search `x` for, will be checked with [as.ab()] if this value is not a column in `x`
|
||||
#' @param verbose a logical to indicate whether additional info should be printed
|
||||
#' @param only_rsi_columns a logical to indicate whether only antibiotic columns must be detected that were transformed to class `<rsi>` (see [as.rsi()]) on beforehand (defaults to `FALSE`)
|
||||
#' @param verbose a [logical] to indicate whether additional info should be printed
|
||||
#' @param only_rsi_columns a [logical] to indicate whether only antibiotic columns must be detected that were transformed to class `<rsi>` (see [as.rsi()]) on beforehand (defaults to `FALSE`)
|
||||
#' @details You can look for an antibiotic (trade) name or abbreviation and it will search `x` and the [antibiotics] data set for any column containing a name or code of that antibiotic. **Longer columns names take precedence over shorter column names.**
|
||||
#' @return A column name of `x`, or `NULL` when no result is found.
|
||||
#' @export
|
||||
@@ -97,24 +97,56 @@ 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 (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$get_column_abx.out)
|
||||
}
|
||||
|
||||
meet_criteria(x, allow_class = "data.frame")
|
||||
meet_criteria(soft_dependencies, allow_class = "character", allow_NULL = TRUE)
|
||||
meet_criteria(hard_dependencies, allow_class = "character", allow_NULL = TRUE)
|
||||
meet_criteria(verbose, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(info, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(sort, allow_class = "logical", has_length = 1)
|
||||
|
||||
if (info == TRUE) {
|
||||
message_("Auto-guessing columns suitable for analysis", appendLF = FALSE, as_note = FALSE)
|
||||
}
|
||||
|
||||
x <- as.data.frame(x, stringsAsFactors = FALSE)
|
||||
x.bak <- x
|
||||
if (only_rsi_columns == TRUE) {
|
||||
x <- x[, which(is.rsi(x)), drop = FALSE]
|
||||
}
|
||||
@@ -147,7 +179,7 @@ get_column_abx <- function(x,
|
||||
} else {
|
||||
return(NA_character_)
|
||||
}
|
||||
})
|
||||
}, USE.NAMES = FALSE)
|
||||
|
||||
x_columns <- x_columns[!is.na(x_columns)]
|
||||
x <- x[, x_columns, drop = FALSE] # without drop = FALSE, x will become a vector when x_columns is length 1
|
||||
@@ -155,56 +187,77 @@ get_column_abx <- function(x,
|
||||
abcode = suppressWarnings(as.ab(colnames(x), info = FALSE)),
|
||||
stringsAsFactors = FALSE)
|
||||
df_trans <- df_trans[!is.na(df_trans$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.")
|
||||
}
|
||||
return(x)
|
||||
pkg_env$get_column_abx.call <- unique_call_id(entire_session = FALSE)
|
||||
pkg_env$get_column_abx.checked_cols <- colnames(x.bak)
|
||||
pkg_env$get_column_abx.out <- out
|
||||
return(out)
|
||||
}
|
||||
|
||||
# sort on name
|
||||
x <- x[order(names(x), x)]
|
||||
duplicates <- c(x[duplicated(x)], x[duplicated(names(x))])
|
||||
if (sort == TRUE) {
|
||||
out <- out[order(names(out), out)]
|
||||
}
|
||||
duplicates <- c(out[duplicated(out)], out[duplicated(names(out))])
|
||||
duplicates <- duplicates[unique(names(duplicates))]
|
||||
x <- c(x[!names(x) %in% names(duplicates)], duplicates)
|
||||
x <- x[order(names(x), x)]
|
||||
out <- c(out[!names(out) %in% names(duplicates)], duplicates)
|
||||
if (sort == TRUE) {
|
||||
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,
|
||||
@@ -214,18 +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)
|
||||
@@ -233,7 +286,33 @@ get_column_abx <- function(x,
|
||||
missing_msg)
|
||||
}
|
||||
}
|
||||
x
|
||||
|
||||
pkg_env$get_column_abx.call <- unique_call_id(entire_session = FALSE)
|
||||
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) {
|
||||
|
||||
@@ -0,0 +1,132 @@
|
||||
# ==================================================================== #
|
||||
# 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/ #
|
||||
# ==================================================================== #
|
||||
|
||||
#' 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 Stable Lifecycle
|
||||
#' @param string a [character] (vector)
|
||||
#' @param type type of conversion of the taxonomic names, either "markdown" or "ansi", see *Details*
|
||||
#' @details
|
||||
#' This function finds the taxonomic names and makes them italic based on the [microorganisms] data set.
|
||||
#'
|
||||
#' The taxonomic names can be italicised using markdown (the default) by adding `*` before and after the taxonomic names, or using ANSI colours by adding `\033[3m` before and `\033[23m` after the taxonomic names. If multiple ANSI colours are not available, no conversion will occur.
|
||||
#'
|
||||
#' This function also supports abbreviation of the genus if it is followed by a species, such as "E. coli" and "K. pneumoniae ozaenae".
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
#' @export
|
||||
#' @examples
|
||||
#' italicise_taxonomy("An overview of Staphylococcus aureus isolates")
|
||||
#' italicise_taxonomy("An overview of S. aureus isolates")
|
||||
#'
|
||||
#' cat(italicise_taxonomy("An overview of S. aureus isolates", type = "ansi"))
|
||||
#'
|
||||
#' # since ggplot2 supports no markdown (yet), use
|
||||
#' # italicise_taxonomy() and the `ggtext` package for titles:
|
||||
#' \donttest{
|
||||
#' if (require("ggplot2") && require("ggtext")) {
|
||||
#' autoplot(example_isolates$AMC,
|
||||
#' title = italicise_taxonomy("Amoxi/clav in E. coli")) +
|
||||
#' theme(plot.title = ggtext::element_markdown())
|
||||
#' }
|
||||
#' }
|
||||
italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
|
||||
if (missing(type)) {
|
||||
type <- "markdown"
|
||||
}
|
||||
meet_criteria(string, allow_class = "character")
|
||||
meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("markdown", "ansi"))
|
||||
|
||||
if (type == "markdown") {
|
||||
before <- "*"
|
||||
after <- "*"
|
||||
} else if (type == "ansi") {
|
||||
if (!has_colour()) {
|
||||
return(string)
|
||||
}
|
||||
before <- "\033[3m"
|
||||
after <- "\033[23m"
|
||||
}
|
||||
|
||||
vapply(FUN.VALUE = character(1),
|
||||
string,
|
||||
function(s) {
|
||||
s_split <- unlist(strsplit(s, " "))
|
||||
|
||||
search_strings <- gsub("[^a-zA-Z-]", "", s_split)
|
||||
|
||||
ind_species <- search_strings != "" &
|
||||
search_strings %in% MO_lookup[which(MO_lookup$rank %in% c("family",
|
||||
"genus",
|
||||
"species",
|
||||
"subspecies",
|
||||
"infraspecies",
|
||||
"subsp.")),
|
||||
"species",
|
||||
drop = TRUE]
|
||||
|
||||
ind_fullname <- search_strings != "" &
|
||||
search_strings %in% c(MO_lookup[which(MO_lookup$rank %in% c("family",
|
||||
"genus",
|
||||
"species",
|
||||
"subspecies",
|
||||
"infraspecies",
|
||||
"subsp.")),
|
||||
"fullname",
|
||||
drop = TRUE],
|
||||
MO_lookup[which(MO_lookup$rank %in% c("family",
|
||||
"genus",
|
||||
"species",
|
||||
"subspecies",
|
||||
"infraspecies",
|
||||
"subsp.")),
|
||||
"subspecies",
|
||||
drop = TRUE])
|
||||
|
||||
# also support E. coli, add "E." to indices
|
||||
has_previous_genera_abbr <- s_split[which(ind_species) - 1] %like_case% "^[A-Z][.]?$"
|
||||
ind_species <- c(which(ind_species), which(ind_species)[has_previous_genera_abbr] - 1)
|
||||
|
||||
ind <- c(ind_species, which(ind_fullname))
|
||||
|
||||
s_split[ind] <- paste0(before, s_split[ind], after)
|
||||
s_paste <- paste(s_split, collapse = " ")
|
||||
|
||||
# clean up a bit
|
||||
s_paste <- gsub(paste0(after, " ", before), " ", s_paste, fixed = TRUE)
|
||||
|
||||
s_paste
|
||||
},
|
||||
USE.NAMES = FALSE)
|
||||
}
|
||||
|
||||
#' @rdname italicise_taxonomy
|
||||
#' @export
|
||||
italicize_taxonomy <- function(string, type = c("markdown", "ansi")) {
|
||||
if (missing(type)) {
|
||||
type <- "markdown"
|
||||
}
|
||||
italicise_taxonomy(string = string, type = type)
|
||||
}
|
||||
+59
-168
@@ -25,23 +25,24 @@
|
||||
|
||||
#' Join [microorganisms] to a Data Set
|
||||
#'
|
||||
#' Join the data set [microorganisms] easily to an existing table or character vector.
|
||||
#' Join the data set [microorganisms] easily to an existing data set or to a [character] vector.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @rdname join
|
||||
#' @name join
|
||||
#' @aliases join inner_join
|
||||
#' @param x existing table to join, or character vector
|
||||
#' @param x existing data set to join, or [character] vector. In case of a [character] vector, the resulting [data.frame] will contain a column 'x' with these values.
|
||||
#' @param by a variable to join by - if left empty will search for a column with class [`mo`] (created with [as.mo()]) or will be `"mo"` if that column name exists in `x`, could otherwise be a column name of `x` with values that exist in `microorganisms$mo` (such as `by = "bacteria_id"`), or another column in [microorganisms] (but then it should be named, like `by = c("bacteria_id" = "fullname")`)
|
||||
#' @param suffix if there are non-joined duplicate variables in `x` and `y`, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.
|
||||
#' @param ... ignored
|
||||
#' @param suffix if there are non-joined duplicate variables in `x` and `y`, these suffixes will be added to the output to disambiguate them. Should be a [character] vector of length 2.
|
||||
#' @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()] function 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
|
||||
#' @examples
|
||||
#' left_join_microorganisms(as.mo("K. pneumoniae"))
|
||||
#' left_join_microorganisms("B_KLBSL_PNE")
|
||||
#' left_join_microorganisms("B_KLBSL_PNMN")
|
||||
#'
|
||||
#' \donttest{
|
||||
#' if (require("dplyr")) {
|
||||
@@ -65,28 +66,7 @@ inner_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
|
||||
meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
|
||||
meet_criteria(suffix, allow_class = "character", has_length = 2)
|
||||
|
||||
check_dataset_integrity()
|
||||
x <- check_groups_before_join(x, "inner_join_microorganisms")
|
||||
checked <- joins_check_df(x, by)
|
||||
x_class <- get_prejoined_class(x)
|
||||
x <- checked$x
|
||||
by <- checked$by
|
||||
# use dplyr if available - it's much faster
|
||||
dplyr_inner <- import_fn("inner_join", "dplyr", error_on_fail = FALSE)
|
||||
if (!is.null(dplyr_inner)) {
|
||||
join <- suppressWarnings(
|
||||
dplyr_inner(x = x, y = microorganisms, by = by, suffix = suffix, ...)
|
||||
)
|
||||
} else {
|
||||
join <- suppressWarnings(
|
||||
pm_inner_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
|
||||
)
|
||||
}
|
||||
if (NROW(join) > NROW(x)) {
|
||||
warning_("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
|
||||
}
|
||||
class(join) <- x_class
|
||||
join
|
||||
join_microorganisms(type = "inner_join", x = x, by = by, suffix = suffix, ...)
|
||||
}
|
||||
|
||||
#' @rdname join
|
||||
@@ -96,28 +76,7 @@ left_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
|
||||
meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
|
||||
meet_criteria(suffix, allow_class = "character", has_length = 2)
|
||||
|
||||
check_dataset_integrity()
|
||||
x <- check_groups_before_join(x, "left_join_microorganisms")
|
||||
checked <- joins_check_df(x, by)
|
||||
x_class <- get_prejoined_class(x)
|
||||
x <- checked$x
|
||||
by <- checked$by
|
||||
# use dplyr if available - it's much faster
|
||||
dplyr_left <- import_fn("left_join", "dplyr", error_on_fail = FALSE)
|
||||
if (!is.null(dplyr_left)) {
|
||||
join <- suppressWarnings(
|
||||
dplyr_left(x = x, y = microorganisms, by = by, suffix = suffix, ...)
|
||||
)
|
||||
} else {
|
||||
join <- suppressWarnings(
|
||||
pm_left_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
|
||||
)
|
||||
}
|
||||
if (NROW(join) > NROW(x)) {
|
||||
warning_("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
|
||||
}
|
||||
class(join) <- x_class
|
||||
join
|
||||
join_microorganisms(type = "left_join", x = x, by = by, suffix = suffix, ...)
|
||||
}
|
||||
|
||||
#' @rdname join
|
||||
@@ -127,28 +86,7 @@ right_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
|
||||
meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
|
||||
meet_criteria(suffix, allow_class = "character", has_length = 2)
|
||||
|
||||
check_dataset_integrity()
|
||||
x <- check_groups_before_join(x, "right_join_microorganisms")
|
||||
checked <- joins_check_df(x, by)
|
||||
x_class <- get_prejoined_class(x)
|
||||
x <- checked$x
|
||||
by <- checked$by
|
||||
# use dplyr if available - it's much faster
|
||||
dplyr_right <- import_fn("right_join", "dplyr", error_on_fail = FALSE)
|
||||
if (!is.null(dplyr_right)) {
|
||||
join <- suppressWarnings(
|
||||
dplyr_right(x = x, y = microorganisms, by = by, suffix = suffix, ...)
|
||||
)
|
||||
} else {
|
||||
join <- suppressWarnings(
|
||||
pm_right_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
|
||||
)
|
||||
}
|
||||
if (NROW(join) > NROW(x)) {
|
||||
warning_("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
|
||||
}
|
||||
class(join) <- x_class
|
||||
join
|
||||
join_microorganisms(type = "right_join", x = x, by = by, suffix = suffix, ...)
|
||||
}
|
||||
|
||||
#' @rdname join
|
||||
@@ -158,28 +96,7 @@ full_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
|
||||
meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
|
||||
meet_criteria(suffix, allow_class = "character", has_length = 2)
|
||||
|
||||
check_dataset_integrity()
|
||||
x <- check_groups_before_join(x, "full_join_microorganisms")
|
||||
checked <- joins_check_df(x, by)
|
||||
x_class <- get_prejoined_class(x)
|
||||
x <- checked$x
|
||||
by <- checked$by
|
||||
# use dplyr if available - it's much faster
|
||||
dplyr_full <- import_fn("full_join", "dplyr", error_on_fail = FALSE)
|
||||
if (!is.null(dplyr_full)) {
|
||||
join <- suppressWarnings(
|
||||
dplyr_full(x = x, y = microorganisms, by = by, suffix = suffix, ...)
|
||||
)
|
||||
} else {
|
||||
join <- suppressWarnings(
|
||||
pm_full_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
|
||||
)
|
||||
}
|
||||
if (NROW(join) > NROW(x)) {
|
||||
warning_("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
|
||||
}
|
||||
class(join) <- x_class
|
||||
join
|
||||
join_microorganisms(type = "full_join", x = x, by = by, suffix = suffix, ...)
|
||||
}
|
||||
|
||||
#' @rdname join
|
||||
@@ -188,25 +105,7 @@ semi_join_microorganisms <- function(x, by = NULL, ...) {
|
||||
meet_criteria(x, allow_class = c("data.frame", "character"))
|
||||
meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
|
||||
|
||||
check_dataset_integrity()
|
||||
x <- check_groups_before_join(x, "semi_join_microorganisms")
|
||||
x_class <- get_prejoined_class(x)
|
||||
checked <- joins_check_df(x, by)
|
||||
x <- checked$x
|
||||
by <- checked$by
|
||||
# use dplyr if available - it's much faster
|
||||
dplyr_semi <- import_fn("semi_join", "dplyr", error_on_fail = FALSE)
|
||||
if (!is.null(dplyr_semi)) {
|
||||
join <- suppressWarnings(
|
||||
dplyr_semi(x = x, y = microorganisms, by = by, ...)
|
||||
)
|
||||
} else {
|
||||
join <- suppressWarnings(
|
||||
pm_semi_join(x = x, y = microorganisms, by = by, ...)
|
||||
)
|
||||
}
|
||||
class(join) <- x_class
|
||||
join
|
||||
join_microorganisms(type = "semi_join", x = x, by = by, ...)
|
||||
}
|
||||
|
||||
#' @rdname join
|
||||
@@ -215,72 +114,64 @@ anti_join_microorganisms <- function(x, by = NULL, ...) {
|
||||
meet_criteria(x, allow_class = c("data.frame", "character"))
|
||||
meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
|
||||
|
||||
check_dataset_integrity()
|
||||
x <- check_groups_before_join(x, "anti_join_microorganisms")
|
||||
checked <- joins_check_df(x, by)
|
||||
x_class <- get_prejoined_class(x)
|
||||
x <- checked$x
|
||||
by <- checked$by
|
||||
# use dplyr if available - it's much faster
|
||||
dplyr_anti <- import_fn("anti_join", "dplyr", error_on_fail = FALSE)
|
||||
if (!is.null(dplyr_anti)) {
|
||||
join <- suppressWarnings(
|
||||
dplyr_anti(x = x, y = microorganisms, by = by, ...)
|
||||
)
|
||||
} else {
|
||||
join <- suppressWarnings(
|
||||
pm_anti_join(x = x, y = microorganisms, by = by, ...)
|
||||
)
|
||||
}
|
||||
class(join) <- x_class
|
||||
join
|
||||
join_microorganisms(type = "anti_join", x = x, by = by, ...)
|
||||
}
|
||||
|
||||
joins_check_df <- function(x, by) {
|
||||
if (!any(class(x) %in% c("data.frame", "matrix"))) {
|
||||
x <- data.frame(mo = as.mo(x), stringsAsFactors = FALSE)
|
||||
if (is.null(by)) {
|
||||
by <- "mo"
|
||||
}
|
||||
join_microorganisms <- function(type, x, by, suffix, ...) {
|
||||
check_dataset_integrity()
|
||||
|
||||
if (!is.data.frame(x)) {
|
||||
x <- data.frame(mo = x, stringsAsFactors = FALSE)
|
||||
by <- "mo"
|
||||
}
|
||||
x <- as.data.frame(x, stringsAsFactors = FALSE)
|
||||
if (is.null(by)) {
|
||||
# search for column with class `mo` and return first one found
|
||||
by <- colnames(x)[lapply(x, is.mo) == TRUE][1]
|
||||
if (is.na(by)) {
|
||||
if ("mo" %in% colnames(x)) {
|
||||
by <- "mo"
|
||||
x[, "mo"] <- as.mo(x[, "mo"])
|
||||
} else {
|
||||
stop("Cannot join - no column found with name 'mo' or with class <mo>.", call. = FALSE)
|
||||
}
|
||||
by <- search_type_in_df(x, "mo", info = FALSE)
|
||||
if (is.null(by) && NCOL(x) == 1) {
|
||||
by <- colnames(x)[1L]
|
||||
} else {
|
||||
stop_if(is.null(by), "no column with microorganism names or codes found, set this column with `by`", call = -2)
|
||||
}
|
||||
message_('Joining, by = "', by, '"', add_fn = font_black, as_note = FALSE) # message same as dplyr::join functions
|
||||
}
|
||||
if (!all(x[, by, drop = TRUE] %in% MO_lookup$mo, na.rm = TRUE)) {
|
||||
x$join.mo <- as.mo(x[, by, drop = TRUE])
|
||||
by <- c("join.mo" = "mo")
|
||||
} else {
|
||||
x[, by] <- as.mo(x[, by, drop = TRUE])
|
||||
}
|
||||
|
||||
if (is.null(names(by))) {
|
||||
joinby <- colnames(microorganisms)[1]
|
||||
names(joinby) <- by
|
||||
# will always be joined to microorganisms$mo, so add name to that
|
||||
by <- stats::setNames("mo", by)
|
||||
}
|
||||
|
||||
# use dplyr if available - it's much faster than poorman alternatives
|
||||
dplyr_join <- import_fn(name = type, pkg = "dplyr", error_on_fail = FALSE)
|
||||
if (!is.null(dplyr_join)) {
|
||||
join_fn <- dplyr_join
|
||||
} else {
|
||||
joinby <- by
|
||||
# otherwise use poorman, see R/aa_helper_pm_functions.R
|
||||
join_fn <- get(paste0("pm_", type), envir = asNamespace("AMR"))
|
||||
}
|
||||
list(x = x,
|
||||
by = joinby)
|
||||
}
|
||||
|
||||
get_prejoined_class <- function(x) {
|
||||
if (is.data.frame(x)) {
|
||||
class(x)
|
||||
if (type %like% "full|left|right|inner") {
|
||||
joined <- join_fn(x = x, y = AMR::microorganisms, by = by, suffix = suffix, ...)
|
||||
} else {
|
||||
"data.frame"
|
||||
joined <- join_fn(x = x, y = AMR::microorganisms, by = by, ...)
|
||||
}
|
||||
}
|
||||
|
||||
check_groups_before_join <- function(x, fn) {
|
||||
if (is.data.frame(x) && !is.null(attributes(x)$groups)) {
|
||||
x <- pm_ungroup(x)
|
||||
attr(x, "groups") <- NULL
|
||||
class(x) <- class(x)[!class(x) %like% "group"]
|
||||
warning_("Groups are dropped, since the ", fn, "() function relies on merge() from base R.", call = FALSE)
|
||||
|
||||
if ("join.mo" %in% colnames(joined)) {
|
||||
if ("mo" %in% colnames(joined)) {
|
||||
ind_mo <- which(colnames(joined) %in% c("mo", "join.mo"))
|
||||
colnames(joined)[ind_mo[1L]] <- paste0("mo", suffix[1L])
|
||||
colnames(joined)[ind_mo[2L]] <- paste0("mo", suffix[2L])
|
||||
} else {
|
||||
colnames(joined)[colnames(joined) == "join.mo"] <- "mo"
|
||||
}
|
||||
}
|
||||
x
|
||||
|
||||
if (type %like% "full|left|right|inner" && NROW(joined) > NROW(x)) {
|
||||
warning_("The newly joined data set contains ", nrow(joined) - nrow(x), " rows more than the number of rows of `x`.", call = FALSE)
|
||||
}
|
||||
|
||||
joined
|
||||
}
|
||||
|
||||
@@ -1,380 +0,0 @@
|
||||
# ==================================================================== #
|
||||
# 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/ #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Key Antibiotics for First (Weighted) Isolates
|
||||
#'
|
||||
#' These function can be used to determine first isolates (see [first_isolate()]). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates can then be called first 'weighted' isolates.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param x a [data.frame] with antibiotics columns, like `AMX` or `amox`. Can be left blank to determine automatically
|
||||
#' @param y,z character vectors to compare
|
||||
#' @inheritParams first_isolate
|
||||
#' @param universal_1,universal_2,universal_3,universal_4,universal_5,universal_6 column names of **broad-spectrum** antibiotics, case-insensitive. See details for which antibiotics will be used at default (which are guessed with [guess_ab_col()]).
|
||||
#' @param GramPos_1,GramPos_2,GramPos_3,GramPos_4,GramPos_5,GramPos_6 column names of antibiotics for **Gram-positives**, case-insensitive. See details for which antibiotics will be used at default (which are guessed with [guess_ab_col()]).
|
||||
#' @param GramNeg_1,GramNeg_2,GramNeg_3,GramNeg_4,GramNeg_5,GramNeg_6 column names of antibiotics for **Gram-negatives**, case-insensitive. See details for which antibiotics will be used at default (which are guessed with [guess_ab_col()]).
|
||||
#' @param warnings give a warning about missing antibiotic columns (they will be ignored)
|
||||
#' @param ... other arguments passed on to functions
|
||||
#' @details
|
||||
#' The [key_antibiotics()] function is context-aware. This means that then the `x` argument can be left blank, see *Examples*.
|
||||
#'
|
||||
#' The function [key_antibiotics()] returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using [key_antibiotics_equal()], to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (`"."`) by [key_antibiotics()] and ignored by [key_antibiotics_equal()].
|
||||
#'
|
||||
#' The [first_isolate()] function only uses this function on the same microbial species from the same patient. Using this, e.g. an MRSA will be included after a susceptible *S. aureus* (MSSA) is found within the same patient episode. Without key antibiotic comparison it would not. See [first_isolate()] for more info.
|
||||
#'
|
||||
#' At default, the antibiotics that are used for **Gram-positive bacteria** are:
|
||||
#' - Amoxicillin
|
||||
#' - Amoxicillin/clavulanic acid
|
||||
#' - Cefuroxime
|
||||
#' - Piperacillin/tazobactam
|
||||
#' - Ciprofloxacin
|
||||
#' - Trimethoprim/sulfamethoxazole
|
||||
#' - Vancomycin
|
||||
#' - Teicoplanin
|
||||
#' - Tetracycline
|
||||
#' - Erythromycin
|
||||
#' - Oxacillin
|
||||
#' - Rifampin
|
||||
#'
|
||||
#' At default the antibiotics that are used for **Gram-negative bacteria** are:
|
||||
#' - Amoxicillin
|
||||
#' - Amoxicillin/clavulanic acid
|
||||
#' - Cefuroxime
|
||||
#' - Piperacillin/tazobactam
|
||||
#' - Ciprofloxacin
|
||||
#' - Trimethoprim/sulfamethoxazole
|
||||
#' - Gentamicin
|
||||
#' - Tobramycin
|
||||
#' - Colistin
|
||||
#' - Cefotaxime
|
||||
#' - Ceftazidime
|
||||
#' - Meropenem
|
||||
#'
|
||||
#' The function [key_antibiotics_equal()] checks the characters returned by [key_antibiotics()] for equality, and returns a [`logical`] vector.
|
||||
#' @inheritSection first_isolate Key Antibiotics
|
||||
#' @rdname key_antibiotics
|
||||
#' @export
|
||||
#' @seealso [first_isolate()]
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
#' @examples
|
||||
#' # `example_isolates` is a data set available in the AMR package.
|
||||
#' # See ?example_isolates.
|
||||
#'
|
||||
#' # output of the `key_antibiotics()` function could be like this:
|
||||
#' strainA <- "SSSRR.S.R..S"
|
||||
#' strainB <- "SSSIRSSSRSSS"
|
||||
#'
|
||||
#' # those strings can be compared with:
|
||||
#' key_antibiotics_equal(strainA, strainB)
|
||||
#' # TRUE, because I is ignored (as well as missing values)
|
||||
#'
|
||||
#' key_antibiotics_equal(strainA, strainB, ignore_I = FALSE)
|
||||
#' # FALSE, because I is not ignored and so the 4th character differs
|
||||
#'
|
||||
#' \donttest{
|
||||
#' if (require("dplyr")) {
|
||||
#' # set key antibiotics to a new variable
|
||||
#' my_patients <- example_isolates %>%
|
||||
#' mutate(keyab = key_antibiotics()) %>% # no need to define `x`
|
||||
#' mutate(
|
||||
#' # now calculate first isolates
|
||||
#' first_regular = first_isolate(col_keyantibiotics = FALSE),
|
||||
#' # and first WEIGHTED isolates
|
||||
#' first_weighted = first_isolate(col_keyantibiotics = "keyab")
|
||||
#' )
|
||||
#'
|
||||
#' # Check the difference, in this data set it results in a lot more isolates:
|
||||
#' sum(my_patients$first_regular, na.rm = TRUE)
|
||||
#' sum(my_patients$first_weighted, na.rm = TRUE)
|
||||
#' }
|
||||
#' }
|
||||
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,
|
||||
...) {
|
||||
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_mo, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(universal_1, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(universal_2, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(universal_3, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(universal_4, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(universal_5, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(universal_6, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(GramPos_1, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(GramPos_2, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(GramPos_3, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(GramPos_4, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(GramPos_5, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(GramPos_6, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(GramNeg_1, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(GramNeg_2, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(GramNeg_3, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(GramNeg_4, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(GramNeg_5, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(GramNeg_6, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(warnings, allow_class = "logical", has_length = 1)
|
||||
|
||||
# force regular data.frame, not a tibble or data.table
|
||||
x <- as.data.frame(x, stringsAsFactors = FALSE)
|
||||
|
||||
dots <- unlist(list(...))
|
||||
if (length(dots) != 0) {
|
||||
# backwards compatibility with old arguments
|
||||
dots.names <- names(dots)
|
||||
if ("info" %in% dots.names) {
|
||||
warnings <- dots[which(dots.names == "info")]
|
||||
}
|
||||
}
|
||||
|
||||
# try to find columns based on type
|
||||
# -- mo
|
||||
if (is.null(col_mo)) {
|
||||
col_mo <- search_type_in_df(x = x, type = "mo")
|
||||
stop_if(is.null(col_mo), "`col_mo` must be set")
|
||||
} else {
|
||||
stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found")
|
||||
}
|
||||
|
||||
# check columns
|
||||
col.list <- c(universal_1, universal_2, universal_3, universal_4, universal_5, universal_6,
|
||||
GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6,
|
||||
GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6)
|
||||
check_available_columns <- function(x, col.list, warnings = TRUE) {
|
||||
# check columns
|
||||
col.list <- col.list[!is.na(col.list) & !is.null(col.list)]
|
||||
names(col.list) <- col.list
|
||||
col.list.bak <- col.list
|
||||
# are they available as upper case or lower case then?
|
||||
for (i in seq_len(length(col.list))) {
|
||||
if (is.null(col.list[i]) | isTRUE(is.na(col.list[i]))) {
|
||||
col.list[i] <- NA
|
||||
} else if (toupper(col.list[i]) %in% colnames(x)) {
|
||||
col.list[i] <- toupper(col.list[i])
|
||||
} else if (tolower(col.list[i]) %in% colnames(x)) {
|
||||
col.list[i] <- tolower(col.list[i])
|
||||
} else if (!col.list[i] %in% colnames(x)) {
|
||||
col.list[i] <- NA
|
||||
}
|
||||
}
|
||||
if (!all(col.list %in% colnames(x))) {
|
||||
if (warnings == TRUE) {
|
||||
warning_("Some columns do not exist and will be ignored: ",
|
||||
col.list.bak[!(col.list %in% colnames(x))] %pm>% toString(),
|
||||
".\nTHIS MAY STRONGLY INFLUENCE THE OUTCOME.",
|
||||
immediate = TRUE,
|
||||
call = FALSE)
|
||||
}
|
||||
}
|
||||
col.list
|
||||
}
|
||||
|
||||
col.list <- check_available_columns(x = x, col.list = col.list, warnings = warnings)
|
||||
universal_1 <- col.list[universal_1]
|
||||
universal_2 <- col.list[universal_2]
|
||||
universal_3 <- col.list[universal_3]
|
||||
universal_4 <- col.list[universal_4]
|
||||
universal_5 <- col.list[universal_5]
|
||||
universal_6 <- col.list[universal_6]
|
||||
GramPos_1 <- col.list[GramPos_1]
|
||||
GramPos_2 <- col.list[GramPos_2]
|
||||
GramPos_3 <- col.list[GramPos_3]
|
||||
GramPos_4 <- col.list[GramPos_4]
|
||||
GramPos_5 <- col.list[GramPos_5]
|
||||
GramPos_6 <- col.list[GramPos_6]
|
||||
GramNeg_1 <- col.list[GramNeg_1]
|
||||
GramNeg_2 <- col.list[GramNeg_2]
|
||||
GramNeg_3 <- col.list[GramNeg_3]
|
||||
GramNeg_4 <- col.list[GramNeg_4]
|
||||
GramNeg_5 <- col.list[GramNeg_5]
|
||||
GramNeg_6 <- col.list[GramNeg_6]
|
||||
|
||||
universal <- c(universal_1, universal_2, universal_3,
|
||||
universal_4, universal_5, universal_6)
|
||||
|
||||
gram_positive <- c(universal,
|
||||
GramPos_1, GramPos_2, GramPos_3,
|
||||
GramPos_4, GramPos_5, GramPos_6)
|
||||
gram_positive <- gram_positive[!is.null(gram_positive)]
|
||||
gram_positive <- gram_positive[!is.na(gram_positive)]
|
||||
if (length(gram_positive) < 12 & message_not_thrown_before("key_antibiotics.grampos")) {
|
||||
warning_("Only using ", length(gram_positive), " different antibiotics as key antibiotics for Gram-positives. See ?key_antibiotics.", call = FALSE)
|
||||
remember_thrown_message("key_antibiotics.grampos")
|
||||
}
|
||||
|
||||
gram_negative <- c(universal,
|
||||
GramNeg_1, GramNeg_2, GramNeg_3,
|
||||
GramNeg_4, GramNeg_5, GramNeg_6)
|
||||
gram_negative <- gram_negative[!is.null(gram_negative)]
|
||||
gram_negative <- gram_negative[!is.na(gram_negative)]
|
||||
if (length(gram_negative) < 12 & message_not_thrown_before("key_antibiotics.gramneg")) {
|
||||
warning_("Only using ", length(gram_negative), " different antibiotics as key antibiotics for Gram-negatives. See ?key_antibiotics.", call = FALSE)
|
||||
remember_thrown_message("key_antibiotics.gramneg")
|
||||
}
|
||||
|
||||
x[, col_mo] <- as.mo(x[, col_mo, drop = TRUE])
|
||||
x$gramstain <- mo_gramstain(x[, col_mo, drop = TRUE], language = NULL)
|
||||
x$key_ab <- NA_character_
|
||||
|
||||
# Gram +
|
||||
x$key_ab <- pm_if_else(x$gramstain == "Gram-positive",
|
||||
tryCatch(apply(X = x[, gram_positive],
|
||||
MARGIN = 1,
|
||||
FUN = function(x) paste(x, collapse = "")),
|
||||
error = function(e) paste0(rep(".", 12), collapse = "")),
|
||||
x$key_ab)
|
||||
|
||||
# Gram -
|
||||
x$key_ab <- pm_if_else(x$gramstain == "Gram-negative",
|
||||
tryCatch(apply(X = x[, gram_negative],
|
||||
MARGIN = 1,
|
||||
FUN = function(x) paste(x, collapse = "")),
|
||||
error = function(e) paste0(rep(".", 12), collapse = "")),
|
||||
x$key_ab)
|
||||
|
||||
# format
|
||||
key_abs <- toupper(gsub("[^SIR]", ".", gsub("(NA|NULL)", ".", x$key_ab)))
|
||||
|
||||
if (pm_n_distinct(key_abs) == 1) {
|
||||
warning_("No distinct key antibiotics determined.", call = FALSE)
|
||||
}
|
||||
|
||||
key_abs
|
||||
|
||||
}
|
||||
|
||||
#' @rdname key_antibiotics
|
||||
#' @export
|
||||
key_antibiotics_equal <- function(y,
|
||||
z,
|
||||
type = c("keyantibiotics", "points"),
|
||||
ignore_I = TRUE,
|
||||
points_threshold = 2,
|
||||
info = FALSE) {
|
||||
meet_criteria(y, allow_class = "character")
|
||||
meet_criteria(z, allow_class = "character")
|
||||
meet_criteria(type, allow_class = "character", has_length = c(1, 2))
|
||||
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)
|
||||
|
||||
stop_ifnot(length(y) == length(z), "length of `y` and `z` must be equal")
|
||||
# y is active row, z is lag
|
||||
x <- y
|
||||
y <- z
|
||||
|
||||
type <- type[1]
|
||||
|
||||
# only show progress bar on points or when at least 5000 isolates
|
||||
info_needed <- info == TRUE & (type == "points" | length(x) > 5000)
|
||||
|
||||
result <- logical(length(x))
|
||||
|
||||
if (info_needed == TRUE) {
|
||||
p <- progress_ticker(length(x))
|
||||
on.exit(close(p))
|
||||
}
|
||||
|
||||
for (i in seq_len(length(x))) {
|
||||
|
||||
if (info_needed == TRUE) {
|
||||
p$tick()
|
||||
}
|
||||
|
||||
if (is.na(x[i])) {
|
||||
x[i] <- ""
|
||||
}
|
||||
if (is.na(y[i])) {
|
||||
y[i] <- ""
|
||||
}
|
||||
|
||||
if (x[i] == y[i]) {
|
||||
|
||||
result[i] <- TRUE
|
||||
|
||||
} else if (nchar(x[i]) != nchar(y[i])) {
|
||||
|
||||
result[i] <- FALSE
|
||||
|
||||
} else {
|
||||
|
||||
x_split <- strsplit(x[i], "")[[1]]
|
||||
y_split <- strsplit(y[i], "")[[1]]
|
||||
|
||||
if (type == "keyantibiotics") {
|
||||
|
||||
if (ignore_I == TRUE) {
|
||||
x_split[x_split == "I"] <- "."
|
||||
y_split[y_split == "I"] <- "."
|
||||
}
|
||||
|
||||
y_split[x_split == "."] <- "."
|
||||
x_split[y_split == "."] <- "."
|
||||
|
||||
result[i] <- all(x_split == y_split)
|
||||
|
||||
} else if (type == "points") {
|
||||
# count points for every single character:
|
||||
# - no change is 0 points
|
||||
# - I <-> S|R is 0.5 point
|
||||
# - S|R <-> R|S is 1 point
|
||||
# use the levels of as.rsi (S = 1, I = 2, R = 3)
|
||||
|
||||
suppressWarnings(x_split <- x_split %pm>% as.rsi() %pm>% as.double())
|
||||
suppressWarnings(y_split <- y_split %pm>% as.rsi() %pm>% as.double())
|
||||
|
||||
points <- (x_split - y_split) %pm>% abs() %pm>% sum(na.rm = TRUE) / 2
|
||||
result[i] <- points >= points_threshold
|
||||
|
||||
} else {
|
||||
stop("`", type, '` is not a valid value for type, must be "points" or "keyantibiotics". See ?key_antibiotics')
|
||||
}
|
||||
}
|
||||
}
|
||||
if (info_needed == TRUE) {
|
||||
close(p)
|
||||
}
|
||||
result
|
||||
}
|
||||
Executable
+334
@@ -0,0 +1,334 @@
|
||||
# ==================================================================== #
|
||||
# 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/ #
|
||||
# ==================================================================== #
|
||||
|
||||
#' (Key) Antimicrobials for First Weighted Isolates
|
||||
#'
|
||||
#' These functions can be used to determine first weighted isolates by considering the phenotype for isolate selection (see [first_isolate()]). Using a phenotype-based method to determine first isolates is more reliable than methods that disregard phenotypes.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param x a [data.frame] with antibiotics columns, like `AMX` or `amox`. Can be left blank to determine automatically
|
||||
#' @param y,z [character] vectors to compare
|
||||
#' @inheritParams first_isolate
|
||||
#' @param universal names of **broad-spectrum** antimicrobial agents, case-insensitive. Set to `NULL` to ignore. See *Details* for the default agents.
|
||||
#' @param gram_negative names of antibiotic agents for **Gram-positives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default agents.
|
||||
#' @param gram_positive names of antibiotic agents for **Gram-negatives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default agents.
|
||||
#' @param antifungal names of antifungal agents for **fungi**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default agents.
|
||||
#' @param only_rsi_columns a [logical] to indicate whether only columns must be included that were transformed to class `<rsi>` (see [as.rsi()]) on beforehand (defaults to `FALSE`)
|
||||
#' @param ... ignored, only in place to allow future extensions
|
||||
#' @details
|
||||
#' The [key_antimicrobials()] and [all_antimicrobials()] functions are context-aware. This means that the `x` argument can be left blank if used inside a [data.frame] call, see *Examples*.
|
||||
#'
|
||||
#' The function [key_antimicrobials()] returns a [character] vector with 12 antimicrobial results for every isolate. The function [all_antimicrobials()] returns a [character] vector with all antimicrobial results for every isolate. These vectors can then be compared using [antimicrobials_equal()], to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (`"."`) by [key_antimicrobials()] and ignored by [antimicrobials_equal()].
|
||||
#'
|
||||
#' Please see the [first_isolate()] function how these important functions enable the 'phenotype-based' method for determination of first isolates.
|
||||
#'
|
||||
#' The default antimicrobial agents used for **all rows** (set in `universal`) are:
|
||||
#'
|
||||
#' - Ampicillin
|
||||
#' - Amoxicillin/clavulanic acid
|
||||
#' - Cefuroxime
|
||||
#' - Ciprofloxacin
|
||||
#' - Piperacillin/tazobactam
|
||||
#' - Trimethoprim/sulfamethoxazole
|
||||
#'
|
||||
#' The default antimicrobial agents used for **Gram-negative bacteria** (set in `gram_negative`) are:
|
||||
#'
|
||||
#' - Cefotaxime
|
||||
#' - Ceftazidime
|
||||
#' - Colistin
|
||||
#' - Gentamicin
|
||||
#' - Meropenem
|
||||
#' - Tobramycin
|
||||
#'
|
||||
#' The default antimicrobial agents used for **Gram-positive bacteria** (set in `gram_positive`) are:
|
||||
#'
|
||||
#' - Erythromycin
|
||||
#' - Oxacillin
|
||||
#' - Rifampin
|
||||
#' - Teicoplanin
|
||||
#' - Tetracycline
|
||||
#' - Vancomycin
|
||||
#'
|
||||
#'
|
||||
#' The default antimicrobial agents used for **fungi** (set in `antifungal`) are:
|
||||
#'
|
||||
#' - Anidulafungin
|
||||
#' - Caspofungin
|
||||
#' - Fluconazole
|
||||
#' - Miconazole
|
||||
#' - Nystatin
|
||||
#' - Voriconazole
|
||||
#' @rdname key_antimicrobials
|
||||
#' @export
|
||||
#' @seealso [first_isolate()]
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
#' @examples
|
||||
#' # `example_isolates` is a data set available in the AMR package.
|
||||
#' # See ?example_isolates.
|
||||
#'
|
||||
#' # output of the `key_antimicrobials()` function could be like this:
|
||||
#' strainA <- "SSSRR.S.R..S"
|
||||
#' strainB <- "SSSIRSSSRSSS"
|
||||
#'
|
||||
#' # those strings can be compared with:
|
||||
#' antimicrobials_equal(strainA, strainB, type = "keyantimicrobials")
|
||||
#' # TRUE, because I is ignored (as well as missing values)
|
||||
#'
|
||||
#' antimicrobials_equal(strainA, strainB, type = "keyantimicrobials", ignore_I = FALSE)
|
||||
#' # FALSE, because I is not ignored and so the 4th [character] differs
|
||||
#'
|
||||
#' \donttest{
|
||||
#' if (require("dplyr")) {
|
||||
#' # set key antibiotics to a new variable
|
||||
#' my_patients <- example_isolates %>%
|
||||
#' mutate(keyab = key_antimicrobials(antifungal = NULL)) %>% # no need to define `x`
|
||||
#' mutate(
|
||||
#' # now calculate first isolates
|
||||
#' first_regular = first_isolate(col_keyantimicrobials = FALSE),
|
||||
#' # and first WEIGHTED isolates
|
||||
#' first_weighted = first_isolate(col_keyantimicrobials = "keyab")
|
||||
#' )
|
||||
#'
|
||||
#' # Check the difference, in this data set it results in more isolates:
|
||||
#' sum(my_patients$first_regular, na.rm = TRUE)
|
||||
#' sum(my_patients$first_weighted, na.rm = TRUE)
|
||||
#' }
|
||||
#' }
|
||||
key_antimicrobials <- function(x = NULL,
|
||||
col_mo = NULL,
|
||||
universal = c("ampicillin", "amoxicillin/clavulanic acid", "cefuroxime",
|
||||
"piperacillin/tazobactam", "ciprofloxacin", "trimethoprim/sulfamethoxazole"),
|
||||
gram_negative = c("gentamicin", "tobramycin", "colistin",
|
||||
"cefotaxime", "ceftazidime", "meropenem"),
|
||||
gram_positive = c("vancomycin", "teicoplanin", "tetracycline",
|
||||
"erythromycin", "oxacillin", "rifampin"),
|
||||
antifungal = c("anidulafungin", "caspofungin", "fluconazole",
|
||||
"miconazole", "nystatin", "voriconazole"),
|
||||
only_rsi_columns = FALSE,
|
||||
...) {
|
||||
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_mo, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE, is_in = colnames(x))
|
||||
meet_criteria(universal, allow_class = "character", allow_NULL = TRUE)
|
||||
meet_criteria(gram_negative, allow_class = "character", allow_NULL = TRUE)
|
||||
meet_criteria(gram_positive, allow_class = "character", allow_NULL = TRUE)
|
||||
meet_criteria(antifungal, allow_class = "character", allow_NULL = TRUE)
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
|
||||
# force regular data.frame, not a tibble or data.table
|
||||
x <- as.data.frame(x, stringsAsFactors = FALSE)
|
||||
cols <- get_column_abx(x, info = FALSE, only_rsi_columns = only_rsi_columns)
|
||||
|
||||
# try to find columns based on type
|
||||
# -- mo
|
||||
if (is.null(col_mo)) {
|
||||
col_mo <- search_type_in_df(x = x, type = "mo", info = FALSE)
|
||||
}
|
||||
if (is.null(col_mo)) {
|
||||
warning_("No column found for `col_mo`, ignoring antibiotics set in `gram_negative` and `gram_positive`, and antimycotics set in `antifungal`", call = FALSE)
|
||||
gramstain <- NA_character_
|
||||
kingdom <- NA_character_
|
||||
} else {
|
||||
x.mo <- as.mo(x[, col_mo, drop = TRUE])
|
||||
gramstain <- mo_gramstain(x.mo, language = NULL)
|
||||
kingdom <- mo_kingdom(x.mo, language = NULL)
|
||||
}
|
||||
|
||||
AMR_string <- function(x, values, name, filter, cols = cols) {
|
||||
if (is.null(values)) {
|
||||
return(rep(NA_character_, length(which(filter))))
|
||||
}
|
||||
|
||||
values_old_length <- length(values)
|
||||
values <- as.ab(values, flag_multiple_results = FALSE, info = FALSE)
|
||||
values <- cols[names(cols) %in% values]
|
||||
values_new_length <- length(values)
|
||||
|
||||
if (values_new_length < values_old_length &
|
||||
any(filter, na.rm = TRUE) &
|
||||
message_not_thrown_before(paste0("key_antimicrobials.", name))) {
|
||||
warning_(ifelse(values_new_length == 0,
|
||||
"No columns available ",
|
||||
paste0("Only using ", values_new_length, " out of ", values_old_length, " defined columns ")),
|
||||
"as key antimicrobials for ", name, "s. See ?key_antimicrobials.",
|
||||
call = FALSE)
|
||||
}
|
||||
|
||||
generate_antimcrobials_string(x[which(filter), c(universal, values), drop = FALSE])
|
||||
}
|
||||
|
||||
if (is.null(universal)) {
|
||||
universal <- character(0)
|
||||
} else {
|
||||
universal <- as.ab(universal, flag_multiple_results = FALSE, info = FALSE)
|
||||
universal <- cols[names(cols) %in% universal]
|
||||
}
|
||||
|
||||
key_ab <- rep(NA_character_, nrow(x))
|
||||
|
||||
key_ab[which(gramstain == "Gram-negative")] <- AMR_string(x = x,
|
||||
values = gram_negative,
|
||||
name = "Gram-negative",
|
||||
filter = gramstain == "Gram-negative",
|
||||
cols = cols)
|
||||
|
||||
key_ab[which(gramstain == "Gram-positive")] <- AMR_string(x = x,
|
||||
values = gram_positive,
|
||||
name = "Gram-positive",
|
||||
filter = gramstain == "Gram-positive",
|
||||
cols = cols)
|
||||
|
||||
key_ab[which(kingdom == "Fungi")] <- AMR_string(x = x,
|
||||
values = antifungal,
|
||||
name = "antifungal",
|
||||
filter = kingdom == "Fungi",
|
||||
cols = cols)
|
||||
|
||||
# back-up - only use `universal`
|
||||
key_ab[which(is.na(key_ab))] <- AMR_string(x = x,
|
||||
values = character(0),
|
||||
name = "",
|
||||
filter = is.na(key_ab),
|
||||
cols = cols)
|
||||
|
||||
if (length(unique(key_ab)) == 1) {
|
||||
warning_("No distinct key antibiotics determined.", call = FALSE)
|
||||
}
|
||||
|
||||
key_ab
|
||||
}
|
||||
|
||||
#' @rdname key_antimicrobials
|
||||
#' @export
|
||||
all_antimicrobials <- function(x = NULL,
|
||||
only_rsi_columns = FALSE,
|
||||
...) {
|
||||
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(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
|
||||
# force regular data.frame, not a tibble or data.table
|
||||
x <- as.data.frame(x, stringsAsFactors = FALSE)
|
||||
cols <- get_column_abx(x, only_rsi_columns = only_rsi_columns, info = FALSE, sort = FALSE)
|
||||
|
||||
generate_antimcrobials_string(x[ , cols, drop = FALSE])
|
||||
}
|
||||
|
||||
generate_antimcrobials_string <- function(df) {
|
||||
if (NCOL(df) == 0) {
|
||||
return(rep("", NROW(df)))
|
||||
}
|
||||
if (NROW(df) == 0) {
|
||||
return(character(0))
|
||||
}
|
||||
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)))
|
||||
}
|
||||
|
||||
#' @rdname key_antimicrobials
|
||||
#' @export
|
||||
antimicrobials_equal <- function(y,
|
||||
z,
|
||||
type = c("points", "keyantimicrobials"),
|
||||
ignore_I = TRUE,
|
||||
points_threshold = 2,
|
||||
...) {
|
||||
meet_criteria(y, allow_class = "character")
|
||||
meet_criteria(z, allow_class = "character")
|
||||
stop_if(missing(type), "argument \"type\" is missing, with no default")
|
||||
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)
|
||||
stop_ifnot(length(y) == length(z), "length of `y` and `z` must be equal")
|
||||
|
||||
key2rsi <- function(val) {
|
||||
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
|
||||
}
|
||||
# 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)) {
|
||||
# incomparable, so not equal
|
||||
return(FALSE)
|
||||
}
|
||||
# ignore NAs on both sides
|
||||
NA_ind <- which(is.na(a) | is.na(b))
|
||||
a[NA_ind] <- NA_real_
|
||||
b[NA_ind] <- NA_real_
|
||||
|
||||
if (type == "points") {
|
||||
# count points for every single character:
|
||||
# - no change is 0 points
|
||||
# - I <-> S|R is 0.5 point
|
||||
# - S|R <-> R|S is 1 point
|
||||
# use the levels of as.rsi (S = 1, I = 2, R = 3)
|
||||
# and divide by 2 (S = 0.5, I = 1, R = 1.5)
|
||||
(sum(abs(a - b), na.rm = TRUE) / 2) < points_threshold
|
||||
} else {
|
||||
if (ignore_I == TRUE) {
|
||||
ind <- which(a == 2 | b == 2) # since as.double(as.rsi("I")) == 2
|
||||
a[ind] <- NA_real_
|
||||
b[ind] <- NA_real_
|
||||
}
|
||||
all(a == b, na.rm = TRUE)
|
||||
}
|
||||
}
|
||||
out <- unlist(mapply(FUN = determine_equality,
|
||||
y,
|
||||
z,
|
||||
MoreArgs = list(type = type,
|
||||
points_threshold = points_threshold,
|
||||
ignore_I = ignore_I),
|
||||
SIMPLIFY = FALSE,
|
||||
USE.NAMES = FALSE))
|
||||
out[is.na(y) | is.na(z)] <- NA
|
||||
out
|
||||
}
|
||||
+2
-2
@@ -28,8 +28,8 @@
|
||||
#' @description Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable. A normal distribution has a kurtosis of 3 and a excess kurtosis of 0.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param x a vector of values, a [matrix] or a [data.frame]
|
||||
#' @param na.rm a logical to indicate whether `NA` values should be stripped before the computation proceeds
|
||||
#' @param excess a logical to indicate whether the *excess kurtosis* should be returned, defined as the kurtosis minus 3.
|
||||
#' @param na.rm a [logical] to indicate whether `NA` values should be stripped before the computation proceeds
|
||||
#' @param excess a [logical] to indicate whether the *excess kurtosis* should be returned, defined as the kurtosis minus 3.
|
||||
#' @seealso [skewness()]
|
||||
#' @rdname kurtosis
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
|
||||
+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.
|
||||
|
||||
@@ -23,30 +23,29 @@
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Pattern Matching with Keyboard Shortcut
|
||||
#' Vectorised Pattern Matching with Keyboard Shortcut
|
||||
#'
|
||||
#' Convenient wrapper around [grepl()] to match a pattern: `x %like% pattern`. It always returns a [`logical`] vector and is always case-insensitive (use `x %like_case% pattern` for case-sensitive matching). Also, `pattern` can be as long as `x` to compare items of each index in both vectors, or they both can have the same length to iterate over all cases.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param x a character vector where matches are sought, or an object which can be coerced by [as.character()] to a character vector.
|
||||
#' @param pattern a character string containing a regular expression (or [character] string for `fixed = TRUE`) to be matched in the given character vector. Coerced by [as.character()] to a character string if possible. If a [character] vector of length 2 or more is supplied, the first element is used with a warning.
|
||||
#' @param x a [character] vector where matches are sought, or an object which can be coerced by [as.character()] to a [character] vector.
|
||||
#' @param pattern a [character] vector containing regular expressions (or a [character] string for `fixed = TRUE`) to be matched in the given [character] vector. Coerced by [as.character()] to a [character] string if possible.
|
||||
#' @param ignore.case if `FALSE`, the pattern matching is *case sensitive* and if `TRUE`, case is ignored during matching.
|
||||
#' @return A [`logical`] vector
|
||||
#' @return A [logical] vector
|
||||
#' @name like
|
||||
#' @rdname like
|
||||
#' @export
|
||||
#' @details
|
||||
#' The `%like%` function:
|
||||
#' * Is case-insensitive (use `%like_case%` for case-sensitive matching)
|
||||
#' * Supports multiple patterns
|
||||
#' * Checks if `pattern` is a regular expression and sets `fixed = TRUE` if not, to greatly improve speed
|
||||
#' * Always uses compatibility with Perl
|
||||
#' These [like()] and `%like%`/`%unlike%` functions:
|
||||
#' * Are case-insensitive (use `%like_case%`/`%unlike_case%` for case-sensitive matching)
|
||||
#' * Support multiple patterns
|
||||
#' * Check if `pattern` is a valid regular expression and sets `fixed = TRUE` if not, to greatly improve speed (vectorised over `pattern`)
|
||||
#' * Always use compatibility with Perl unless `fixed = TRUE`, to greatly improve speed
|
||||
#'
|
||||
#' Using RStudio? The text `%like%` can also be directly inserted in your code from the Addins menu and can have its own Keyboard Shortcut like `Ctrl+Shift+L` or `Cmd+Shift+L` (see `Tools` > `Modify Keyboard Shortcuts...`).
|
||||
#' @source Idea from the [`like` function from the `data.table` package](https://github.com/Rdatatable/data.table/blob/master/R/like.R)
|
||||
#' Using RStudio? The `%like%`/`%unlike%` functions can also be directly inserted in your code from the Addins menu and can have its own keyboard shortcut like `Shift+Ctrl+L` or `Shift+Cmd+L` (see menu `Tools` > `Modify Keyboard Shortcuts...`). If you keep pressing your shortcut, the inserted text will be iterated over `%like%` -> `%unlike%` -> `%like_case%` -> `%unlike_case%`.
|
||||
#' @source Idea from the [`like` function from the `data.table` package](https://github.com/Rdatatable/data.table/blob/ec1259af1bf13fc0c96a1d3f9e84d55d8106a9a4/R/like.R), although altered as explained in *Details*.
|
||||
#' @seealso [grepl()]
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
#' @examples
|
||||
#' # simple test
|
||||
#' a <- "This is a test"
|
||||
#' b <- "TEST"
|
||||
#' a %like% b
|
||||
@@ -59,16 +58,23 @@
|
||||
#' b <- c( "case", "diff", "yet")
|
||||
#' a %like% b
|
||||
#' #> TRUE TRUE TRUE
|
||||
#' a %unlike% b
|
||||
#' #> FALSE FALSE FALSE
|
||||
#'
|
||||
#' a[1] %like% b
|
||||
#' #> TRUE FALSE FALSE
|
||||
#' a %like% b[1]
|
||||
#' #> TRUE FALSE FALSE
|
||||
#'
|
||||
#' # get isolates whose name start with 'Ent' or 'ent'
|
||||
#' example_isolates[which(mo_name(example_isolates$mo) %like% "^ent"), ]
|
||||
#' \donttest{
|
||||
#' # faster way, only works in R 3.2 and later:
|
||||
#' example_isolates[which(mo_name() %like% "^ent"), ]
|
||||
#'
|
||||
#' if (require("dplyr")) {
|
||||
#' example_isolates %>%
|
||||
#' filter(mo_name(mo) %like% "^ent")
|
||||
#' filter(mo_name() %like% "^ent")
|
||||
#' }
|
||||
#' }
|
||||
like <- function(x, pattern, ignore.case = TRUE) {
|
||||
@@ -79,9 +85,10 @@ like <- function(x, pattern, ignore.case = TRUE) {
|
||||
if (all(is.na(x))) {
|
||||
return(rep(FALSE, length(x)))
|
||||
}
|
||||
|
||||
# set to fixed if no regex found
|
||||
fixed <- !any(is_possibly_regex(pattern))
|
||||
|
||||
# set to fixed if no valid regex (vectorised)
|
||||
fixed <- !is_valid_regex(pattern)
|
||||
|
||||
if (ignore.case == TRUE) {
|
||||
# set here, otherwise if fixed = TRUE, this warning will be thrown: argument `ignore.case = TRUE` will be ignored
|
||||
x <- tolower(x)
|
||||
@@ -91,21 +98,26 @@ like <- function(x, pattern, ignore.case = TRUE) {
|
||||
if (is.factor(x)) {
|
||||
x <- as.character(x)
|
||||
}
|
||||
|
||||
|
||||
if (length(pattern) == 1) {
|
||||
grepl(pattern, x, ignore.case = FALSE, fixed = fixed, perl = !fixed)
|
||||
} else {
|
||||
if (length(x) == 1) {
|
||||
x <- rep(x, length(pattern))
|
||||
} else if (length(pattern) != length(x)) {
|
||||
stop_("arguments `x` and `pattern` must be of same length, or either one must be 1")
|
||||
stop_("arguments `x` and `pattern` must be of same length, or either one must be 1 ",
|
||||
"(`x` has length ", length(x), " and `pattern` has length ", length(pattern), ")")
|
||||
}
|
||||
unlist(
|
||||
Map(f = grepl,
|
||||
pattern,
|
||||
x,
|
||||
MoreArgs = list(ignore.case = FALSE, fixed = fixed, perl = !fixed)),
|
||||
use.names = FALSE)
|
||||
mapply(FUN = grepl,
|
||||
x = x,
|
||||
pattern = pattern,
|
||||
fixed = fixed,
|
||||
perl = !fixed,
|
||||
MoreArgs = list(ignore.case = FALSE),
|
||||
SIMPLIFY = FALSE,
|
||||
USE.NAMES = FALSE)
|
||||
)
|
||||
}
|
||||
}
|
||||
|
||||
@@ -117,6 +129,14 @@ like <- function(x, pattern, ignore.case = TRUE) {
|
||||
like(x, pattern, ignore.case = TRUE)
|
||||
}
|
||||
|
||||
#' @rdname like
|
||||
#' @export
|
||||
"%unlike%" <- function(x, pattern) {
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(pattern, allow_NA = FALSE)
|
||||
!like(x, pattern, ignore.case = TRUE)
|
||||
}
|
||||
|
||||
#' @rdname like
|
||||
#' @export
|
||||
"%like_case%" <- function(x, pattern) {
|
||||
@@ -124,3 +144,11 @@ like <- function(x, pattern, ignore.case = TRUE) {
|
||||
meet_criteria(pattern, allow_NA = FALSE)
|
||||
like(x, pattern, ignore.case = FALSE)
|
||||
}
|
||||
|
||||
#' @rdname like
|
||||
#' @export
|
||||
"%unlike_case%" <- function(x, pattern) {
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(pattern, allow_NA = FALSE)
|
||||
!like(x, pattern, ignore.case = FALSE)
|
||||
}
|
||||
|
||||
@@ -34,10 +34,10 @@
|
||||
#' @inheritParams eucast_rules
|
||||
#' @param pct_required_classes minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for *S. aureus*. Setting this `pct_required_classes` argument to `0.5` (default) means that for every *S. aureus* isolate at least 8 different classes must be available. Any lower number of available classes will return `NA` for that isolate.
|
||||
#' @param combine_SI a [logical] to indicate whether all values of S and I must be merged into one, so resistance is only considered when isolates are R, not I. As this is the default behaviour of the [mdro()] function, it follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. When using `combine_SI = FALSE`, resistance is considered when isolates are R or I.
|
||||
#' @param verbose a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function 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.
|
||||
#' @param verbose a [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.
|
||||
#' @inheritSection eucast_rules Antibiotics
|
||||
#' @details
|
||||
#' These functions are context-aware. This means that then the `x` argument can be left blank, see *Examples*.
|
||||
#' These functions are context-aware. This means that the `x` argument can be left blank if used inside a [data.frame] call, see *Examples*.
|
||||
#'
|
||||
#' For the `pct_required_classes` argument, values above 1 will be divided by 100. This is to support both fractions (`0.75` or `3/4`) and percentages (`75`).
|
||||
#'
|
||||
@@ -78,7 +78,7 @@
|
||||
#'
|
||||
#' Custom guidelines can be set with the [custom_mdro_guideline()] function. This is of great importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.
|
||||
#'
|
||||
#' If you are familiar with `case_when()` of the `dplyr` package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation':
|
||||
#' If you are familiar with the [`case_when()`][dplyr::case_when()] function of the `dplyr` package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule is written *before* the tilde (`~`) and the consequence of the rule is written *after* the tilde:
|
||||
#'
|
||||
#' ```
|
||||
#' custom <- custom_mdro_guideline(CIP == "R" & age > 60 ~ "Elderly Type A",
|
||||
@@ -102,10 +102,22 @@
|
||||
#' The outcome of the function can be used for the `guideline` argument in the [mdro()] function:
|
||||
#'
|
||||
#' ```
|
||||
#' x <- mdro(example_isolates, guideline = custom)
|
||||
#' x <- mdro(example_isolates,
|
||||
#' guideline = custom)
|
||||
#' table(x)
|
||||
#' #> Elderly Type A Elderly Type B Negative
|
||||
#' #> 43 891 1066
|
||||
#' #> Negative Elderly Type A Elderly Type B
|
||||
#' #> 1070 198 732
|
||||
#' ```
|
||||
#'
|
||||
#' Rules can also be combined with other custom rules by using [c()]:
|
||||
#'
|
||||
#' ```
|
||||
#' x <- mdro(example_isolates,
|
||||
#' guideline = c(custom,
|
||||
#' custom_mdro_guideline(ERY == "R" & age > 50 ~ "Elderly Type C")))
|
||||
#' table(x)
|
||||
#' #> Negative Elderly Type A Elderly Type B Elderly Type C
|
||||
#' #> 961 198 732 109
|
||||
#' ```
|
||||
#'
|
||||
#' The rules set (the `custom` object in this case) could be exported to a shared file location using [saveRDS()] if you collaborate with multiple users. The custom rules set could then be imported using [readRDS()].
|
||||
@@ -124,7 +136,7 @@
|
||||
#' @export
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
#' @source
|
||||
#' See the supported guidelines above for the list of publications used for this function.
|
||||
#' See the supported guidelines above for the [list] of publications used for this function.
|
||||
#' @examples
|
||||
#' mdro(example_isolates, guideline = "EUCAST")
|
||||
#'
|
||||
@@ -175,13 +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.:",
|
||||
@@ -220,7 +228,7 @@ mdro <- function(x = NULL,
|
||||
}
|
||||
}
|
||||
|
||||
# force regular data.frame, not a tibble or data.table
|
||||
# force regular [data.frame], not a tibble or data.table
|
||||
x <- as.data.frame(x, stringsAsFactors = FALSE)
|
||||
|
||||
if (pct_required_classes > 1) {
|
||||
@@ -246,7 +254,7 @@ mdro <- function(x = NULL,
|
||||
txt <- word_wrap(txt)
|
||||
cat(txt, "\n", sep = "")
|
||||
}
|
||||
x <- run_custom_mdro_guideline(x, guideline)
|
||||
x <- run_custom_mdro_guideline(df = x, guideline = guideline, info = info)
|
||||
if (info.bak == TRUE) {
|
||||
cat(group_msg)
|
||||
if (sum(!is.na(x$MDRO)) == 0) {
|
||||
@@ -294,12 +302,11 @@ mdro <- function(x = NULL,
|
||||
}
|
||||
if (is.null(col_mo) & guideline$code == "tb") {
|
||||
message_("No column found as input for `col_mo`, ",
|
||||
font_bold(paste0("assuming all records contain", font_italic("Mycobacterium tuberculosis"), ".")))
|
||||
font_bold(paste0("assuming all rows contain ", font_italic("Mycobacterium tuberculosis"), ".")))
|
||||
x$mo <- as.mo("Mycobacterium tuberculosis") # consider overkill at all times: MO_lookup[which(MO_lookup$fullname == "Mycobacterium tuberculosis"), "mo", drop = TRUE]
|
||||
col_mo <- "mo"
|
||||
}
|
||||
stop_if(is.null(col_mo), "`col_mo` must be set")
|
||||
stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found")
|
||||
|
||||
if (guideline$code == "cmi2012") {
|
||||
guideline$name <- "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance."
|
||||
@@ -350,7 +357,7 @@ mdro <- function(x = NULL,
|
||||
if (guideline$code == "cmi2012") {
|
||||
cols_ab <- get_column_abx(x = x,
|
||||
soft_dependencies = c(
|
||||
# table 1 (S aureus):
|
||||
# [table] 1 (S aureus):
|
||||
"GEN",
|
||||
"RIF",
|
||||
"CPT",
|
||||
@@ -373,7 +380,7 @@ mdro <- function(x = NULL,
|
||||
"TCY",
|
||||
"DOX",
|
||||
"MNO",
|
||||
# table 2 (Enterococcus)
|
||||
# [table] 2 (Enterococcus)
|
||||
"GEH",
|
||||
"STH",
|
||||
"IPM",
|
||||
@@ -391,7 +398,7 @@ mdro <- function(x = NULL,
|
||||
"QDA",
|
||||
"DOX",
|
||||
"MNO",
|
||||
# table 3 (Enterobacteriaceae)
|
||||
# [table] 3 (Enterobacteriaceae)
|
||||
"GEN",
|
||||
"TOB",
|
||||
"AMK",
|
||||
@@ -423,7 +430,7 @@ mdro <- function(x = NULL,
|
||||
"TCY",
|
||||
"DOX",
|
||||
"MNO",
|
||||
# table 4 (Pseudomonas)
|
||||
# [table] 4 (Pseudomonas)
|
||||
"GEN",
|
||||
"TOB",
|
||||
"AMK",
|
||||
@@ -441,7 +448,7 @@ mdro <- function(x = NULL,
|
||||
"FOS",
|
||||
"COL",
|
||||
"PLB",
|
||||
# table 5 (Acinetobacter)
|
||||
# [table] 5 (Acinetobacter)
|
||||
"GEN",
|
||||
"TOB",
|
||||
"AMK",
|
||||
@@ -529,6 +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"]
|
||||
@@ -731,7 +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])),
|
||||
@@ -745,13 +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")
|
||||
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)
|
||||
@@ -802,6 +824,9 @@ mdro <- function(x = NULL,
|
||||
}
|
||||
|
||||
x[, col_mo] <- as.mo(as.character(x[, col_mo, drop = TRUE]))
|
||||
# rename col_mo to prevent interference with joined columns
|
||||
colnames(x)[colnames(x) == col_mo] <- ".col_mo"
|
||||
col_mo <- ".col_mo"
|
||||
# join to microorganisms data set
|
||||
x <- left_join_microorganisms(x, by = col_mo)
|
||||
x$MDRO <- ifelse(!is.na(x$genus), 1, NA_integer_)
|
||||
@@ -1015,7 +1040,10 @@ mdro <- function(x = NULL,
|
||||
# PDR (=4): all agents are R
|
||||
x[which(x$classes_affected == 999 & x$classes_in_guideline == x$classes_available), "MDRO"] <- 4
|
||||
if (verbose == TRUE) {
|
||||
x[which(x$MDRO == 4), "reason"] <- paste("all antibiotics in all", x$classes_in_guideline[which(x$MDRO == 4)], "classes were tested R or I")
|
||||
x[which(x$MDRO == 4), "reason"] <- paste("all antibiotics in all",
|
||||
x$classes_in_guideline[which(x$MDRO == 4)],
|
||||
"classes were tested R",
|
||||
ifelse(!isTRUE(combine_SI), " or I", ""))
|
||||
}
|
||||
|
||||
# not enough classes available
|
||||
@@ -1319,7 +1347,7 @@ mdro <- function(x = NULL,
|
||||
ab
|
||||
}
|
||||
drug_is_R <- function(ab) {
|
||||
# returns logical vector
|
||||
# returns [logical] vector
|
||||
ab <- prepare_drug(ab)
|
||||
if (length(ab) == 0) {
|
||||
rep(FALSE, NROW(x))
|
||||
@@ -1330,7 +1358,7 @@ mdro <- function(x = NULL,
|
||||
}
|
||||
}
|
||||
drug_is_not_R <- function(ab) {
|
||||
# returns logical vector
|
||||
# returns [logical] vector
|
||||
ab <- prepare_drug(ab)
|
||||
if (length(ab) == 0) {
|
||||
rep(TRUE, NROW(x))
|
||||
@@ -1365,23 +1393,43 @@ mdro <- function(x = NULL,
|
||||
x$reason <- "PDR/MDR/XDR criteria were met"
|
||||
}
|
||||
|
||||
# some more info on negative results
|
||||
if (verbose == TRUE) {
|
||||
if (guideline$code == "cmi2012") {
|
||||
x[which(x$MDRO == 1 & !is.na(x$classes_affected)), "reason"] <- paste0(x$classes_affected[which(x$MDRO == 1 & !is.na(x$classes_affected))],
|
||||
" of ",
|
||||
x$classes_available[which(x$MDRO == 1 & !is.na(x$classes_affected))],
|
||||
" available classes contain R",
|
||||
ifelse(!isTRUE(combine_SI), " or I", ""),
|
||||
" (3 required for MDR)")
|
||||
} else {
|
||||
x[which(x$MDRO == 1), "reason"] <- "too few antibiotics are R"
|
||||
}
|
||||
}
|
||||
|
||||
if (info.bak == TRUE) {
|
||||
cat(group_msg)
|
||||
if (sum(!is.na(x$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$MDRO)))), ")\n")))
|
||||
" isolates (", trimws(percentage(sum(x$MDRO %in% c(2:5), na.rm = TRUE) / sum(!is.na(x$MDRO)))), ")")))
|
||||
}
|
||||
}
|
||||
|
||||
# some more info on negative results
|
||||
if (verbose == TRUE) {
|
||||
if (guideline$code == "cmi2012") {
|
||||
x[which(x$MDRO == 1 & !is.na(x$classes_affected)), "reason"] <- paste0(x$classes_affected[which(x$MDRO == 1 & !is.na(x$classes_affected))], " of ", x$classes_available[which(x$MDRO == 1 & !is.na(x$classes_affected))], " available classes contain R or I (3 required for MDR)")
|
||||
} else {
|
||||
x[which(x$MDRO == 1), "reason"] <- "too few antibiotics are R"
|
||||
}
|
||||
# Fill in blanks ----
|
||||
# for rows that have no results
|
||||
x_transposed <- as.list(as.data.frame(t(x[, cols_ab, drop = FALSE]),
|
||||
stringsAsFactors = FALSE))
|
||||
rows_empty <- which(vapply(FUN.VALUE = logical(1),
|
||||
x_transposed,
|
||||
function(y) all(is.na(y))))
|
||||
if (length(rows_empty) > 0) {
|
||||
cat(font_italic(paste0(" (", length(rows_empty), " isolates had no test results)\n")))
|
||||
x[rows_empty, "MDRO"] <- NA
|
||||
x[rows_empty, "reason"] <- "none of the antibiotics have test results"
|
||||
} else {
|
||||
cat("\n")
|
||||
}
|
||||
|
||||
# Results ----
|
||||
@@ -1390,7 +1438,6 @@ mdro <- function(x = NULL,
|
||||
if (message_not_thrown_before("mdro.availability")) {
|
||||
warning_("NA introduced for isolates where the available percentage of antimicrobial classes was below ",
|
||||
percentage(pct_required_classes), " (set with `pct_required_classes`)", call = FALSE)
|
||||
remember_thrown_message("mdro.availability")
|
||||
}
|
||||
# set these -1s to NA
|
||||
x[which(x$MDRO == -1), "MDRO"] <- NA_integer_
|
||||
@@ -1419,8 +1466,10 @@ mdro <- function(x = NULL,
|
||||
}
|
||||
|
||||
if (verbose == TRUE) {
|
||||
colnames(x)[colnames(x) == col_mo] <- "microorganism"
|
||||
x$microorganism <- mo_name(x$microorganism, language = NULL)
|
||||
x[, c("row_number",
|
||||
col_mo,
|
||||
"microorganism",
|
||||
"MDRO",
|
||||
"reason",
|
||||
"columns_nonsusceptible"),
|
||||
@@ -1434,6 +1483,8 @@ mdro <- function(x = NULL,
|
||||
#' @rdname mdro
|
||||
#' @export
|
||||
custom_mdro_guideline <- function(..., as_factor = TRUE) {
|
||||
meet_criteria(as_factor, allow_class = "logical", has_length = 1)
|
||||
|
||||
dots <- tryCatch(list(...),
|
||||
error = function(e) "error")
|
||||
stop_if(identical(dots, "error"),
|
||||
@@ -1470,11 +1521,49 @@ custom_mdro_guideline <- function(..., as_factor = TRUE) {
|
||||
|
||||
names(out) <- paste0("rule", seq_len(n_dots))
|
||||
out <- set_clean_class(out, new_class = c("custom_mdro_guideline", "list"))
|
||||
attr(out, "values") <- c("Negative", vapply(FUN.VALUE = character(1), out, function(x) x$value))
|
||||
attr(out, "values") <- unname(c("Negative", vapply(FUN.VALUE = character(1), unclass(out), function(x) x$value)))
|
||||
attr(out, "as_factor") <- as_factor
|
||||
out
|
||||
}
|
||||
|
||||
#' @method c custom_mdro_guideline
|
||||
#' @noRd
|
||||
#' @export
|
||||
c.custom_mdro_guideline <- function(x, ..., as_factor = NULL) {
|
||||
if (length(list(...)) == 0) {
|
||||
return(x)
|
||||
}
|
||||
if (!is.null(as_factor)) {
|
||||
meet_criteria(as_factor, allow_class = "logical", has_length = 1)
|
||||
} else {
|
||||
as_factor <- attributes(x)$as_factor
|
||||
}
|
||||
for (g in list(...)) {
|
||||
stop_ifnot(inherits(g, "custom_mdro_guideline"),
|
||||
"for combining custom MDRO guidelines, all rules must be created with `custom_mdro_guideline()`",
|
||||
call = FALSE)
|
||||
vals <- attributes(x)$values
|
||||
if (!all(attributes(g)$values %in% vals)) {
|
||||
vals <- unname(unique(c(vals, attributes(g)$values)))
|
||||
}
|
||||
attributes(g) <- NULL
|
||||
x <- c(unclass(x), unclass(g))
|
||||
attr(x, "values") <- vals
|
||||
}
|
||||
names(x) <- paste0("rule", seq_len(length(x)))
|
||||
x <- set_clean_class(x, new_class = c("custom_mdro_guideline", "list"))
|
||||
attr(x, "values") <- vals
|
||||
attr(x, "as_factor") <- as_factor
|
||||
x
|
||||
}
|
||||
|
||||
#' @method as.list custom_mdro_guideline
|
||||
#' @noRd
|
||||
#' @export
|
||||
as.list.custom_mdro_guideline <- function(x, ...) {
|
||||
c(x, ...)
|
||||
}
|
||||
|
||||
#' @method print custom_mdro_guideline
|
||||
#' @export
|
||||
#' @noRd
|
||||
@@ -1482,23 +1571,10 @@ print.custom_mdro_guideline <- function(x, ...) {
|
||||
cat("A set of custom MDRO rules:\n")
|
||||
for (i in seq_len(length(x))) {
|
||||
rule <- x[[i]]
|
||||
rule$query <- gsub(" & ", font_black(font_italic(" and ")), rule$query, fixed = TRUE)
|
||||
rule$query <- gsub(" | ", font_black(" or "), rule$query, fixed = TRUE)
|
||||
rule$query <- gsub(" + ", font_black(" plus "), rule$query, fixed = TRUE)
|
||||
rule$query <- gsub(" - ", font_black(" minus "), rule$query, fixed = TRUE)
|
||||
rule$query <- gsub(" / ", font_black(" divided by "), rule$query, fixed = TRUE)
|
||||
rule$query <- gsub(" * ", font_black(" times "), rule$query, fixed = TRUE)
|
||||
rule$query <- gsub(" == ", font_black(" is "), rule$query, fixed = TRUE)
|
||||
rule$query <- gsub(" > ", font_black(" is higher than "), rule$query, fixed = TRUE)
|
||||
rule$query <- gsub(" < ", font_black(" is lower than "), rule$query, fixed = TRUE)
|
||||
rule$query <- gsub(" >= ", font_black(" is higher than or equal to "), rule$query, fixed = TRUE)
|
||||
rule$query <- gsub(" <= ", font_black(" is lower than or equal to "), rule$query, fixed = TRUE)
|
||||
rule$query <- gsub(" ^ ", font_black(" to the power of "), rule$query, fixed = TRUE)
|
||||
# replace the black colour 'stops' with blue colour 'starts'
|
||||
rule$query <- gsub("\033[39m", "\033[34m", as.character(rule$query), fixed = TRUE)
|
||||
cat(" ", i, ". ", font_blue(rule$query), font_bold(" -> "), font_red(rule$value), "\n", sep = "")
|
||||
rule$query <- format_custom_query_rule(rule$query)
|
||||
cat(" ", i, ". ", font_bold("If "), font_blue(rule$query), font_bold(" then: "), font_red(rule$value), "\n", sep = "")
|
||||
}
|
||||
cat(" ", i + 1, ". Otherwise", font_bold(" -> "), font_red(paste0("Negative")), "\n", sep = "")
|
||||
cat(" ", i + 1, ". ", font_bold("Otherwise: "), font_red(paste0("Negative")), "\n", sep = "")
|
||||
cat("\nUnmatched rows will return ", font_red("NA"), ".\n", sep = "")
|
||||
if (isTRUE(attributes(x)$as_factor)) {
|
||||
cat("Results will be of class <factor>, with ordered levels: ", paste0(attributes(x)$values, collapse = " < "), "\n", sep = "")
|
||||
@@ -1507,7 +1583,7 @@ print.custom_mdro_guideline <- function(x, ...) {
|
||||
}
|
||||
}
|
||||
|
||||
run_custom_mdro_guideline <- function(df, guideline) {
|
||||
run_custom_mdro_guideline <- function(df, guideline, info) {
|
||||
n_dots <- length(guideline)
|
||||
stop_if(n_dots == 0, "no custom guidelines set", call = -2)
|
||||
out <- character(length = NROW(df))
|
||||
@@ -1520,7 +1596,7 @@ run_custom_mdro_guideline <- function(df, guideline) {
|
||||
})
|
||||
if (identical(qry, "error")) {
|
||||
warning_("in custom_mdro_guideline(): rule ", i,
|
||||
" (`", guideline[[i]]$query, "`) was ignored because of this error message: ",
|
||||
" (`", as.character(guideline[[i]]$query), "`) was ignored because of this error message: ",
|
||||
pkg_env$err_msg,
|
||||
call = FALSE,
|
||||
add_fn = font_red)
|
||||
@@ -1529,9 +1605,16 @@ run_custom_mdro_guideline <- function(df, guideline) {
|
||||
stop_ifnot(is.logical(qry), "in custom_mdro_guideline(): rule ", i, " (`", guideline[[i]]$query,
|
||||
"`) must return `TRUE` or `FALSE`, not ",
|
||||
format_class(class(qry), plural = FALSE), call = FALSE)
|
||||
|
||||
new_mdros <- which(qry == TRUE & out == "")
|
||||
|
||||
if (info == TRUE) {
|
||||
cat(word_wrap("- Custom MDRO rule ", i, ": `", as.character(guideline[[i]]$query),
|
||||
"` (", length(new_mdros), " rows matched)"), "\n", sep = "")
|
||||
}
|
||||
val <- guideline[[i]]$value
|
||||
out[which(qry)] <- val
|
||||
reasons[which(qry)] <- paste0("matched rule ", gsub("rule", "", names(guideline)[i]), ": ", as.character(guideline[[i]]$query))
|
||||
out[new_mdros] <- val
|
||||
reasons[new_mdros] <- paste0("matched rule ", gsub("rule", "", names(guideline)[i]), ": ", as.character(guideline[[i]]$query))
|
||||
}
|
||||
out[out == ""] <- "Negative"
|
||||
reasons[out == "Negative"] <- "no rules matched"
|
||||
@@ -1540,8 +1623,7 @@ run_custom_mdro_guideline <- function(df, guideline) {
|
||||
out <- factor(out, levels = attributes(guideline)$values, ordered = TRUE)
|
||||
}
|
||||
|
||||
rsi_cols <- vapply(FUN.VALUE = logical(1), df, function(x) is.rsi(x))
|
||||
columns_nonsusceptible <- as.data.frame(t(df[, rsi_cols] == "R"))
|
||||
columns_nonsusceptible <- as.data.frame(t(df[, is.rsi(df)] == "R"))
|
||||
columns_nonsusceptible <- vapply(FUN.VALUE = character(1),
|
||||
columns_nonsusceptible,
|
||||
function(x) paste0(rownames(columns_nonsusceptible)[which(x)], collapse = " "))
|
||||
|
||||
@@ -23,16 +23,33 @@
|
||||
# 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 character or numeric vector
|
||||
#' @param na.rm a logical indicating whether missing values should be removed
|
||||
#' @param x a [character] or [numeric] vector
|
||||
#' @param na.rm a [logical] indicating whether missing values should be removed
|
||||
#' @details To interpret MIC values as RSI values, use [as.rsi()] on MIC values. It supports guidelines from EUCAST and CLSI.
|
||||
#'
|
||||
#' This class for MIC values is a quite a special data type: formally it is an ordered factor with valid MIC values as factor levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:
|
||||
#' This class for MIC values is a quite a special data type: formally it is an ordered [factor] with valid MIC values as [factor] levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:
|
||||
#'
|
||||
#' ```
|
||||
#' x <- random_mic(10)
|
||||
@@ -50,7 +67,7 @@
|
||||
#' #> [1] 26
|
||||
#' ```
|
||||
#'
|
||||
#' This makes it possible to maintain operators that often come with MIC values, such ">=" and "<=", even when filtering using numeric values in data analysis, e.g.:
|
||||
#' This makes it possible to maintain operators that often come with MIC values, such ">=" and "<=", even when filtering using [numeric] values in data analysis, e.g.:
|
||||
#'
|
||||
#' ```
|
||||
#' x[x > 4]
|
||||
@@ -69,7 +86,7 @@
|
||||
#' ```
|
||||
#'
|
||||
#' The following [generic functions][groupGeneric()] are implemented for the MIC class: `!`, `!=`, `%%`, `%/%`, `&`, `*`, `+`, `-`, `/`, `<`, `<=`, `==`, `>`, `>=`, `^`, `|`, [abs()], [acos()], [acosh()], [all()], [any()], [asin()], [asinh()], [atan()], [atanh()], [ceiling()], [cos()], [cosh()], [cospi()], [cummax()], [cummin()], [cumprod()], [cumsum()], [digamma()], [exp()], [expm1()], [floor()], [gamma()], [lgamma()], [log()], [log1p()], [log2()], [log10()], [max()], [mean()], [min()], [prod()], [range()], [round()], [sign()], [signif()], [sin()], [sinh()], [sinpi()], [sqrt()], [sum()], [tan()], [tanh()], [tanpi()], [trigamma()] and [trunc()]. Some functions of the `stats` package are also implemented: [median()], [quantile()], [mad()], [IQR()], [fivenum()]. Also, [boxplot.stats()] is supported. Since [sd()] and [var()] are non-generic functions, these could not be extended. Use [mad()] as an alternative, or use e.g. `sd(as.numeric(x))` where `x` is your vector of MIC values.
|
||||
#' @return Ordered [factor] with additional class [`mic`], that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a numeric value.
|
||||
#' @return Ordered [factor] with additional class [`mic`], that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a [numeric] value.
|
||||
#' @aliases mic
|
||||
#' @export
|
||||
#' @seealso [as.rsi()]
|
||||
@@ -81,7 +98,7 @@
|
||||
#' # this can also coerce combined MIC/RSI values:
|
||||
#' as.mic("<=0.002; S") # will return <=0.002
|
||||
#'
|
||||
#' # mathematical processing treats MICs as numeric values
|
||||
#' # mathematical processing treats MICs as [numeric] values
|
||||
#' fivenum(mic_data)
|
||||
#' quantile(mic_data)
|
||||
#' all(mic_data < 512)
|
||||
@@ -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 <=
|
||||
@@ -133,7 +152,7 @@ as.mic <- function(x, na.rm = FALSE) {
|
||||
# keep only one zero before dot
|
||||
x <- gsub("0+[.]", "0.", x, perl = TRUE)
|
||||
# starting 00 is probably 0.0 if there's no dot yet
|
||||
x[!x %like% "[.]"] <- gsub("^00", "0.0", x[!x %like% "[.]"])
|
||||
x[x %unlike% "[.]"] <- gsub("^00", "0.0", x[!x %like% "[.]"])
|
||||
# remove last zeroes
|
||||
x <- gsub("([.].?)0+$", "\\1", x, perl = TRUE)
|
||||
x <- gsub("(.*[.])0+$", "\\10", x, perl = TRUE)
|
||||
@@ -141,27 +160,14 @@ as.mic <- function(x, na.rm = FALSE) {
|
||||
x[x %like% "[.]"] <- gsub("0+$", "", 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) {
|
||||
@@ -307,10 +319,8 @@ as.matrix.mic <- function(x, ...) {
|
||||
#' @method c mic
|
||||
#' @export
|
||||
#' @noRd
|
||||
c.mic <- function(x, ...) {
|
||||
y <- unlist(lapply(list(...), as.character))
|
||||
x <- as.character(x)
|
||||
as.mic(c(x, y))
|
||||
c.mic <- function(...) {
|
||||
as.mic(unlist(lapply(list(...), as.character)))
|
||||
}
|
||||
|
||||
#' @method unique mic
|
||||
@@ -322,6 +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
|
||||
@@ -339,7 +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))
|
||||
}
|
||||
|
||||
@@ -347,11 +366,12 @@ hist.mic <- function(x, ...) {
|
||||
get_skimmers.mic <- function(column) {
|
||||
skimr::sfl(
|
||||
skim_type = "mic",
|
||||
min = ~min(., na.rm = TRUE),
|
||||
max = ~max(., na.rm = TRUE),
|
||||
median = ~stats::median(., na.rm = TRUE),
|
||||
n_unique = ~pm_n_distinct(., na.rm = TRUE),
|
||||
hist_log2 = ~skimr::inline_hist(log2(stats::na.omit(.)))
|
||||
p0 = ~stats::quantile(., probs = 0, na.rm = TRUE, names = FALSE),
|
||||
p25 = ~stats::quantile(., probs = 0.25, na.rm = TRUE, names = FALSE),
|
||||
p50 = ~stats::quantile(., probs = 0.5, na.rm = TRUE, names = FALSE),
|
||||
p75 = ~stats::quantile(., probs = 0.75, na.rm = TRUE, names = FALSE),
|
||||
p100 = ~stats::quantile(., probs = 1, na.rm = TRUE, names = FALSE),
|
||||
hist = ~skimr::inline_hist(log2(stats::na.omit(.)), 5)
|
||||
)
|
||||
}
|
||||
|
||||
|
||||
@@ -23,21 +23,22 @@
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Transform Input to a Microorganism ID
|
||||
#' Transform Input to a Microorganism Code
|
||||
#'
|
||||
#' Use this function to determine a valid microorganism ID ([`mo`]). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see *Source*). The input can be almost anything: a full name (like `"Staphylococcus aureus"`), an abbreviated name (such as `"S. aureus"`), an abbreviation known in the field (such as `"MRSA"`), or just a genus. See *Examples*.
|
||||
#' Use this function to determine a valid microorganism code ([`mo`]). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see *Source*). The input can be almost anything: a full name (like `"Staphylococcus aureus"`), an abbreviated name (such as `"S. aureus"`), an abbreviation known in the field (such as `"MRSA"`), or just a genus. See *Examples*.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param x a character vector or a [data.frame] with one or two columns
|
||||
#' @param Becker a logical to indicate whether staphylococci should be categorised into coagulase-negative staphylococci ("CoNS") and coagulase-positive staphylococci ("CoPS") instead of their own species, according to Karsten Becker *et al.* (1,2,3).
|
||||
#' @param x a [character] vector or a [data.frame] with one or two columns
|
||||
#' @param Becker a [logical] to indicate whether staphylococci should be categorised into coagulase-negative staphylococci ("CoNS") and coagulase-positive staphylococci ("CoPS") instead of their own species, according to Karsten Becker *et al.* (1,2,3).
|
||||
#'
|
||||
#' This excludes *Staphylococcus aureus* at default, use `Becker = "all"` to also categorise *S. aureus* as "CoPS".
|
||||
#' @param Lancefield a logical to indicate whether beta-haemolytic *Streptococci* should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (4). These *Streptococci* will be categorised in their first group, e.g. *Streptococcus dysgalactiae* will be group C, although officially it was also categorised into groups G and L.
|
||||
#' @param Lancefield a [logical] to indicate whether beta-haemolytic *Streptococci* should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (4). These *Streptococci* will be categorised in their first group, e.g. *Streptococcus dysgalactiae* will be group C, although officially it was also categorised into groups G and L.
|
||||
#'
|
||||
#' This excludes *Enterococci* at default (who are in group D), use `Lancefield = "all"` to also categorise all *Enterococci* as group D.
|
||||
#' @param allow_uncertain a number between `0` (or `"none"`) and `3` (or `"all"`), or `TRUE` (= `2`) or `FALSE` (= `0`) to indicate whether the input should be checked for less probable results, see *Details*
|
||||
#' @param reference_df a [data.frame] to be used for extra reference when translating `x` to a valid [`mo`]. See [set_mo_source()] and [get_mo_source()] to automate the usage of your own codes (e.g. used in your analysis or organisation).
|
||||
#' @param ignore_pattern a regular expression (case-insensitive) of which all matches in `x` must return `NA`. This can be convenient to exclude known non-relevant input and can also be set with the option `AMR_ignore_pattern`, e.g. `options(AMR_ignore_pattern = "(not reported|contaminated flora)")`.
|
||||
#' @param language language to translate text like "no growth", which defaults to the system language (see [get_locale()])
|
||||
#' @param info a [logical] to indicate if a progress bar should be printed if more than 25 items are to be coerced, defaults to `TRUE` only in interactive mode
|
||||
#' @param ... other arguments passed on to functions
|
||||
#' @rdname as.mo
|
||||
#' @aliases mo
|
||||
@@ -45,7 +46,7 @@
|
||||
#' @details
|
||||
#' ## General Info
|
||||
#'
|
||||
#' A microorganism ID from this package (class: [`mo`]) is human readable and typically looks like these examples:
|
||||
#' A microorganism (MO) code from this package (class: [`mo`]) is human readable and typically looks like these examples:
|
||||
#' ```
|
||||
#' Code Full name
|
||||
#' --------------- --------------------------------------
|
||||
@@ -161,6 +162,7 @@ as.mo <- function(x,
|
||||
reference_df = get_mo_source(),
|
||||
ignore_pattern = getOption("AMR_ignore_pattern"),
|
||||
language = get_locale(),
|
||||
info = interactive(),
|
||||
...) {
|
||||
meet_criteria(x, allow_class = c("mo", "data.frame", "list", "character", "numeric", "integer", "factor"), allow_NA = TRUE)
|
||||
meet_criteria(Becker, allow_class = c("logical", "character"), has_length = 1)
|
||||
@@ -169,7 +171,8 @@ as.mo <- function(x,
|
||||
meet_criteria(reference_df, allow_class = "data.frame", allow_NULL = TRUE)
|
||||
meet_criteria(ignore_pattern, allow_class = "character", has_length = 1, allow_NULL = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
meet_criteria(info, allow_class = "logical", has_length = 1)
|
||||
|
||||
check_dataset_integrity()
|
||||
|
||||
if (tryCatch(all(x[!is.na(x)] %in% MO_lookup$mo)
|
||||
@@ -198,7 +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)
|
||||
@@ -227,9 +231,10 @@ as.mo <- function(x,
|
||||
reference_df = reference_df,
|
||||
ignore_pattern = ignore_pattern,
|
||||
language = language,
|
||||
info = info,
|
||||
...)
|
||||
}
|
||||
|
||||
|
||||
set_clean_class(y,
|
||||
new_class = c("mo", "character"))
|
||||
}
|
||||
@@ -241,10 +246,10 @@ is.mo <- function(x) {
|
||||
}
|
||||
|
||||
# param property a column name of microorganisms
|
||||
# param initial_search logical - is FALSE when coming from uncertain tries, which uses exec_as.mo internally too
|
||||
# param dyslexia_mode logical - also check for characters that resemble others
|
||||
# param debug logical - show different lookup texts while searching
|
||||
# param reference_data_to_use data.frame - the data set to check for
|
||||
# param initial_search [logical] - is FALSE when coming from uncertain tries, which uses exec_as.mo internally too
|
||||
# param dyslexia_mode [logical] - also check for characters that resemble others
|
||||
# param debug [logical] - show different lookup texts while searching
|
||||
# param reference_data_to_use [data.frame] - the data set to check for
|
||||
# param actual_uncertainty - (only for initial_search = FALSE) the actual uncertainty level used in the function for score calculation (sometimes passed as 2 or 3 by uncertain_fn())
|
||||
# param actual_input - (only for initial_search = FALSE) the actual, original input
|
||||
# param language - used for translating "no growth", etc.
|
||||
@@ -253,6 +258,7 @@ exec_as.mo <- function(x,
|
||||
Lancefield = FALSE,
|
||||
allow_uncertain = TRUE,
|
||||
reference_df = get_mo_source(),
|
||||
info = interactive(),
|
||||
property = "mo",
|
||||
initial_search = TRUE,
|
||||
dyslexia_mode = FALSE,
|
||||
@@ -299,7 +305,7 @@ exec_as.mo <- function(x,
|
||||
}
|
||||
|
||||
# `column` can be NULL for all columns, or a selection
|
||||
# returns a character (vector) - if `column` > length 1 then with columns as names
|
||||
# returns a [character] (vector) - if `column` > length 1 then with columns as names
|
||||
if (isTRUE(debug_mode)) {
|
||||
cat(font_silver("Looking up: ", substitute(needle), collapse = ""),
|
||||
"\n ", time_track())
|
||||
@@ -367,7 +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()
|
||||
@@ -464,7 +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))) {
|
||||
@@ -487,12 +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)) {
|
||||
@@ -600,7 +610,7 @@ exec_as.mo <- function(x,
|
||||
}
|
||||
|
||||
if (initial_search == TRUE) {
|
||||
progress <- progress_ticker(n = length(x[!already_known]), n_min = 25) # start if n >= 25
|
||||
progress <- progress_ticker(n = length(x[!already_known]), n_min = 25, print = info) # start if n >= 25
|
||||
on.exit(close(progress))
|
||||
}
|
||||
|
||||
@@ -703,7 +713,7 @@ exec_as.mo <- function(x,
|
||||
|
||||
# check for very small input, but ignore the O antigens of E. coli
|
||||
if (nchar(gsub("[^a-zA-Z]", "", x_trimmed[i])) < 3
|
||||
& !toupper(x_backup_without_spp[i]) %like_case% "O?(26|103|104|104|111|121|145|157)") {
|
||||
& toupper(x_backup_without_spp[i]) %unlike_case% "O?(26|103|104|104|111|121|145|157)") {
|
||||
# fewer than 3 chars and not looked for species, add as failure
|
||||
x[i] <- lookup(mo == "UNKNOWN")
|
||||
if (initial_search == TRUE) {
|
||||
@@ -794,7 +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
|
||||
@@ -855,7 +865,7 @@ exec_as.mo <- function(x,
|
||||
x[i] <- lookup(genus == "Salmonella", uncertainty = -1)
|
||||
next
|
||||
} else if (x_backup[i] %like_case% "[sS]almonella [A-Z][a-z]+ ?.*" &
|
||||
!x_backup[i] %like% "t[iy](ph|f)[iy]") {
|
||||
x_backup[i] %unlike% "t[iy](ph|f)[iy]") {
|
||||
# Salmonella with capital letter species like "Salmonella Goettingen" - they're all S. enterica
|
||||
# except for S. typhi, S. paratyphi, S. typhimurium
|
||||
x[i] <- lookup(fullname == "Salmonella enterica", uncertainty = -1)
|
||||
@@ -911,7 +921,7 @@ exec_as.mo <- function(x,
|
||||
# FIRST TRY FULLNAMES AND CODES ----
|
||||
# if only genus is available, return only genus
|
||||
|
||||
if (all(!c(x[i], b.x_trimmed) %like_case% " ")) {
|
||||
if (all(c(x[i], b.x_trimmed) %unlike_case% " ")) {
|
||||
found <- lookup(fullname_lower %in% c(h.x_species, i.x_trimmed_species),
|
||||
haystack = data_to_check)
|
||||
if (!is.na(found)) {
|
||||
@@ -1118,8 +1128,8 @@ exec_as.mo <- function(x,
|
||||
if (isTRUE(debug)) {
|
||||
cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (3) look for genus only, part of name\n"))
|
||||
}
|
||||
if (nchar(g.x_backup_without_spp) > 4 & !b.x_trimmed %like_case% " ") {
|
||||
if (!b.x_trimmed %like_case% "^[A-Z][a-z]+") {
|
||||
if (nchar(g.x_backup_without_spp) > 4 & b.x_trimmed %unlike_case% " ") {
|
||||
if (b.x_trimmed %unlike_case% "^[A-Z][a-z]+") {
|
||||
if (isTRUE(debug)) {
|
||||
message("Running '", paste(b.x_trimmed, "species"), "'")
|
||||
}
|
||||
@@ -1263,7 +1273,7 @@ exec_as.mo <- function(x,
|
||||
stringsAsFactors = FALSE)
|
||||
return(found)
|
||||
}
|
||||
if (b.x_trimmed %like_case% "(fungus|fungi)" & !b.x_trimmed %like_case% "fungiphrya") {
|
||||
if (b.x_trimmed %like_case% "(fungus|fungi)" & b.x_trimmed %unlike_case% "fungiphrya") {
|
||||
found <- "F_FUNGUS"
|
||||
found_result <- found
|
||||
found <- lookup(mo == found)
|
||||
@@ -1490,20 +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$mo %in% MO_CONS), property, drop = TRUE]
|
||||
x[x %in% CoNS] <- lookup(mo == "B_STPHY_CONS", uncertainty = -1)
|
||||
@@ -1546,16 +1559,7 @@ exec_as.mo <- function(x,
|
||||
& !identical(x_input, "")
|
||||
& !identical(x_input, "xxx")])
|
||||
|
||||
# left join the found results to the original input values (x_input)
|
||||
df_found <- data.frame(input = as.character(x_input_unique_nonempty),
|
||||
found = as.character(x),
|
||||
stringsAsFactors = FALSE)
|
||||
df_input <- data.frame(input = as.character(x_input),
|
||||
stringsAsFactors = FALSE)
|
||||
|
||||
# super fast using match() which is a lot faster than merge()
|
||||
x <- df_found$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"))
|
||||
}
|
||||
@@ -1654,11 +1658,36 @@ pillar_shaft.mo <- function(x, ...) {
|
||||
out[!is.na(x)] <- gsub("^([A-Z]+_)(.*)", paste0(font_subtle("\\1"), "\\2"), out[!is.na(x)], perl = TRUE)
|
||||
# and grey out every _
|
||||
out[!is.na(x)] <- gsub("_", font_subtle("_"), out[!is.na(x)])
|
||||
|
||||
|
||||
# markup NA and UNKNOWN
|
||||
out[is.na(x)] <- font_na(" NA")
|
||||
out[x == "UNKNOWN"] <- font_na(" UNKNOWN")
|
||||
|
||||
|
||||
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(s)
|
||||
if (!is.null(mo_cols)) {
|
||||
col <- paste0("Column ", vector_or(colnames(df)[mo_cols], quotes = TRUE, sort = FALSE))
|
||||
} else {
|
||||
col <- "The data"
|
||||
}
|
||||
warning_(col, " contains old MO codes (from a previous AMR package version). ",
|
||||
"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)) {
|
||||
@@ -1709,9 +1738,9 @@ freq.mo <- function(x, ...) {
|
||||
get_skimmers.mo <- function(column) {
|
||||
skimr::sfl(
|
||||
skim_type = "mo",
|
||||
unique_total = ~pm_n_distinct(., na.rm = TRUE),
|
||||
gram_negative = ~sum(mo_is_gram_negative(stats::na.omit(.))),
|
||||
gram_positive = ~sum(mo_is_gram_positive(stats::na.omit(.))),
|
||||
unique_total = ~length(unique(stats::na.omit(.))),
|
||||
gram_negative = ~sum(mo_is_gram_negative(.), na.rm = TRUE),
|
||||
gram_positive = ~sum(mo_is_gram_positive(.), na.rm = TRUE),
|
||||
top_genus = ~names(sort(-table(mo_genus(stats::na.omit(.), language = NULL))))[1L],
|
||||
top_species = ~names(sort(-table(mo_name(stats::na.omit(.), language = NULL))))[1L]
|
||||
)
|
||||
@@ -1728,6 +1757,11 @@ print.mo <- function(x, print.shortnames = FALSE, ...) {
|
||||
}
|
||||
x <- as.character(x)
|
||||
names(x) <- x_names
|
||||
if (!all(x[!is.na(x)] %in% MO_lookup$mo)) {
|
||||
warning_("Some MO codes are from a previous AMR package version. ",
|
||||
"Please update these MO codes with `as.mo()`.",
|
||||
call = FALSE)
|
||||
}
|
||||
print.default(x, quote = FALSE)
|
||||
}
|
||||
|
||||
@@ -1753,11 +1787,16 @@ summary.mo <- function(object, ...) {
|
||||
#' @export
|
||||
#' @noRd
|
||||
as.data.frame.mo <- function(x, ...) {
|
||||
if (!all(x[!is.na(x)] %in% MO_lookup$mo)) {
|
||||
warning_("The data contains old MO codes (from a previous AMR package version). ",
|
||||
"Please update your MO codes with `as.mo()`.",
|
||||
call = FALSE)
|
||||
}
|
||||
nm <- deparse1(substitute(x))
|
||||
if (!"nm" %in% names(list(...))) {
|
||||
as.data.frame.vector(as.mo(x), ..., nm = nm)
|
||||
as.data.frame.vector(x, ..., nm = nm)
|
||||
} else {
|
||||
as.data.frame.vector(as.mo(x), ...)
|
||||
as.data.frame.vector(x, ...)
|
||||
}
|
||||
}
|
||||
|
||||
@@ -1784,8 +1823,7 @@ as.data.frame.mo <- function(x, ...) {
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(i)
|
||||
# must only contain valid MOs
|
||||
class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
|
||||
as.character(microorganisms.translation$mo_old)))
|
||||
return_after_integrity_check(y, "microorganism code", as.character(microorganisms$mo))
|
||||
}
|
||||
#' @method [[<- mo
|
||||
#' @export
|
||||
@@ -1794,18 +1832,16 @@ as.data.frame.mo <- function(x, ...) {
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(i)
|
||||
# must only contain valid MOs
|
||||
class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
|
||||
as.character(microorganisms.translation$mo_old)))
|
||||
return_after_integrity_check(y, "microorganism code", as.character(microorganisms$mo))
|
||||
}
|
||||
#' @method c mo
|
||||
#' @export
|
||||
#' @noRd
|
||||
c.mo <- function(x, ...) {
|
||||
c.mo <- function(...) {
|
||||
x <- list(...)[[1L]]
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(x)
|
||||
# must only contain valid MOs
|
||||
class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
|
||||
as.character(microorganisms.translation$mo_old)))
|
||||
return_after_integrity_check(y, "microorganism code", as.character(microorganisms$mo))
|
||||
}
|
||||
|
||||
#' @method unique mo
|
||||
@@ -1850,35 +1886,30 @@ print.mo_uncertainties <- function(x, ...) {
|
||||
if (NROW(x) == 0) {
|
||||
return(NULL)
|
||||
}
|
||||
message_("Matching scores are based on human pathogenic prevalence and the resemblance between the input and the full taxonomic name. See `?mo_matching_score`.", as_note = FALSE)
|
||||
|
||||
msg <- ""
|
||||
cat(word_wrap("Matching scores", ifelse(has_colour(), " (in blue)", ""), " are based on human pathogenic prevalence and the resemblance between the input and the full taxonomic name. See `?mo_matching_score`.\n\n", add_fn = font_blue))
|
||||
|
||||
txt <- ""
|
||||
for (i in seq_len(nrow(x))) {
|
||||
if (x[i, ]$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(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 <- ""
|
||||
}
|
||||
@@ -1886,23 +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
|
||||
@@ -2008,33 +2040,78 @@ 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$message, call. = FALSE)) # this will also be thrown when running `as.mo(no_existing_object)`
|
||||
parsed
|
||||
}
|
||||
|
||||
replace_old_mo_codes <- function(x, property) {
|
||||
if (any(toupper(x) %in% microorganisms.translation$mo_old, na.rm = TRUE)) {
|
||||
# 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
|
||||
matched <- match(toupper(x), microorganisms.translation$mo_old)
|
||||
# and their new codes
|
||||
mo_new <- microorganisms.translation$mo_new[matched]
|
||||
affected <- x[ind]
|
||||
affected_unique <- unique(affected)
|
||||
all_direct_matches <- TRUE
|
||||
# find their new codes, once per code
|
||||
solved_unique <- unlist(lapply(strsplit(affected_unique, ""),
|
||||
function(m) {
|
||||
kingdom <- paste0("^", m[1])
|
||||
name <- m[3:length(m)]
|
||||
name[name == "_"] <- " "
|
||||
name <- tolower(paste0(name, ".*", collapse = ""))
|
||||
name <- gsub(" .*", " ", name, fixed = TRUE)
|
||||
name <- paste0("^", name)
|
||||
results <- MO_lookup$mo[MO_lookup$kingdom %like_case% kingdom &
|
||||
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)
|
||||
solved <- solved_unique[match(affected, affected_unique)]
|
||||
# assign on places where a match was found
|
||||
x[which(!is.na(matched))] <- mo_new[which(!is.na(matched))]
|
||||
n_matched <- length(matched[!is.na(matched)])
|
||||
if (property != "mo") {
|
||||
message_(font_blue("The input contained old microbial codes (from previous package versions). Please update your MO codes with `as.mo()`."))
|
||||
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, ")
|
||||
} else {
|
||||
if (n_matched == 1) {
|
||||
message_(font_blue("1 old microbial code (from previous package versions) was updated to a current used MO code."))
|
||||
} else {
|
||||
message_(font_blue(n_matched, "old microbial codes (from previous package versions) were updated to current used MO codes."))
|
||||
}
|
||||
n_unique <- ""
|
||||
}
|
||||
if (property != "mo") {
|
||||
warning_(paste0("The input contained ", n_matched,
|
||||
" old MO code", ifelse(n_matched == 1, "", "s"),
|
||||
" (", n_unique, "from a previous AMR package version). ",
|
||||
"Please update your MO codes with `as.mo()` to increase speed."),
|
||||
call = FALSE)
|
||||
} else {
|
||||
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_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)
|
||||
}
|
||||
}
|
||||
x
|
||||
@@ -2069,7 +2146,7 @@ repair_reference_df <- function(reference_df) {
|
||||
reference_df[, "x"] <- as.character(reference_df[, "x", drop = TRUE])
|
||||
reference_df[, "mo"] <- as.character(reference_df[, "mo", drop = TRUE])
|
||||
|
||||
# some microbial codes might be old
|
||||
# some MO codes might be old
|
||||
reference_df[, "mo"] <- as.mo(reference_df[, "mo", drop = TRUE])
|
||||
reference_df
|
||||
}
|
||||
|
||||
@@ -44,7 +44,9 @@
|
||||
#' * \ifelse{html}{\out{<i>p<sub>n</sub></i> is the human pathogenic prevalence group of <i>n</i>, as described below;}}{p_n is the human pathogenic prevalence group of \eqn{n}, as described below;}
|
||||
#' * \ifelse{html}{\out{<i>k<sub>n</sub></i> is the taxonomic kingdom of <i>n</i>, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.}}{l_n is the taxonomic kingdom of \eqn{n}, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.}
|
||||
#'
|
||||
#' 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.
|
||||
#' 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
|
||||
|
||||
+58
-77
@@ -27,7 +27,7 @@
|
||||
#'
|
||||
#' Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with [as.mo()], which makes it possible to use microbial abbreviations, codes and names as input. See *Examples*.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param x any character (vector) that can be coerced to a valid microorganism code with [as.mo()]. Can be left blank for auto-guessing the column containing microorganism codes if used in a data set, see *Examples*.
|
||||
#' @param x any [character] (vector) that can be coerced to a valid microorganism code with [as.mo()]. Can be left blank for auto-guessing the column containing microorganism codes if used in a data set, see *Examples*.
|
||||
#' @param property one of the column names of the [microorganisms] data set: `r vector_or(colnames(microorganisms), sort = FALSE, quotes = TRUE)`, or must be `"shortname"`
|
||||
#' @param language language of the returned text, defaults to system language (see [get_locale()]) and can be overwritten by setting the option `AMR_locale`, e.g. `options(AMR_locale = "de")`, see [translate]. Also used to translate text like "no growth". Use `language = NULL` or `language = ""` to prevent translation.
|
||||
#' @param ... other arguments passed on to [as.mo()], such as 'allow_uncertain' and 'ignore_pattern'
|
||||
@@ -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
|
||||
@@ -152,6 +152,7 @@
|
||||
#' mo_is_yeast(c("Candida", "E. coli")) # TRUE, FALSE
|
||||
#'
|
||||
#' # gram stains and intrinsic resistance can also be used as a filter in dplyr verbs
|
||||
#' \donttest{
|
||||
#' if (require("dplyr")) {
|
||||
#' example_isolates %>%
|
||||
#' filter(mo_is_gram_positive())
|
||||
@@ -167,6 +168,7 @@
|
||||
#' # SNOMED codes, and URL to the online database
|
||||
#' mo_info("E. coli")
|
||||
#' }
|
||||
#' }
|
||||
mo_name <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this tries to find the data and an <mo> column
|
||||
@@ -178,7 +180,7 @@ mo_name <- function(x, language = get_locale(), ...) {
|
||||
translate_AMR(mo_validate(x = x, property = "fullname", language = language, ...),
|
||||
language = language,
|
||||
only_unknown = FALSE,
|
||||
affect_mo_name = TRUE)
|
||||
only_affect_mo_names = TRUE)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
@@ -214,15 +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, affect_mo_name = TRUE)
|
||||
translate_AMR(shortnames, language = language, only_unknown = FALSE, only_affect_mo_names = TRUE)
|
||||
}
|
||||
|
||||
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_subspecies <- function(x, language = get_locale(), ...) {
|
||||
@@ -360,25 +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)
|
||||
@@ -473,11 +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)
|
||||
@@ -522,7 +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)
|
||||
}
|
||||
|
||||
@@ -538,7 +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})$", "\\1", x[!is.na(x)], perl = TRUE)
|
||||
suppressWarnings(as.integer(x))
|
||||
}
|
||||
|
||||
@@ -568,17 +564,17 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
|
||||
x <- as.mo(x, language = language, ...)
|
||||
metadata <- get_mo_failures_uncertainties_renamed()
|
||||
|
||||
result <- list(kingdom = mo_kingdom(x, language = language),
|
||||
phylum = mo_phylum(x, language = language),
|
||||
class = mo_class(x, language = language),
|
||||
order = mo_order(x, language = language),
|
||||
family = mo_family(x, language = language),
|
||||
genus = mo_genus(x, language = language),
|
||||
species = mo_species(x, language = language),
|
||||
subspecies = mo_subspecies(x, language = language))
|
||||
out <- list(kingdom = mo_kingdom(x, language = language),
|
||||
phylum = mo_phylum(x, language = language),
|
||||
class = mo_class(x, language = language),
|
||||
order = mo_order(x, language = language),
|
||||
family = mo_family(x, language = language),
|
||||
genus = mo_genus(x, language = language),
|
||||
species = mo_species(x, language = language),
|
||||
subspecies = mo_subspecies(x, language = language))
|
||||
|
||||
load_mo_failures_uncertainties_renamed(metadata)
|
||||
result
|
||||
out
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
@@ -656,31 +652,23 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
|
||||
meet_criteria(open, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
mo <- as.mo(x = x, language = language, ... = ...)
|
||||
mo_names <- mo_name(mo)
|
||||
x.mo <- as.mo(x = x, language = language, ... = ...)
|
||||
metadata <- get_mo_failures_uncertainties_renamed()
|
||||
|
||||
df <- data.frame(mo, stringsAsFactors = FALSE) %pm>%
|
||||
pm_left_join(pm_select(microorganisms, mo, source, species_id), by = "mo")
|
||||
df$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$fullname
|
||||
|
||||
names(u) <- mo_names
|
||||
|
||||
if (open == TRUE) {
|
||||
if (isTRUE(open)) {
|
||||
if (length(u) > 1) {
|
||||
warning_("Only the first URL will be opened, as `browseURL()` only suports one string.")
|
||||
}
|
||||
@@ -721,23 +709,17 @@ mo_validate <- function(x, property, language, ...) {
|
||||
|
||||
if (tryCatch(all(x[!is.na(x)] %in% MO_lookup$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$mo), property, drop = TRUE])
|
||||
}
|
||||
x <- MO_lookup[match(x, MO_lookup$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$message, call. = FALSE))
|
||||
|
||||
if (is.mo(x)
|
||||
& !Becker %in% c(TRUE, "all")
|
||||
& !Lancefield %in% c(TRUE, "all")) {
|
||||
# this will not reset mo_uncertainties and mo_failures
|
||||
# because it's already a valid MO
|
||||
x <- exec_as.mo(x, property = property, initial_search = FALSE, language = language, ...)
|
||||
} else if (!all(x %in% MO_lookup[, property, drop = TRUE])
|
||||
| has_Becker_or_Lancefield) {
|
||||
x <- exec_as.mo(x, property = property, language = language, ...)
|
||||
} else {
|
||||
# try to catch an error when inputting an invalid argument
|
||||
# so the 'call.' can be set to FALSE
|
||||
tryCatch(x[1L] %in% MO_lookup[1, property, drop = TRUE],
|
||||
error = function(e) stop(e$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") {
|
||||
@@ -759,8 +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 {
|
||||
|
||||
+2
-2
@@ -275,9 +275,9 @@ check_validity_mo_source <- function(x, refer_to_name = "`reference_df`", stop_o
|
||||
return(FALSE)
|
||||
}
|
||||
}
|
||||
if (!all(x$mo %in% c("", microorganisms$mo, microorganisms.translation$mo_old), na.rm = TRUE)) {
|
||||
if (!all(x$mo %in% c("", microorganisms$mo), na.rm = TRUE)) {
|
||||
if (stop_on_error == TRUE) {
|
||||
invalid <- x[which(!x$mo %in% c("", microorganisms$mo, microorganisms.translation$mo_old)), , drop = FALSE]
|
||||
invalid <- x[which(!x$mo %in% c("", microorganisms$mo)), , drop = FALSE]
|
||||
if (nrow(invalid) > 1) {
|
||||
plural <- "s"
|
||||
} else {
|
||||
|
||||
@@ -27,12 +27,12 @@
|
||||
#'
|
||||
#' Performs a principal component analysis (PCA) based on a data set with automatic determination for afterwards plotting the groups and labels, and automatic filtering on only suitable (i.e. non-empty and numeric) variables.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param x a [data.frame] containing numeric columns
|
||||
#' @param x a [data.frame] containing [numeric] columns
|
||||
#' @param ... columns of `x` to be selected for PCA, can be unquoted since it supports quasiquotation.
|
||||
#' @inheritParams stats::prcomp
|
||||
#' @details The [pca()] function takes a [data.frame] as input and performs the actual PCA with the \R function [prcomp()].
|
||||
#'
|
||||
#' The result of the [pca()] function is a [prcomp] object, with an additional attribute `non_numeric_cols` which is a vector with the column names of all columns that do not contain numeric values. These are probably the groups and labels, and will be used by [ggplot_pca()].
|
||||
#' The result of the [pca()] function is a [prcomp] object, with an additional attribute `non_numeric_cols` which is a vector with the column names of all columns that do not contain [numeric] values. These are probably the groups and labels, and will be used by [ggplot_pca()].
|
||||
#' @return An object of classes [pca] and [prcomp]
|
||||
#' @importFrom stats prcomp
|
||||
#' @export
|
||||
@@ -42,7 +42,6 @@
|
||||
#' # See ?example_isolates.
|
||||
#'
|
||||
#' \donttest{
|
||||
#'
|
||||
#' if (require("dplyr")) {
|
||||
#' # calculate the resistance per group first
|
||||
#' resistance_data <- example_isolates %>%
|
||||
@@ -91,7 +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
|
||||
}
|
||||
}
|
||||
@@ -99,7 +98,7 @@ pca <- function(x,
|
||||
|
||||
x <- as.data.frame(new_list, stringsAsFactors = FALSE)
|
||||
if (any(vapply(FUN.VALUE = logical(1), x, function(y) !is.numeric(y)))) {
|
||||
warning_("Be sure to first calculate the resistance (or susceptibility) of variables with antimicrobial test results, since PCA works with numeric variables only. See Examples in ?pca.", call = FALSE)
|
||||
warning_("Be sure to first calculate the resistance (or susceptibility) of variables with antimicrobial test results, since PCA works with [numeric] variables only. See Examples in ?pca.", call = FALSE)
|
||||
}
|
||||
|
||||
# set column names
|
||||
@@ -120,7 +119,7 @@ pca <- function(x,
|
||||
message_("Columns selected for PCA: ", vector_and(font_bold(colnames(pca_data), collapse = NULL), quotes = TRUE),
|
||||
". Total observations available: ", nrow(pca_data), ".")
|
||||
|
||||
if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.4) {
|
||||
if (getRversion() < "3.4.0") {
|
||||
# stats::prcomp prior to 3.4.0 does not have the 'rank.' argument
|
||||
pca_model <- prcomp(pca_data, retx = retx, center = center, scale. = scale., tol = tol)
|
||||
} else {
|
||||
|
||||
@@ -25,19 +25,18 @@
|
||||
|
||||
#' 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 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.
|
||||
#' @param expand a [logical] to indicate whether the range on the x axis should be expanded between the lowest and highest value. For MIC values, intermediate values will be factors of 2 starting from the highest MIC value. For disk diameters, the whole diameter range will be filled.
|
||||
#' @details
|
||||
#' The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
|
||||
#'
|
||||
@@ -46,8 +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")
|
||||
@@ -61,10 +62,12 @@
|
||||
#' plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")
|
||||
#' plot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
|
||||
#'
|
||||
#' \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
|
||||
|
||||
@@ -73,26 +76,34 @@ 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)
|
||||
|
||||
# translate if not specifically set
|
||||
if (missing(ylab)) {
|
||||
ylab <- translate_AMR(ylab, language = language)
|
||||
}
|
||||
if (missing(xlab)) {
|
||||
xlab <- translate_AMR(xlab, language = language)
|
||||
}
|
||||
|
||||
if (length(colours_RSI) == 1) {
|
||||
colours_RSI <- rep(colours_RSI, 3)
|
||||
}
|
||||
@@ -135,13 +146,14 @@ plot.mic <- function(x,
|
||||
legend_txt <- c(legend_txt, "Resistant")
|
||||
legend_col <- c(legend_col, colours_RSI[1])
|
||||
}
|
||||
legend("top",
|
||||
legend("top",
|
||||
x.intersp = 0.5,
|
||||
legend = translate_AMR(legend_txt, language = language),
|
||||
fill = legend_col,
|
||||
horiz = TRUE,
|
||||
cex = 0.75,
|
||||
box.lwd = 0,
|
||||
cex = 0.75,
|
||||
box.lwd = 0,
|
||||
box.col = "#FFFFFF55",
|
||||
bg = "#FFFFFF55")
|
||||
}
|
||||
}
|
||||
@@ -150,12 +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,
|
||||
@@ -170,6 +182,14 @@ barplot.mic <- function(height,
|
||||
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)
|
||||
|
||||
# translate if not specifically set
|
||||
if (missing(ylab)) {
|
||||
ylab <- translate_AMR(ylab, language = language)
|
||||
}
|
||||
if (missing(xlab)) {
|
||||
xlab <- translate_AMR(xlab, language = language)
|
||||
}
|
||||
|
||||
main <- gsub(" +", " ", paste0(main, collapse = " "))
|
||||
|
||||
plot(x = height,
|
||||
@@ -183,32 +203,39 @@ 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)
|
||||
|
||||
# translate if not specifically set
|
||||
if (missing(ylab)) {
|
||||
ylab <- translate_AMR(ylab, language = language)
|
||||
}
|
||||
if (missing(xlab)) {
|
||||
xlab <- translate_AMR(xlab, language = language)
|
||||
}
|
||||
|
||||
if ("main" %in% names(list(...))) {
|
||||
title <- list(...)$main
|
||||
}
|
||||
@@ -216,7 +243,7 @@ ggplot.mic <- function(data,
|
||||
title <- gsub(" +", " ", paste0(title, collapse = " "))
|
||||
}
|
||||
|
||||
x <- plot_prepare_table(data, expand = expand)
|
||||
x <- plot_prepare_table(object, expand = expand)
|
||||
cols_sub <- plot_colours_subtitle_guideline(x = x,
|
||||
mo = mo,
|
||||
ab = ab,
|
||||
@@ -235,22 +262,20 @@ ggplot.mic <- function(data,
|
||||
levels = translate_AMR(c("Susceptible", plot_name_of_I(cols_sub$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$cols)) {
|
||||
vals <- c("Resistant" = colours_RSI[1],
|
||||
"Susceptible" = colours_RSI[2],
|
||||
"Incr. exposure" = colours_RSI[3],
|
||||
"Susceptible, incr. exp." = colours_RSI[3],
|
||||
"Intermediate" = colours_RSI[3])
|
||||
names(vals) <- translate_AMR(names(vals), language = language)
|
||||
p <- p +
|
||||
ggplot2::geom_col(ggplot2::aes(x = mic, y = count, fill = cols)) +
|
||||
# limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
|
||||
ggplot2::scale_fill_manual(values = vals,
|
||||
name = NULL)
|
||||
name = NULL,
|
||||
limits = force)
|
||||
} else {
|
||||
p <- p +
|
||||
ggplot2::geom_col(ggplot2::aes(x = mic, y = count))
|
||||
@@ -260,6 +285,14 @@ ggplot.mic <- function(data,
|
||||
ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$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
|
||||
@@ -285,6 +318,14 @@ plot.disk <- function(x,
|
||||
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)
|
||||
|
||||
# translate if not specifically set
|
||||
if (missing(ylab)) {
|
||||
ylab <- translate_AMR(ylab, language = language)
|
||||
}
|
||||
if (missing(xlab)) {
|
||||
xlab <- translate_AMR(xlab, language = language)
|
||||
}
|
||||
|
||||
if (length(colours_RSI) == 1) {
|
||||
colours_RSI <- rep(colours_RSI, 3)
|
||||
}
|
||||
@@ -333,8 +374,9 @@ plot.disk <- function(x,
|
||||
legend = translate_AMR(legend_txt, language = language),
|
||||
fill = legend_col,
|
||||
horiz = TRUE,
|
||||
cex = 0.75,
|
||||
box.lwd = 0,
|
||||
cex = 0.75,
|
||||
box.lwd = 0,
|
||||
box.col = "#FFFFFF55",
|
||||
bg = "#FFFFFF55")
|
||||
}
|
||||
}
|
||||
@@ -363,6 +405,14 @@ barplot.disk <- function(height,
|
||||
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)
|
||||
|
||||
# translate if not specifically set
|
||||
if (missing(ylab)) {
|
||||
ylab <- translate_AMR(ylab, language = language)
|
||||
}
|
||||
if (missing(xlab)) {
|
||||
xlab <- translate_AMR(xlab, language = language)
|
||||
}
|
||||
|
||||
main <- gsub(" +", " ", paste0(main, collapse = " "))
|
||||
|
||||
plot(x = height,
|
||||
@@ -376,21 +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)
|
||||
@@ -402,6 +451,14 @@ ggplot.disk <- function(data,
|
||||
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)
|
||||
|
||||
# translate if not specifically set
|
||||
if (missing(ylab)) {
|
||||
ylab <- translate_AMR(ylab, language = language)
|
||||
}
|
||||
if (missing(xlab)) {
|
||||
xlab <- translate_AMR(xlab, language = language)
|
||||
}
|
||||
|
||||
if ("main" %in% names(list(...))) {
|
||||
title <- list(...)$main
|
||||
}
|
||||
@@ -409,7 +466,7 @@ ggplot.disk <- function(data,
|
||||
title <- gsub(" +", " ", paste0(title, collapse = " "))
|
||||
}
|
||||
|
||||
x <- plot_prepare_table(data, expand = expand)
|
||||
x <- plot_prepare_table(object, expand = expand)
|
||||
cols_sub <- plot_colours_subtitle_guideline(x = x,
|
||||
mo = mo,
|
||||
ab = ab,
|
||||
@@ -429,22 +486,20 @@ ggplot.disk <- function(data,
|
||||
levels = translate_AMR(c("Susceptible", plot_name_of_I(cols_sub$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$cols)) {
|
||||
vals <- c("Resistant" = colours_RSI[1],
|
||||
"Susceptible" = colours_RSI[2],
|
||||
"Incr. exposure" = colours_RSI[3],
|
||||
"Susceptible, incr. exp." = colours_RSI[3],
|
||||
"Intermediate" = colours_RSI[3])
|
||||
names(vals) <- translate_AMR(names(vals), language = language)
|
||||
p <- p +
|
||||
ggplot2::geom_col(ggplot2::aes(x = disk, y = count, fill = cols)) +
|
||||
# limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
|
||||
ggplot2::scale_fill_manual(values = vals,
|
||||
name = NULL)
|
||||
name = NULL,
|
||||
limits = force)
|
||||
} else {
|
||||
p <- p +
|
||||
ggplot2::geom_col(ggplot2::aes(x = disk, y = count))
|
||||
@@ -454,77 +509,12 @@ ggplot.disk <- function(data,
|
||||
ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
|
||||
}
|
||||
|
||||
plot_prepare_table <- function(x, expand) {
|
||||
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
|
||||
extra_range <- max(x) / 2
|
||||
while (min(extra_range) / 2 > min(x)) {
|
||||
extra_range <- c(min(extra_range) / 2, extra_range)
|
||||
}
|
||||
nms <- extra_range
|
||||
extra_range <- rep(0, length(extra_range))
|
||||
names(extra_range) <- nms
|
||||
x <- table(droplevels(x, as.mic = FALSE))
|
||||
extra_range <- extra_range[!names(extra_range) %in% names(x)]
|
||||
x <- as.table(c(x, extra_range))
|
||||
} else {
|
||||
x <- table(droplevels(x, as.mic = FALSE))
|
||||
}
|
||||
x <- x[order(as.double(as.mic(names(x))))]
|
||||
} else if (is.disk(x)) {
|
||||
if (expand == TRUE) {
|
||||
# expand range for disks from lowest to highest so all mm's in between also print
|
||||
extra_range <- rep(0, max(x) - min(x) - 1)
|
||||
names(extra_range) <- seq(min(x) + 1, max(x) - 1)
|
||||
x <- table(x)
|
||||
extra_range <- extra_range[!names(extra_range) %in% names(x)]
|
||||
x <- as.table(c(x, extra_range))
|
||||
} else {
|
||||
x <- table(x)
|
||||
}
|
||||
x <- x[order(as.double(names(x)))]
|
||||
}
|
||||
as.table(x)
|
||||
}
|
||||
|
||||
plot_name_of_I <- function(guideline) {
|
||||
if (!guideline %like% "CLSI" && as.double(gsub("[^0-9]+", "", guideline)) >= 2019) {
|
||||
# interpretation since 2019
|
||||
"Incr. exposure"
|
||||
} else {
|
||||
# interpretation until 2019
|
||||
"Intermediate"
|
||||
}
|
||||
}
|
||||
|
||||
plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_RSI, fn, language, ...) {
|
||||
guideline <- get_guideline(guideline, AMR::rsi_translation)
|
||||
if (!is.null(mo) && !is.null(ab)) {
|
||||
# interpret and give colour based on MIC values
|
||||
mo <- as.mo(mo)
|
||||
ab <- as.ab(ab)
|
||||
rsi <- suppressWarnings(suppressMessages(as.rsi(fn(names(x)), mo = mo, ab = ab, guideline = guideline, ...)))
|
||||
cols <- character(length = length(rsi))
|
||||
cols[is.na(rsi)] <- "#BEBEBE"
|
||||
cols[rsi == "R"] <- colours_RSI[1]
|
||||
cols[rsi == "S"] <- colours_RSI[2]
|
||||
cols[rsi == "I"] <- colours_RSI[3]
|
||||
moname <- mo_name(mo, language = language)
|
||||
abname <- ab_name(ab, language = language)
|
||||
if (all(cols == "#BEBEBE")) {
|
||||
message_("No ", guideline, " interpretations found for ",
|
||||
ab_name(ab, language = NULL, tolower = TRUE), " in ", moname)
|
||||
guideline_txt <- ""
|
||||
} else {
|
||||
guideline_txt <- paste0("(", guideline, ")")
|
||||
}
|
||||
sub <- bquote(.(abname)~"in"~italic(.(moname))~.(guideline_txt))
|
||||
} else {
|
||||
cols <- "#BEBEBE"
|
||||
sub <- NULL
|
||||
}
|
||||
list(cols = cols, count = as.double(x), sub = sub, guideline = guideline)
|
||||
#' @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
|
||||
@@ -599,8 +589,18 @@ barplot.rsi <- function(height,
|
||||
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)
|
||||
|
||||
# translate if not specifically set
|
||||
if (missing(ylab)) {
|
||||
ylab <- translate_AMR(ylab, language = language)
|
||||
}
|
||||
if (missing(xlab)) {
|
||||
xlab <- translate_AMR(xlab, language = language)
|
||||
}
|
||||
|
||||
if (length(colours_RSI) == 1) {
|
||||
colours_RSI <- rep(colours_RSI, 3)
|
||||
} else {
|
||||
colours_RSI <- c(colours_RSI[2], colours_RSI[3], colours_RSI[1])
|
||||
}
|
||||
main <- gsub(" +", " ", paste0(main, collapse = " "))
|
||||
|
||||
@@ -615,22 +615,30 @@ 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"),
|
||||
...) {
|
||||
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)
|
||||
meet_criteria(xlab, allow_class = "character", has_length = 1)
|
||||
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
|
||||
|
||||
# translate if not specifically set
|
||||
if (missing(ylab)) {
|
||||
ylab <- translate_AMR(ylab, language = language)
|
||||
}
|
||||
if (missing(xlab)) {
|
||||
xlab <- translate_AMR(xlab, language = language)
|
||||
}
|
||||
|
||||
if ("main" %in% names(list(...))) {
|
||||
title <- list(...)$main
|
||||
}
|
||||
@@ -642,19 +650,99 @@ 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)
|
||||
}
|
||||
nms <- extra_range
|
||||
extra_range <- rep(0, length(extra_range))
|
||||
names(extra_range) <- nms
|
||||
x <- table(droplevels(x, as.mic = FALSE))
|
||||
extra_range <- extra_range[!names(extra_range) %in% names(x) & names(extra_range) %in% valid_lvls]
|
||||
x <- as.table(c(x, extra_range))
|
||||
} else {
|
||||
x <- table(droplevels(x, as.mic = FALSE))
|
||||
}
|
||||
x <- x[order(as.double(as.mic(names(x))))]
|
||||
} else if (is.disk(x)) {
|
||||
if (expand == TRUE) {
|
||||
# expand range for disks from lowest to highest so all mm's in between also print
|
||||
extra_range <- rep(0, max(x) - min(x) - 1)
|
||||
names(extra_range) <- seq(min(x) + 1, max(x) - 1)
|
||||
x <- table(x)
|
||||
extra_range <- extra_range[!names(extra_range) %in% names(x)]
|
||||
x <- as.table(c(x, extra_range))
|
||||
} else {
|
||||
x <- table(x)
|
||||
}
|
||||
x <- x[order(as.double(names(x)))]
|
||||
}
|
||||
as.table(x)
|
||||
}
|
||||
|
||||
plot_name_of_I <- function(guideline) {
|
||||
if (guideline %unlike% "CLSI" && as.double(gsub("[^0-9]+", "", guideline)) >= 2019) {
|
||||
# interpretation since 2019
|
||||
"Susceptible, incr. exp."
|
||||
} else {
|
||||
# interpretation until 2019
|
||||
"Intermediate"
|
||||
}
|
||||
}
|
||||
|
||||
plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_RSI, fn, language, ...) {
|
||||
guideline <- get_guideline(guideline, AMR::rsi_translation)
|
||||
if (!is.null(mo) && !is.null(ab)) {
|
||||
# interpret and give colour based on MIC values
|
||||
mo <- as.mo(mo)
|
||||
ab <- as.ab(ab)
|
||||
rsi <- suppressWarnings(suppressMessages(as.rsi(fn(names(x)), mo = mo, ab = ab, guideline = guideline, ...)))
|
||||
cols <- character(length = length(rsi))
|
||||
cols[is.na(rsi)] <- "#BEBEBE"
|
||||
cols[rsi == "R"] <- colours_RSI[1]
|
||||
cols[rsi == "S"] <- colours_RSI[2]
|
||||
cols[rsi == "I"] <- colours_RSI[3]
|
||||
moname <- mo_name(mo, language = language)
|
||||
abname <- ab_name(ab, language = language)
|
||||
if (all(cols == "#BEBEBE")) {
|
||||
message_("No ", guideline, " interpretations found for ",
|
||||
ab_name(ab, language = NULL, tolower = TRUE), " in ", moname)
|
||||
guideline_txt <- ""
|
||||
} else {
|
||||
guideline_txt <- paste0("(", guideline, ")")
|
||||
}
|
||||
sub <- bquote(.(abname)~"-"~italic(.(moname))~.(guideline_txt))
|
||||
} else {
|
||||
cols <- "#BEBEBE"
|
||||
sub <- NULL
|
||||
}
|
||||
list(cols = cols, count = as.double(x), sub = sub, guideline = guideline)
|
||||
}
|
||||
|
||||
+74
-56
@@ -31,18 +31,18 @@
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param ... one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with [as.rsi()] if needed. Use multiple columns to calculate (the lack of) co-resistance: the probability where one of two drugs have a resistant or susceptible result. See *Examples*.
|
||||
#' @param minimum the minimum allowed number of available (tested) isolates. Any isolate count lower than `minimum` will return `NA` with a warning. The default number of `30` isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see *Source*.
|
||||
#' @param as_percent a logical to indicate whether the output must be returned as a hundred fold with % sign (a character). A value of `0.123456` will then be returned as `"12.3%"`.
|
||||
#' @param only_all_tested (for combination therapies, i.e. using more than one variable for `...`): a logical to indicate that isolates must be tested for all antibiotics, see section *Combination Therapy* below
|
||||
#' @param as_percent a [logical] to indicate whether the output must be returned as a hundred fold with % sign (a character). A value of `0.123456` will then be returned as `"12.3%"`.
|
||||
#' @param only_all_tested (for combination therapies, i.e. using more than one variable for `...`): a [logical] to indicate that isolates must be tested for all antibiotics, see section *Combination Therapy* below
|
||||
#' @param data a [data.frame] containing columns with class [`rsi`] (see [as.rsi()])
|
||||
#' @param translate_ab a column name of the [antibiotics] data set to translate the antibiotic abbreviations to, using [ab_property()]
|
||||
#' @inheritParams ab_property
|
||||
#' @param combine_SI a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the argument `combine_IR`, but this now follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is `TRUE`.
|
||||
#' @param combine_IR a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see argument `combine_SI`.
|
||||
#' @param combine_SI a [logical] to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the argument `combine_IR`, but this now follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is `TRUE`.
|
||||
#' @param combine_IR a [logical] to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see argument `combine_SI`.
|
||||
#' @inheritSection as.rsi Interpretation of R and S/I
|
||||
#' @details
|
||||
#' The function [resistance()] is equal to the function [proportion_R()]. The function [susceptibility()] is equal to the function [proportion_SI()].
|
||||
#'
|
||||
#' **Remember that you should filter your table to let it contain only first isolates!** This is needed to exclude duplicates and to reduce selection bias. Use [first_isolate()] to determine them in your data set.
|
||||
#' **Remember that you should filter your data to let it contain only first isolates!** This is needed to exclude duplicates and to reduce selection bias. Use [first_isolate()] to determine them in your data set.
|
||||
#'
|
||||
#' These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the [`count()`][AMR::count()] functions to count isolates. The function [susceptibility()] is essentially equal to `count_susceptible() / count_all()`. *Low counts can influence the outcome - the `proportion` functions may camouflage this, since they only return the proportion (albeit being dependent on the `minimum` argument).*
|
||||
#'
|
||||
@@ -103,6 +103,7 @@
|
||||
#' proportion_IR(example_isolates$AMX)
|
||||
#' proportion_R(example_isolates$AMX)
|
||||
#'
|
||||
#' \donttest{
|
||||
#' if (require("dplyr")) {
|
||||
#' example_isolates %>%
|
||||
#' group_by(hospital_id) %>%
|
||||
@@ -161,16 +162,19 @@
|
||||
#' group_by(hospital_id) %>%
|
||||
#' proportion_df(translate = FALSE)
|
||||
#' }
|
||||
#' }
|
||||
resistance <- function(...,
|
||||
minimum = 30,
|
||||
as_percent = FALSE,
|
||||
only_all_tested = FALSE) {
|
||||
rsi_calc(...,
|
||||
ab_result = "R",
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = FALSE)
|
||||
tryCatch(
|
||||
rsi_calc(...,
|
||||
ab_result = "R",
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = FALSE),
|
||||
error = function(e) stop_(e$message, call = -5))
|
||||
}
|
||||
|
||||
#' @rdname proportion
|
||||
@@ -179,12 +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$message, call = -5))
|
||||
}
|
||||
|
||||
#' @rdname proportion
|
||||
@@ -193,12 +199,14 @@ proportion_R <- function(...,
|
||||
minimum = 30,
|
||||
as_percent = FALSE,
|
||||
only_all_tested = FALSE) {
|
||||
rsi_calc(...,
|
||||
ab_result = "R",
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = FALSE)
|
||||
tryCatch(
|
||||
rsi_calc(...,
|
||||
ab_result = "R",
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = FALSE),
|
||||
error = function(e) stop_(e$message, call = -5))
|
||||
}
|
||||
|
||||
#' @rdname proportion
|
||||
@@ -207,12 +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$message, call = -5))
|
||||
}
|
||||
|
||||
#' @rdname proportion
|
||||
@@ -221,12 +231,14 @@ proportion_I <- function(...,
|
||||
minimum = 30,
|
||||
as_percent = FALSE,
|
||||
only_all_tested = FALSE) {
|
||||
rsi_calc(...,
|
||||
ab_result = "I",
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = FALSE)
|
||||
tryCatch(
|
||||
rsi_calc(...,
|
||||
ab_result = "I",
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = FALSE),
|
||||
error = function(e) stop_(e$message, call = -5))
|
||||
}
|
||||
|
||||
#' @rdname proportion
|
||||
@@ -235,12 +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$message, call = -5))
|
||||
}
|
||||
|
||||
#' @rdname proportion
|
||||
@@ -249,12 +263,14 @@ proportion_S <- function(...,
|
||||
minimum = 30,
|
||||
as_percent = FALSE,
|
||||
only_all_tested = FALSE) {
|
||||
rsi_calc(...,
|
||||
ab_result = "S",
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = FALSE)
|
||||
tryCatch(
|
||||
rsi_calc(...,
|
||||
ab_result = "S",
|
||||
minimum = minimum,
|
||||
as_percent = as_percent,
|
||||
only_all_tested = only_all_tested,
|
||||
only_count = FALSE),
|
||||
error = function(e) stop_(e$message, call = -5))
|
||||
}
|
||||
|
||||
#' @rdname proportion
|
||||
@@ -266,13 +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))
|
||||
}
|
||||
|
||||
+40
-24
@@ -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 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 ... extension for future versions, not used at the moment
|
||||
#' @details The base R function [sample()] is used for generating values.
|
||||
#' @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 ... ignored, only in place to allow future extensions
|
||||
#' @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)])
|
||||
|
||||
+34
-9
@@ -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`
|
||||
@@ -34,11 +35,11 @@
|
||||
#' @param year_every unit of sequence between lowest year found in the data and `year_max`
|
||||
#' @param minimum minimal amount of available isolates per year to include. Years containing less observations will be estimated by the model.
|
||||
#' @param model the statistical model of choice. This could be a generalised linear regression model with binomial distribution (i.e. using `glm(..., family = binomial)``, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See *Details* for all valid options.
|
||||
#' @param I_as_S a logical to indicate whether values `"I"` should be treated as `"S"` (will otherwise be treated as `"R"`). The default, `TRUE`, follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section *Interpretation of S, I and R* below.
|
||||
#' @param preserve_measurements a logical to indicate whether predictions of years that are actually available in the data should be overwritten by the original data. The standard errors of those years will be `NA`.
|
||||
#' @param info a logical to indicate whether textual analysis should be printed with the name and [summary()] of the statistical model.
|
||||
#' @param I_as_S a [logical] to indicate whether values `"I"` should be treated as `"S"` (will otherwise be treated as `"R"`). The default, `TRUE`, follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section *Interpretation of S, I and R* below.
|
||||
#' @param preserve_measurements a [logical] to indicate whether predictions of years that are actually available in the data should be overwritten by the original data. The standard errors of those years will be `NA`.
|
||||
#' @param info a [logical] to indicate whether textual analysis should be printed with the name and [summary()] of the statistical model.
|
||||
#' @param main title of the plot
|
||||
#' @param ribbon a logical to indicate whether a ribbon should be shown (default) or error bars
|
||||
#' @param ribbon a [logical] to indicate whether a ribbon should be shown (default) or error bars
|
||||
#' @param ... arguments passed on to functions
|
||||
#' @inheritSection as.rsi Interpretation of R and S/I
|
||||
#' @inheritParams first_isolate
|
||||
@@ -70,6 +71,7 @@
|
||||
#' year_min = 2010,
|
||||
#' model = "binomial")
|
||||
#' plot(x)
|
||||
#' \donttest{
|
||||
#' if (require("ggplot2")) {
|
||||
#' ggplot_rsi_predict(x)
|
||||
#' }
|
||||
@@ -97,6 +99,8 @@
|
||||
#' model = "binomial",
|
||||
#' info = FALSE,
|
||||
#' minimum = 15)
|
||||
#'
|
||||
#' autoplot(data)
|
||||
#'
|
||||
#' ggplot(data,
|
||||
#' aes(x = year)) +
|
||||
@@ -114,6 +118,7 @@
|
||||
#' x = "Year") +
|
||||
#' theme_minimal(base_size = 13)
|
||||
#' }
|
||||
#' }
|
||||
resistance_predict <- function(x,
|
||||
col_ab,
|
||||
col_date = NULL,
|
||||
@@ -139,7 +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
|
||||
@@ -317,7 +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),
|
||||
@@ -360,14 +365,14 @@ ggplot_rsi_predict <- function(x,
|
||||
stop_ifnot_installed("ggplot2")
|
||||
stop_ifnot(inherits(x, "resistance_predict"), "`x` must be a resistance prediction model created with resistance_predict()")
|
||||
|
||||
|
||||
if (attributes(x)$I_as_S == TRUE) {
|
||||
ylab <- "%R"
|
||||
} else {
|
||||
ylab <- "%IR"
|
||||
}
|
||||
|
||||
p <- ggplot2::ggplot(x, ggplot2::aes(x = year, y = value)) +
|
||||
p <- ggplot2::ggplot(as.data.frame(x, stringsAsFactors = FALSE),
|
||||
ggplot2::aes(x = year, y = value)) +
|
||||
ggplot2::geom_point(data = subset(x, !is.na(observations)),
|
||||
size = 2) +
|
||||
scale_y_percent(limits = c(0, 1)) +
|
||||
@@ -389,3 +394,23 @@ ggplot_rsi_predict <- function(x,
|
||||
colour = "grey40")
|
||||
p
|
||||
}
|
||||
|
||||
#' @method autoplot resistance_predict
|
||||
#' @rdname resistance_predict
|
||||
# will be exported using s3_register() in R/zzz.R
|
||||
autoplot.resistance_predict <- function(object,
|
||||
main = paste("Resistance Prediction of", x_name),
|
||||
ribbon = TRUE,
|
||||
...) {
|
||||
x_name <- paste0(ab_name(attributes(object)$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)
|
||||
}
|
||||
|
||||
@@ -25,17 +25,17 @@
|
||||
|
||||
#' Interpret MIC and Disk Values, or Clean Raw R/SI Data
|
||||
#'
|
||||
#' Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class [`rsi`], which is an ordered factor with levels `S < I < R`. Values that cannot be interpreted will be returned as `NA` with a warning.
|
||||
#' Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class [`rsi`], which is an ordered [factor] with levels `S < I < R`.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @rdname as.rsi
|
||||
#' @param x vector of values (for class [`mic`]: an MIC value in mg/L, for class [`disk`]: a disk diffusion radius in millimetres)
|
||||
#' @param mo any (vector of) text that can be coerced to a valid microorganism code with [as.mo()], can be left empty to determine it automatically
|
||||
#' @param x vector of values (for class [`mic`]: MIC values in mg/L, for class [`disk`]: a disk diffusion radius in millimetres)
|
||||
#' @param mo any (vector of) text that can be coerced to valid microorganism codes with [as.mo()], can be left empty to determine it automatically
|
||||
#' @param ab any (vector of) text that can be coerced to a valid antimicrobial code with [as.ab()]
|
||||
#' @param uti (Urinary Tract Infection) A vector with [logical]s (`TRUE` or `FALSE`) to specify whether a UTI specific interpretation from the guideline should be chosen. For using [as.rsi()] on a [data.frame], this can also be a column containing [logical]s or when left blank, the data set will be searched for a 'specimen' and rows containing 'urin' (such as 'urine', 'urina') in that column will be regarded isolates from a UTI. See *Examples*.
|
||||
#' @param uti (Urinary Tract Infection) A vector with [logical]s (`TRUE` or `FALSE`) to specify whether a UTI specific interpretation from the guideline should be chosen. For using [as.rsi()] on a [data.frame], this can also be a column containing [logical]s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See *Examples*.
|
||||
#' @inheritParams first_isolate
|
||||
#' @param guideline defaults to the latest included EUCAST guideline, see *Details* for all options
|
||||
#' @param conserve_capped_values a logical to indicate that MIC values starting with `">"` (but not `">="`) must always return "R" , and that MIC values starting with `"<"` (but not `"<="`) must always return "S"
|
||||
#' @param add_intrinsic_resistance *(only useful when using a EUCAST guideline)* a logical to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in *Klebsiella* species. Determination is based on the [intrinsic_resistant] data set, that itself is based on `r format_eucast_version_nr(3.2)`.
|
||||
#' @param conserve_capped_values a [logical] to indicate that MIC values starting with `">"` (but not `">="`) must always return "R" , and that MIC values starting with `"<"` (but not `"<="`) must always return "S"
|
||||
#' @param add_intrinsic_resistance *(only useful when using a EUCAST guideline)* a [logical] to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in *Klebsiella* species. Determination is based on the [intrinsic_resistant] data set, that itself is based on `r format_eucast_version_nr(3.2)`.
|
||||
#' @param reference_data a [data.frame] to be used for interpretation, which defaults to the [rsi_translation] data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the [rsi_translation] data set (same column names and column types). Please note that the `guideline` argument will be ignored when `reference_data` is manually set.
|
||||
#' @param threshold maximum fraction of invalid antimicrobial interpretations of `x`, see *Examples*
|
||||
#' @param ... for using on a [data.frame]: names of columns to apply [as.rsi()] on (supports tidy selection like `AMX:VAN`). Otherwise: arguments passed on to methods.
|
||||
@@ -49,25 +49,25 @@
|
||||
#' 2. For **interpreting minimum inhibitory concentration (MIC) values** according to EUCAST or CLSI. You must clean your MIC values first using [as.mic()], that also gives your columns the new data class [`mic`]. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the `mo` argument.
|
||||
#' * Using `dplyr`, R/SI interpretation can be done very easily with either:
|
||||
#' ```
|
||||
#' your_data %>% mutate_if(is.mic, as.rsi) # until dplyr 1.0.0
|
||||
#' your_data %>% mutate(across((is.mic), as.rsi)) # since dplyr 1.0.0
|
||||
#' your_data %>% mutate_if(is.mic, as.rsi) # until dplyr 1.0.0
|
||||
#' your_data %>% mutate(across(where(is.mic), as.rsi)) # since dplyr 1.0.0
|
||||
#' ```
|
||||
#' * Operators like "<=" will be stripped before interpretation. When using `conserve_capped_values = TRUE`, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (`conserve_capped_values = FALSE`) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".
|
||||
#'
|
||||
#' 3. For **interpreting disk diffusion diameters** according to EUCAST or CLSI. You must clean your disk zones first using [as.disk()], that also gives your columns the new data class [`disk`]. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the `mo` argument.
|
||||
#' * Using `dplyr`, R/SI interpretation can be done very easily with either:
|
||||
#' ```
|
||||
#' your_data %>% mutate_if(is.disk, as.rsi) # until dplyr 1.0.0
|
||||
#' your_data %>% mutate(across((is.disk), as.rsi)) # since dplyr 1.0.0
|
||||
#' your_data %>% mutate_if(is.disk, as.rsi) # until dplyr 1.0.0
|
||||
#' your_data %>% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0
|
||||
#' ```
|
||||
#'
|
||||
#' 4. For **interpreting a complete data set**, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running `as.rsi(data)`.
|
||||
#'
|
||||
#' ## Supported Guidelines
|
||||
#'
|
||||
#' For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the `guideline` argument are: `r vector_and(AMR::rsi_translation$guideline, quotes = TRUE, reverse = TRUE)`.
|
||||
#' For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`).
|
||||
#'
|
||||
#' Simply using `"CLSI"` or `"EUCAST"` as input will automatically select the latest version of that guideline. You can set your own data set using the `reference_data` argument. The `guideline` argument will then be ignored.
|
||||
#' Thus, the `guideline` argument must be set to e.g., ``r paste0('"', subset(rsi_translation, guideline %like% "EUCAST")$guideline[1], '"')`` or ``r paste0('"', subset(rsi_translation, guideline %like% "CLSI")$guideline[1], '"')``. By simply using `"EUCAST"` (the default) or `"CLSI"` as input, the latest version of that guideline will automatically be selected. You can set your own data set using the `reference_data` argument. The `guideline` argument will then be ignored.
|
||||
#'
|
||||
#' ## After Interpretation
|
||||
#'
|
||||
@@ -75,13 +75,13 @@
|
||||
#'
|
||||
#' ## 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
|
||||
#'
|
||||
#' The function [is.rsi()] detects if the input contains class `<rsi>`. If the input is a data.frame, it iterates over all columns and returns a logical vector.
|
||||
#' The function [is.rsi()] detects if the input contains class `<rsi>`. If the input is a [data.frame], it iterates over all columns and returns a [logical] vector.
|
||||
#'
|
||||
#' The function [is.rsi.eligible()] returns `TRUE` when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and `FALSE` otherwise. The threshold of 5% can be set with the `threshold` argument. If the input is a data.frame, it iterates over all columns and returns a logical vector.
|
||||
#' The function [is.rsi.eligible()] returns `TRUE` when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and `FALSE` otherwise. The threshold of 5% can be set with the `threshold` argument. If the input is a [data.frame], it iterates over all columns and returns a [logical] vector.
|
||||
#' @section Interpretation of R and S/I:
|
||||
#' In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (<https://www.eucast.org/newsiandr/>).
|
||||
#'
|
||||
@@ -89,11 +89,11 @@
|
||||
#' 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.
|
||||
#' @return Ordered factor with new class `<rsi>`
|
||||
#' 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.
|
||||
#' @return Ordered [factor] with new class `<rsi>`
|
||||
#' @aliases rsi
|
||||
#' @export
|
||||
#' @seealso [as.mic()], [as.disk()], [as.mo()]
|
||||
@@ -101,12 +101,12 @@
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
#' @examples
|
||||
#' summary(example_isolates) # see all R/SI results at a glance
|
||||
#'
|
||||
#' \donttest{
|
||||
#' if (require("skimr")) {
|
||||
#' # class <rsi> supported in skim() too:
|
||||
#' skim(example_isolates)
|
||||
#' }
|
||||
#'
|
||||
#' }
|
||||
#' # For INTERPRETING disk diffusion and MIC values -----------------------
|
||||
#'
|
||||
#' # a whole data set, even with combined MIC values and disk zones
|
||||
@@ -135,7 +135,7 @@
|
||||
#' if (require("dplyr")) {
|
||||
#' df %>% mutate_if(is.mic, as.rsi)
|
||||
#' df %>% mutate_if(function(x) is.mic(x) | is.disk(x), as.rsi)
|
||||
#' df %>% mutate(across((is.mic), as.rsi))
|
||||
#' df %>% mutate(across(where(is.mic), as.rsi))
|
||||
#' df %>% mutate_at(vars(AMP:TOB), as.rsi)
|
||||
#' df %>% mutate(across(AMP:TOB, as.rsi))
|
||||
#'
|
||||
@@ -181,13 +181,19 @@
|
||||
#'
|
||||
#' # note: from dplyr 1.0.0 on, this will be:
|
||||
#' # example_isolates %>%
|
||||
#' # mutate(across((is.rsi.eligible), as.rsi))
|
||||
#' # mutate(across(where(is.rsi.eligible), as.rsi))
|
||||
#' }
|
||||
#' }
|
||||
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) {
|
||||
@@ -215,7 +221,6 @@ is.rsi.eligible <- function(x, threshold = 0.05) {
|
||||
"ab",
|
||||
"Date",
|
||||
"POSIXt",
|
||||
"rsi",
|
||||
"raw",
|
||||
"hms",
|
||||
"mic",
|
||||
@@ -258,44 +263,63 @@ as.rsi.default <- function(x, ...) {
|
||||
return(x)
|
||||
}
|
||||
|
||||
if (inherits(x, c("integer", "numeric", "double")) && all(x %in% c(1:3, NA))) {
|
||||
x[x == 1] <- "S"
|
||||
x[x == 2] <- "I"
|
||||
x[x == 3] <- "R"
|
||||
|
||||
} else if (!all(is.na(x)) && !identical(levels(x), c("S", "I", "R"))) {
|
||||
|
||||
if (!any(x %like% "(R|S|I)", na.rm = TRUE)) {
|
||||
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.bak)$labels
|
||||
if (!is.null(lbls) && all(c("R", "S", "I") %in% names(lbls)) && all(c(1:3) %in% lbls)) {
|
||||
x[x.bak == 1] <- names(lbls[lbls == 1])
|
||||
x[x.bak == 2] <- names(lbls[lbls == 2])
|
||||
x[x.bak == 3] <- names(lbls[lbls == 3])
|
||||
} else {
|
||||
x[x.bak == 1] <- "S"
|
||||
x[x.bak == 2] <- "I"
|
||||
x[x.bak == 3] <- "R"
|
||||
}
|
||||
|
||||
} else if (!all(is.na(x)) && !identical(levels(x), c("R", "S", "I")) && !all(x %in% c("R", "S", "I", NA))) {
|
||||
|
||||
if (all(x %unlike% "(R|S|I)", na.rm = TRUE)) {
|
||||
# check if they are actually MICs or disks
|
||||
if (all_valid_mics(x)) {
|
||||
warning_("The input seems to be MIC values. Transform them with `as.mic()` before running `as.rsi()` to interpret them.")
|
||||
warning_("The input seems to contain MIC values. You can transform them with `as.mic()` before running `as.rsi()` to interpret them.", call = FALSE)
|
||||
} else if (all_valid_disks(x)) {
|
||||
warning_("The input seems to be disk diffusion values. Transform them with `as.disk()` before running `as.rsi()` to interpret them.")
|
||||
warning_("The input seems to contain disk diffusion values. You can transform them with `as.disk()` before running `as.rsi()` to interpret them.", call = FALSE)
|
||||
}
|
||||
}
|
||||
|
||||
x <- as.character(unlist(x))
|
||||
# trim leading and trailing spaces, new lines, etc.
|
||||
x <- trimws2(as.character(unlist(x)))
|
||||
x.bak <- x
|
||||
|
||||
na_before <- length(x[is.na(x) | x == ""])
|
||||
# remove all spaces
|
||||
x <- gsub(" +", "", x)
|
||||
# remove all MIC-like values: numbers, operators and periods
|
||||
x <- gsub("[0-9.,;:<=>]+", "", x)
|
||||
# remove everything between brackets, and 'high' and 'low'
|
||||
x <- gsub("([(].*[)])", "", x)
|
||||
x <- gsub("(high|low)", "", x, ignore.case = TRUE)
|
||||
# disallow more than 3 characters
|
||||
x[nchar(x) > 3] <- NA
|
||||
|
||||
# correct for translations
|
||||
trans_R <- unlist(TRANSLATIONS[which(TRANSLATIONS$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
|
||||
@@ -339,7 +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)
|
||||
@@ -385,13 +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)
|
||||
|
||||
@@ -428,7 +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)
|
||||
@@ -474,13 +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)
|
||||
|
||||
@@ -535,7 +569,7 @@ as.rsi.data.frame <- function(x,
|
||||
}
|
||||
if (!is.null(col_uti)) {
|
||||
if (is.logical(col_uti)) {
|
||||
# already a logical vector as input
|
||||
# already a [logical] vector as input
|
||||
if (length(col_uti) == 1) {
|
||||
uti <- rep(col_uti, NROW(x))
|
||||
} else {
|
||||
@@ -544,7 +578,7 @@ as.rsi.data.frame <- function(x,
|
||||
} else {
|
||||
# column found, transform to logical
|
||||
stop_if(length(col_uti) != 1 | !col_uti %in% colnames(x),
|
||||
"argument `uti` must be a logical vector, of must be a single column name of `x`")
|
||||
"argument `uti` must be a [logical] vector, of must be a single column name of `x`")
|
||||
uti <- as.logical(x[, col_uti, drop = TRUE])
|
||||
}
|
||||
} else {
|
||||
@@ -570,7 +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]
|
||||
}
|
||||
@@ -614,10 +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>%
|
||||
@@ -648,11 +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)
|
||||
@@ -660,7 +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)
|
||||
@@ -683,7 +720,7 @@ get_guideline <- function(guideline, reference_data) {
|
||||
if (guideline_param %in% c("CLSI", "EUCAST")) {
|
||||
guideline_param <- rev(sort(subset(reference_data, guideline %like% guideline_param)$guideline))[1L]
|
||||
}
|
||||
if (!guideline_param %like% " ") {
|
||||
if (guideline_param %unlike% " ") {
|
||||
# like 'EUCAST2020', should be 'EUCAST 2020'
|
||||
guideline_param <- gsub("([a-z]+)([0-9]+)", "\\1 \\2", guideline_param, ignore.case = TRUE)
|
||||
}
|
||||
@@ -740,7 +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")
|
||||
}
|
||||
}
|
||||
|
||||
@@ -776,10 +812,9 @@ exec_as.rsi <- function(method,
|
||||
any_is_intrinsic_resistant <- any_is_intrinsic_resistant | is_intrinsic_r
|
||||
|
||||
if (isTRUE(add_intrinsic_resistance) & is_intrinsic_r) {
|
||||
if (!guideline_coerced %like% "EUCAST") {
|
||||
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"
|
||||
@@ -844,7 +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
|
||||
}
|
||||
@@ -905,7 +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)))
|
||||
@@ -923,28 +957,16 @@ get_skimmers.rsi <- function(column) {
|
||||
# get the variable name 'skim_variable'
|
||||
name_call <- function(.data) {
|
||||
calls <- sys.calls()
|
||||
frms <- sys.frames()
|
||||
calls_txt <- vapply(calls, function(x) paste(deparse(x), collapse = ""), FUN.VALUE = character(1))
|
||||
if (any(calls_txt %like% "skim_variable", na.rm = TRUE)) {
|
||||
ind <- which(calls_txt %like% "skim_variable")[1L]
|
||||
vars <- tryCatch(eval(parse(text = ".data$skim_variable"), envir = sys.frame(ind)),
|
||||
vars <- tryCatch(eval(parse(text = ".data$skim_variable$rsi"), envir = frms[[ind]]),
|
||||
error = function(e) NULL)
|
||||
tryCatch(ab_name(as.character(calls[[length(calls)]][[2]]), language = NULL),
|
||||
error = function(e) NA_character_)
|
||||
} else {
|
||||
vars <- NULL
|
||||
}
|
||||
i <- tryCatch(attributes(calls[[length(calls)]])$position,
|
||||
error = function(e) NULL)
|
||||
if (is.null(vars) | is.null(i)) {
|
||||
NA_character_
|
||||
} else {
|
||||
lengths <- vapply(FUN.VALUE = double(1), vars, length)
|
||||
when_starts_rsi <- which(names(vapply(FUN.VALUE = double(1), vars, length)) == "rsi")
|
||||
offset <- sum(lengths[c(1:when_starts_rsi - 1)])
|
||||
var <- vars$rsi[i - offset]
|
||||
if (!isFALSE(var == "data")) {
|
||||
NA_character_
|
||||
} else{
|
||||
ab_name(var)
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@@ -1027,10 +1049,8 @@ summary.rsi <- function(object, ...) {
|
||||
#' @method c rsi
|
||||
#' @export
|
||||
#' @noRd
|
||||
c.rsi <- function(x, ...) {
|
||||
y <- unlist(lapply(list(...), as.character))
|
||||
x <- as.character(x)
|
||||
as.rsi(c(x, y))
|
||||
c.rsi <- function(...) {
|
||||
as.rsi(unlist(lapply(list(...), as.character)))
|
||||
}
|
||||
|
||||
#' @method unique rsi
|
||||
@@ -1042,6 +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 "))
|
||||
|
||||
+27
-5
@@ -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(...,
|
||||
@@ -150,9 +150,8 @@ rsi_calc <- function(...,
|
||||
if (message_not_thrown_before("rsi_calc")) {
|
||||
warning_("Increase speed by transforming to class <rsi> on beforehand:\n",
|
||||
" your_data %>% mutate_if(is.rsi.eligible, as.rsi)\n",
|
||||
" your_data %>% mutate(across((is.rsi.eligible), as.rsi))",
|
||||
" 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
|
||||
}
|
||||
|
||||
|
||||
+1
-1
@@ -30,7 +30,7 @@
|
||||
#' When negative ('left-skewed'): the left tail is longer; the mass of the distribution is concentrated on the right of a histogram. When positive ('right-skewed'): the right tail is longer; the mass of the distribution is concentrated on the left of a histogram. A normal distribution has a skewness of 0.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param x a vector of values, a [matrix] or a [data.frame]
|
||||
#' @param na.rm a logical value indicating whether `NA` values should be stripped before the computation proceeds
|
||||
#' @param na.rm a [logical] value indicating whether `NA` values should be stripped before the computation proceeds
|
||||
#' @seealso [kurtosis()]
|
||||
#' @rdname skewness
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
|
||||
Binary file not shown.
+38
-18
@@ -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)) {
|
||||
@@ -123,7 +129,11 @@ coerce_language_setting <- function(lang) {
|
||||
}
|
||||
|
||||
# translate strings based on inst/translations.tsv
|
||||
translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE, affect_mo_name = FALSE) {
|
||||
translate_AMR <- function(from,
|
||||
language = get_locale(),
|
||||
only_unknown = FALSE,
|
||||
only_affect_ab_names = FALSE,
|
||||
only_affect_mo_names = FALSE) {
|
||||
|
||||
if (is.null(language)) {
|
||||
return(from)
|
||||
@@ -132,7 +142,7 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE, a
|
||||
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
|
||||
@@ -144,12 +154,20 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE, a
|
||||
|
||||
# only keep lines where translation is available for this language
|
||||
df_trans <- df_trans[which(!is.na(df_trans[, language, drop = TRUE])), , drop = FALSE]
|
||||
# and where the original string is not equal to the string in the target language
|
||||
df_trans <- df_trans[which(df_trans[, "pattern", drop = TRUE] != df_trans[, language, drop = TRUE]), , drop = FALSE]
|
||||
if (only_unknown == TRUE) {
|
||||
df_trans <- subset(df_trans, pattern %like% "unknown")
|
||||
}
|
||||
if (affect_mo_name == TRUE) {
|
||||
if (only_affect_ab_names == TRUE) {
|
||||
df_trans <- subset(df_trans, affect_ab_name == TRUE)
|
||||
}
|
||||
if (only_affect_mo_names == TRUE) {
|
||||
df_trans <- subset(df_trans, affect_mo_name == TRUE)
|
||||
}
|
||||
if (NROW(df_trans) == 0) {
|
||||
return(from)
|
||||
}
|
||||
|
||||
# default: case sensitive if value if 'case_sensitive' is missing:
|
||||
df_trans$case_sensitive[is.na(df_trans$case_sensitive)] <- TRUE
|
||||
@@ -157,11 +175,13 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE, a
|
||||
df_trans$regular_expr[is.na(df_trans$regular_expr)] <- FALSE
|
||||
|
||||
# check if text to look for is in one of the patterns
|
||||
any_form_in_patterns <- tryCatch(any(from_unique %like% paste0("(", paste(df_trans$pattern, collapse = "|"), ")")),
|
||||
error = function(e) {
|
||||
warning_("Translation not possible. Please open an issue on GitHub (https://github.com/msberends/AMR/issues).", call = FALSE)
|
||||
return(FALSE)
|
||||
})
|
||||
any_form_in_patterns <- tryCatch(
|
||||
any(from_unique %like% paste0("(", paste(gsub(" +\\(.*", "", df_trans$pattern), collapse = "|"), ")")),
|
||||
error = function(e) {
|
||||
warning_("Translation not possible. Please open an issue on GitHub (https://github.com/msberends/AMR/issues).", call = FALSE)
|
||||
return(FALSE)
|
||||
})
|
||||
|
||||
if (NROW(df_trans) == 0 | !any_form_in_patterns) {
|
||||
return(from)
|
||||
}
|
||||
@@ -170,7 +190,7 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE, a
|
||||
function(i) from_unique_translated <<- gsub(pattern = df_trans$pattern[i],
|
||||
replacement = df_trans[i, language, drop = TRUE],
|
||||
x = from_unique_translated,
|
||||
ignore.case = !df_trans$case_sensitive[i],
|
||||
ignore.case = !df_trans$case_sensitive[i] & df_trans$regular_expr[i],
|
||||
fixed = !df_trans$regular_expr[i],
|
||||
perl = df_trans$regular_expr[i]))
|
||||
|
||||
|
||||
@@ -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)
|
||||
}
|
||||
@@ -28,7 +28,7 @@
|
||||
#' All antimicrobial drugs and their official names, ATC codes, ATC groups and defined daily dose (DDD) are included in this package, using the WHO Collaborating Centre for Drug Statistics Methodology.
|
||||
#' @section WHOCC:
|
||||
#' \if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
|
||||
#' This package contains **all ~550 antibiotic, antimycotic and antiviral drugs** and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <https://www.whocc.no>) and the Pharmaceuticals Community Register of the European Commission (<http://ec.europa.eu/health/documents/community-register/html/atc.htm>).
|
||||
#' This package contains **all ~550 antibiotic, antimycotic and antiviral drugs** and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <https://www.whocc.no>) and the Pharmaceuticals Community Register of the European Commission (<https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm>).
|
||||
#'
|
||||
#' These have become the gold standard for international drug utilisation monitoring and research.
|
||||
#'
|
||||
|
||||
@@ -27,7 +27,18 @@
|
||||
pkg_env <- new.env(hash = FALSE)
|
||||
pkg_env$mo_failed <- character(0)
|
||||
|
||||
.onLoad <- function(libname, pkgname) {
|
||||
# determine info icon for messages
|
||||
utf8_supported <- isTRUE(base::l10n_info()$`UTF-8`)
|
||||
is_latex <- tryCatch(import_fn("is_latex_output", "knitr", error_on_fail = FALSE)(),
|
||||
error = function(e) FALSE)
|
||||
if (utf8_supported && !is_latex) {
|
||||
# \u2139 is a symbol officially named 'information source'
|
||||
pkg_env$info_icon <- "\u2139"
|
||||
} else {
|
||||
pkg_env$info_icon <- "i"
|
||||
}
|
||||
|
||||
.onLoad <- function(...) {
|
||||
# Support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
|
||||
# without the need to depend on other packages. This was suggested by the
|
||||
# developers of the vctrs package:
|
||||
@@ -45,14 +56,33 @@ pkg_env$mo_failed <- character(0)
|
||||
# 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")
|
||||
# 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({
|
||||
@@ -60,21 +90,81 @@ pkg_env$mo_failed <- character(0)
|
||||
invisible(get_mo_source())
|
||||
}
|
||||
}, silent = TRUE)
|
||||
|
||||
|
||||
# reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed
|
||||
# they cannott be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
|
||||
assign(x = "AB_lookup", value = create_AB_lookup(), envir = asNamespace("AMR"))
|
||||
assign(x = "MO_lookup", value = create_MO_lookup(), envir = asNamespace("AMR"))
|
||||
assign(x = "MO.old_lookup", value = create_MO.old_lookup(), envir = asNamespace("AMR"))
|
||||
# for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
|
||||
assign(x = "INTRINSIC_R", value = create_intr_resistance(), envir = asNamespace("AMR"))
|
||||
|
||||
# for building the website, only print first 5 rows of a data set
|
||||
# if (Sys.getenv("IN_PKGDOWN") != "" && !interactive()) {
|
||||
# ...
|
||||
# }
|
||||
}
|
||||
|
||||
.onAttach <- function(...) {
|
||||
# show notice in 10% of cases in interactive session
|
||||
if (!interactive() || stats::runif(1) > 0.1 || isTRUE(as.logical(getOption("AMR_silentstart", FALSE)))) {
|
||||
return()
|
||||
}
|
||||
packageStartupMessage(word_wrap("Thank you for using the AMR package! ",
|
||||
"If you have a minute, please anonymously fill in this short questionnaire to improve the package and its functionalities: ",
|
||||
font_blue("https://msberends.github.io/AMR/survey.html\n"),
|
||||
"[prevent his notice with ",
|
||||
font_bold("suppressPackageStartupMessages(library(AMR))"),
|
||||
" or use ",
|
||||
font_bold("options(AMR_silentstart = TRUE)"), "]"))
|
||||
# Helper functions --------------------------------------------------------
|
||||
|
||||
create_AB_lookup <- function() {
|
||||
AB_lookup <- AMR::antibiotics
|
||||
AB_lookup$generalised_name <- generalise_antibiotic_name(AB_lookup$name)
|
||||
AB_lookup$generalised_synonyms <- lapply(AB_lookup$synonyms, generalise_antibiotic_name)
|
||||
AB_lookup$generalised_abbreviations <- lapply(AB_lookup$abbreviations, generalise_antibiotic_name)
|
||||
AB_lookup$generalised_loinc <- lapply(AB_lookup$loinc, generalise_antibiotic_name)
|
||||
AB_lookup$generalised_all <- unname(lapply(as.list(as.data.frame(t(AB_lookup[,
|
||||
c("ab", "atc", "cid", "name",
|
||||
colnames(AB_lookup)[colnames(AB_lookup) %like% "generalised"]),
|
||||
drop = FALSE]),
|
||||
stringsAsFactors = FALSE)),
|
||||
function(x) {
|
||||
x <- generalise_antibiotic_name(unname(unlist(x)))
|
||||
x[x != ""]
|
||||
}))
|
||||
AB_lookup
|
||||
}
|
||||
|
||||
create_MO_lookup <- function() {
|
||||
MO_lookup <- AMR::microorganisms
|
||||
|
||||
MO_lookup$kingdom_index <- NA_real_
|
||||
MO_lookup[which(MO_lookup$kingdom == "Bacteria" | MO_lookup$mo == "UNKNOWN"), "kingdom_index"] <- 1
|
||||
MO_lookup[which(MO_lookup$kingdom == "Fungi"), "kingdom_index"] <- 2
|
||||
MO_lookup[which(MO_lookup$kingdom == "Protozoa"), "kingdom_index"] <- 3
|
||||
MO_lookup[which(MO_lookup$kingdom == "Archaea"), "kingdom_index"] <- 4
|
||||
# all the rest
|
||||
MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5
|
||||
|
||||
# use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
|
||||
MO_lookup$fullname_lower <- tolower(trimws(paste(MO_lookup$genus,
|
||||
MO_lookup$species,
|
||||
MO_lookup$subspecies)))
|
||||
ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname, perl = TRUE)
|
||||
MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname"])
|
||||
MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
|
||||
|
||||
# add a column with only "e coli" like combinations
|
||||
MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower, perl = TRUE)
|
||||
|
||||
# so arrange data on prevalence first, then kingdom, then full name
|
||||
MO_lookup[order(MO_lookup$prevalence, MO_lookup$kingdom_index, MO_lookup$fullname_lower), ]
|
||||
}
|
||||
|
||||
create_MO.old_lookup <- function() {
|
||||
MO.old_lookup <- AMR::microorganisms.old
|
||||
MO.old_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", tolower(trimws(MO.old_lookup$fullname))))
|
||||
|
||||
# add a column with only "e coli"-like combinations
|
||||
MO.old_lookup$g_species <- trimws(gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO.old_lookup$fullname_lower))
|
||||
|
||||
# so arrange data on prevalence first, then full name
|
||||
MO.old_lookup[order(MO.old_lookup$prevalence, MO.old_lookup$fullname_lower), ]
|
||||
}
|
||||
|
||||
create_intr_resistance <- function() {
|
||||
# for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
|
||||
paste(AMR::microorganisms[match(AMR::intrinsic_resistant$microorganism, AMR::microorganisms$fullname), "mo", drop = TRUE],
|
||||
AMR::antibiotics[match(AMR::intrinsic_resistant$antibiotic, AMR::antibiotics$name), "ab", drop = TRUE])
|
||||
}
|
||||
|
||||
@@ -2,19 +2,17 @@
|
||||
|
||||
# `AMR` (for R)
|
||||
|
||||
[](https://cran.r-project.org/package=AMR)
|
||||
[](https://cran.r-project.org/package=AMR)
|
||||
|
||||
|
||||
[](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.
|
||||
|
||||
@@ -25,11 +23,17 @@ This is the development source of the `AMR` package for R. Not a developer? Then
|
||||
### How to get this package
|
||||
Please see [our website](https://msberends.github.io/AMR/#get-this-package).
|
||||
|
||||
Bottom line: `install.packages("AMR")`
|
||||
You can install or update the `AMR` package from CRAN using:
|
||||
|
||||
```r
|
||||
install.packages("AMR")
|
||||
```
|
||||
|
||||
It will be downloaded and installed automatically. For RStudio, click on the menu *Tools* > *Install Packages...* and then type in "AMR" and press <kbd>Install</kbd>.
|
||||
|
||||
### 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
|
||||
|
||||
|
||||
+35
-43
@@ -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.
|
||||
@@ -143,27 +123,48 @@ reference:
|
||||
- "`as.mic`"
|
||||
- "`as.disk`"
|
||||
- "`eucast_rules`"
|
||||
- "`custom_eucast_rules`"
|
||||
|
||||
- title: "Analysing data: antimicrobial resistance"
|
||||
desc: >
|
||||
Use these function for the analysis part. You can use `susceptibility()` or `resistance()` on any antibiotic column.
|
||||
Be sure to first select the isolates that are appropiate for analysis, by using `first_isolate()` or `is_new_episode()`.
|
||||
You can also filter your data on certain resistance in certain antibiotic classes (`filter_ab_class()`), or determine multi-drug resistant microorganisms (MDRO, `mdro()`).
|
||||
You can also filter your data on certain resistance in certain antibiotic classes (`carbapenems()`, `aminoglycosides()`), or determine multi-drug resistant microorganisms (MDRO, `mdro()`).
|
||||
contents:
|
||||
- "`proportion`"
|
||||
- "`count`"
|
||||
- "`is_new_episode`"
|
||||
- "`first_isolate`"
|
||||
- "`key_antibiotics`"
|
||||
- "`key_antimicrobials`"
|
||||
- "`mdro`"
|
||||
- "`count`"
|
||||
- "`plot`"
|
||||
- "`ggplot_rsi`"
|
||||
- "`bug_drug_combinations`"
|
||||
- "`antibiotic_class_selectors`"
|
||||
- "`filter_ab_class`"
|
||||
- "`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: >
|
||||
@@ -176,6 +177,7 @@ reference:
|
||||
- "`availability`"
|
||||
- "`get_locale`"
|
||||
- "`ggplot_pca`"
|
||||
- "`italicise_taxonomy`"
|
||||
- "`join`"
|
||||
- "`like`"
|
||||
- "`mo_matching_score`"
|
||||
@@ -198,23 +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
|
||||
|
||||
|
||||
+1
-1
@@ -1 +1 @@
|
||||
* This package has a tarball size of over 7 MB and an installation size of over 5 MB, which will return a NOTE on R CMD CHECK. The package size is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package. This was written and explained in a manuscript that was accepted for publication in the Journal of Statistical Software 4 weeks ago. We will add the paper as a vignette in the next version. Please allow this exception in package size for CRAN. We already compressed all data sets using `compression = "xz"` to make them as small as possible.
|
||||
* This package now has a data folder size of ~2.8 MB (this was ~5.6 MB), which will return a NOTE on R CMD CHECK. This package size is needed to provide users reference data for the complete taxonomy of microorganisms - one of the most important features of this package, following 15 previous releases of this package. All data sets were compressed using `compression = "xz"` to make them as small as possible.
|
||||
|
||||
Binary file not shown.
Regular → Executable
+549
-545
File diff suppressed because it is too large
Load Diff
Executable
+20996
File diff suppressed because it is too large
Load Diff
Binary file not shown.
@@ -0,0 +1,82 @@
|
||||
# ==================================================================== #
|
||||
# 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/ #
|
||||
# ==================================================================== #
|
||||
|
||||
# some old R instances have trouble installing tinytest, so we ship it too
|
||||
install.packages("data-raw/tinytest_1.3.1.tar.gz", dependencies = c("Depends", "Imports", "LinkingTo"))
|
||||
install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
|
||||
|
||||
pkg_suggests <- gsub("[^a-zA-Z0-9]+", "",
|
||||
unlist(strsplit(unlist(packageDescription("AMR",
|
||||
fields = c("Suggests", "Enhances", "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$OS.type != "unix") {
|
||||
# no compiling on Windows here
|
||||
options(install.packages.compile.from.source = FALSE)
|
||||
}
|
||||
|
||||
to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())]
|
||||
if (length(to_install) == 0) {
|
||||
message("\nNothing to install\n")
|
||||
}
|
||||
for (i in seq_len(length(to_install))) {
|
||||
cat("Installing package", to_install[i], "\n")
|
||||
tryCatch(install.packages(to_install[i],
|
||||
type = "source",
|
||||
repos = "https://cran.rstudio.com/",
|
||||
dependencies = c("Depends", "Imports", "LinkingTo"),
|
||||
quiet = FALSE),
|
||||
# message = function(m) invisible(),
|
||||
warning = function(w) message(w$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)
|
||||
to_update <- to_update[which(to_update$Package %in% pkg_suggests), "Package", drop = TRUE]
|
||||
if (length(to_update) == 0) {
|
||||
message("\nNothing to update\n")
|
||||
}
|
||||
for (i in seq_len(length(to_update))) {
|
||||
cat("Updating package '", to_update[i], "' v", as.character(packageVersion(to_update[i])), "\n", sep = "")
|
||||
tryCatch(update.packages(to_update[i], repos = "https://cran.rstudio.com/", ask = FALSE),
|
||||
# message = function(m) invisible(),
|
||||
warning = function(w) message(w$message),
|
||||
error = function(e) message(e$message))
|
||||
cat("Updated to '", to_update[i], "' v", as.character(packageVersion(to_update[i])), "\n", sep = "")
|
||||
}
|
||||
+112
-124
@@ -31,8 +31,48 @@ devtools::load_all(quiet = TRUE)
|
||||
|
||||
old_globalenv <- ls(envir = globalenv())
|
||||
|
||||
# Helper functions --------------------------------------------------------
|
||||
# Save internal data to R/sysdata.rda -------------------------------------
|
||||
|
||||
# See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
|
||||
EUCAST_RULES_DF <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
|
||||
skip = 10,
|
||||
sep = "\t",
|
||||
stringsAsFactors = FALSE,
|
||||
header = TRUE,
|
||||
strip.white = TRUE,
|
||||
na = c(NA, "", NULL)) %>%
|
||||
# take the order of the reference.rule_group column in the original data file
|
||||
mutate(reference.rule_group = factor(reference.rule_group,
|
||||
levels = unique(reference.rule_group),
|
||||
ordered = TRUE),
|
||||
sorting_rule = ifelse(grepl("^Table", reference.rule, ignore.case = TRUE), 1, 2)) %>%
|
||||
arrange(reference.rule_group,
|
||||
reference.version,
|
||||
sorting_rule,
|
||||
reference.rule) %>%
|
||||
mutate(reference.rule_group = as.character(reference.rule_group)) %>%
|
||||
select(-sorting_rule)
|
||||
|
||||
# Translations
|
||||
TRANSLATIONS <- utils::read.delim(file = "data-raw/translations.tsv",
|
||||
sep = "\t",
|
||||
stringsAsFactors = FALSE,
|
||||
header = TRUE,
|
||||
blank.lines.skip = TRUE,
|
||||
fill = TRUE,
|
||||
strip.white = TRUE,
|
||||
encoding = "UTF-8",
|
||||
fileEncoding = "UTF-8",
|
||||
na.strings = c(NA, "", NULL),
|
||||
allowEscapes = TRUE, # else "\\1" will be imported as "\\\\1"
|
||||
quote = "")
|
||||
|
||||
# for checking input in `language` argument in e.g. mo_*() and ab_*() functions
|
||||
LANGUAGES_SUPPORTED <- sort(c("en", colnames(TRANSLATIONS)[nchar(colnames(TRANSLATIONS)) == 2]))
|
||||
|
||||
# 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")) {
|
||||
# Determination of which staphylococcal species are CoNS/CoPS according to:
|
||||
# - Becker et al. 2014, PMID 25278577
|
||||
@@ -55,7 +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$subspecies %in% c("schleiferi", ""))),
|
||||
"mo", drop = TRUE]
|
||||
} else if (type == "CoPS") {
|
||||
@@ -65,140 +107,86 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
|
||||
"delphini", "lutrae",
|
||||
"hyicus", "intermedius",
|
||||
"pseudintermedius", "pseudointermedius",
|
||||
"schweitzeri", "simiae")
|
||||
"schweitzeri", "simiae",
|
||||
"roterodami")
|
||||
| (MO_staph$species == "schleiferi" & MO_staph$subspecies == "coagulans")),
|
||||
"mo", drop = TRUE]
|
||||
}
|
||||
}
|
||||
|
||||
create_AB_lookup <- function() {
|
||||
AB_lookup <- AMR::antibiotics
|
||||
AB_lookup$generalised_name <- generalise_antibiotic_name(AB_lookup$name)
|
||||
AB_lookup$generalised_synonyms <- lapply(AB_lookup$synonyms, generalise_antibiotic_name)
|
||||
AB_lookup$generalised_abbreviations <- lapply(AB_lookup$abbreviations, generalise_antibiotic_name)
|
||||
AB_lookup$generalised_loinc <- lapply(AB_lookup$loinc, generalise_antibiotic_name)
|
||||
AB_lookup$generalised_all <- unname(lapply(as.list(as.data.frame(t(AB_lookup[,
|
||||
c("ab", "atc", "cid", "name",
|
||||
colnames(AB_lookup)[colnames(AB_lookup) %like% "generalised"]),
|
||||
drop = FALSE]),
|
||||
stringsAsFactors = FALSE)),
|
||||
function(x) {
|
||||
x <- generalise_antibiotic_name(unname(unlist(x)))
|
||||
x[x != ""]
|
||||
}))
|
||||
AB_lookup
|
||||
}
|
||||
|
||||
create_MO_lookup <- function() {
|
||||
MO_lookup <- AMR::microorganisms
|
||||
|
||||
MO_lookup$kingdom_index <- NA_real_
|
||||
MO_lookup[which(MO_lookup$kingdom == "Bacteria" | MO_lookup$mo == "UNKNOWN"), "kingdom_index"] <- 1
|
||||
MO_lookup[which(MO_lookup$kingdom == "Fungi"), "kingdom_index"] <- 2
|
||||
MO_lookup[which(MO_lookup$kingdom == "Protozoa"), "kingdom_index"] <- 3
|
||||
MO_lookup[which(MO_lookup$kingdom == "Archaea"), "kingdom_index"] <- 4
|
||||
# all the rest
|
||||
MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5
|
||||
|
||||
# use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
|
||||
MO_lookup$fullname_lower <- tolower(trimws(paste(MO_lookup$genus,
|
||||
MO_lookup$species,
|
||||
MO_lookup$subspecies)))
|
||||
ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname)
|
||||
MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname"])
|
||||
MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
|
||||
|
||||
# add a column with only "e coli" like combinations
|
||||
MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower, perl = TRUE)
|
||||
|
||||
# so arrange data on prevalence first, then kingdom, then full name
|
||||
MO_lookup[order(MO_lookup$prevalence, MO_lookup$kingdom_index, MO_lookup$fullname_lower), ]
|
||||
}
|
||||
|
||||
create_MO.old_lookup <- function() {
|
||||
MO.old_lookup <- AMR::microorganisms.old
|
||||
MO.old_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", tolower(trimws(MO.old_lookup$fullname))))
|
||||
|
||||
# add a column with only "e coli"-like combinations
|
||||
MO.old_lookup$g_species <- trimws(gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO.old_lookup$fullname_lower))
|
||||
|
||||
# so arrange data on prevalence first, then full name
|
||||
MO.old_lookup[order(MO.old_lookup$prevalence, MO.old_lookup$fullname_lower), ]
|
||||
}
|
||||
|
||||
create_intr_resistance <- function() {
|
||||
# for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
|
||||
paste(AMR::microorganisms[match(AMR::intrinsic_resistant$microorganism, AMR::microorganisms$fullname), "mo", drop = TRUE],
|
||||
AMR::antibiotics[match(AMR::intrinsic_resistant$antibiotic, AMR::antibiotics$name), "ab", drop = TRUE])
|
||||
}
|
||||
|
||||
|
||||
|
||||
# Save internal data sets 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",
|
||||
skip = 10,
|
||||
sep = "\t",
|
||||
stringsAsFactors = FALSE,
|
||||
header = TRUE,
|
||||
strip.white = TRUE,
|
||||
na = c(NA, "", NULL)) %>%
|
||||
# take the order of the reference.rule_group column in the original data file
|
||||
mutate(reference.rule_group = factor(reference.rule_group,
|
||||
levels = unique(reference.rule_group),
|
||||
ordered = TRUE),
|
||||
sorting_rule = ifelse(grepl("^Table", reference.rule, ignore.case = TRUE), 1, 2)) %>%
|
||||
arrange(reference.rule_group,
|
||||
reference.version,
|
||||
sorting_rule,
|
||||
reference.rule) %>%
|
||||
mutate(reference.rule_group = as.character(reference.rule_group)) %>%
|
||||
select(-sorting_rule)
|
||||
|
||||
# Translations
|
||||
translations_file <- utils::read.delim(file = "data-raw/translations.tsv",
|
||||
sep = "\t",
|
||||
stringsAsFactors = FALSE,
|
||||
header = TRUE,
|
||||
blank.lines.skip = TRUE,
|
||||
fill = TRUE,
|
||||
strip.white = TRUE,
|
||||
encoding = "UTF-8",
|
||||
fileEncoding = "UTF-8",
|
||||
na.strings = c(NA, "", NULL),
|
||||
allowEscapes = TRUE, # else "\\1" will be imported as "\\\\1"
|
||||
quote = "")
|
||||
|
||||
# Old microorganism codes
|
||||
microorganisms.translation <- readRDS("data-raw/microorganisms.translation.rds")
|
||||
|
||||
# for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
|
||||
INTRINSIC_R <- create_intr_resistance()
|
||||
|
||||
# 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]))
|
||||
|
||||
# vectors of CoNS and CoPS, improves speed in as.mo()
|
||||
MO_CONS <- create_species_cons_cops("CoNS")
|
||||
MO_COPS <- create_species_cons_cops("CoPS")
|
||||
|
||||
# reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed
|
||||
AB_lookup <- create_AB_lookup()
|
||||
MO_lookup <- create_MO_lookup()
|
||||
MO.old_lookup <- create_MO.old_lookup()
|
||||
# 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")
|
||||
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,
|
||||
microorganisms.translation,
|
||||
INTRINSIC_R,
|
||||
usethis::use_data(EUCAST_RULES_DF,
|
||||
TRANSLATIONS,
|
||||
LANGUAGES_SUPPORTED,
|
||||
# EXAMPLE_ISOLATES,
|
||||
MO_CONS,
|
||||
MO_COPS,
|
||||
AB_lookup,
|
||||
MO_lookup,
|
||||
MO.old_lookup,
|
||||
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,
|
||||
version = 2,
|
||||
|
||||
+1
-1
@@ -1 +1 @@
|
||||
77f6cca42687a0e3b1b1045a2d70b226
|
||||
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\", \"fluo\")" "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(\"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\", \"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\")" "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\", \"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" "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(\"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(\"\", \"kahl\")" "" ""
|
||||
"KAC" "Kanamycin/cephalexin" "Aminoglycosides" "" "" ""
|
||||
"KET" "J02AB02" 456201 "Ketoconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Imidazole derivatives" "keto" "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\", \"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(\"\", \"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\", \"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(\"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\", \"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\", \"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" "vori" "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.
+156
-38
@@ -1,20 +1,20 @@
|
||||
# -------------------------------------------------------------------------------------------------------------------------------
|
||||
# For editing this EUCAST reference file, these values can all be used for targeting antibiotics:
|
||||
# 'all_betalactams', 'aminoglycosides', 'aminopenicillins', 'carbapenems', 'cephalosporins', 'cephalosporins_1st', 'cephalosporins_2nd', 'cephalosporins_3rd', 'cephalosporins_except_CAZ',
|
||||
# 'fluoroquinolones', 'glycopeptides', 'lincosamides', 'lipoglycopeptides', 'macrolides', 'oxazolidinones', 'polymyxins', 'streptogramins', 'tetracyclines', 'ureidopenicillins',
|
||||
# 'betalactams', 'aminoglycosides', 'aminopenicillins', 'carbapenems', 'cephalosporins', 'cephalosporins_1st', 'cephalosporins_2nd', 'cephalosporins_3rd', 'cephalosporins_except_CAZ',
|
||||
# 'fluoroquinolones', 'glycopeptides', 'glycopeptides_except_lipo', 'lincosamides', 'lipoglycopeptides', 'macrolides', 'oxazolidinones', 'polymyxins', 'streptogramins', 'tetracyclines', 'tetracyclines_except_TGC', 'ureidopenicillins',
|
||||
# and all separate EARS-Net letter codes like 'AMC'. They can be separated by comma: 'AMC, fluoroquinolones'.
|
||||
# The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
|
||||
# The 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
|
||||
order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 10
|
||||
genus is Staphylococcus PEN, FOX S AMP, AMX, PIP, TIC S Staphylococcus Breakpoints 10
|
||||
genus is Staphylococcus PEN, FOX R, S OXA, FLC S Staphylococcus Breakpoints 10
|
||||
genus is Staphylococcus FOX R all_betalactams R Staphylococcus Breakpoints 10
|
||||
genus is Staphylococcus FOX R betalactams R Staphylococcus Breakpoints 10
|
||||
genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 10
|
||||
genus is Staphylococcus FOX S carbapenems, cephalosporins_except_CAZ S Staphylococcus Breakpoints 10
|
||||
genus is Staphylococcus FOX I carbapenems, cephalosporins_except_CAZ I Staphylococcus Breakpoints 10
|
||||
@@ -120,7 +120,7 @@ order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 11
|
||||
order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 11
|
||||
genus is Staphylococcus PEN, FOX S AMP, AMX, PIP, TIC S Staphylococcus Breakpoints 11
|
||||
genus is Staphylococcus PEN, FOX R, S OXA, FLC S Staphylococcus Breakpoints 11
|
||||
genus is Staphylococcus FOX R all_betalactams R Staphylococcus Breakpoints 11
|
||||
genus is Staphylococcus FOX R betalactams R Staphylococcus Breakpoints 11
|
||||
genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 11
|
||||
genus is Staphylococcus FOX S carbapenems, cephalosporins_except_CAZ S Staphylococcus Breakpoints 11
|
||||
genus is Staphylococcus FOX I carbapenems, cephalosporins_except_CAZ I Staphylococcus Breakpoints 11
|
||||
@@ -224,7 +224,7 @@ genus_species is Burkholderia pseudomallei TCY R DOX R Burkholderia pseudomallei
|
||||
genus is Bacillus NOR S fluoroquinolones S Bacillus Breakpoints 11 added in 11
|
||||
genus is Bacillus NOR I fluoroquinolones I Bacillus Breakpoints 11 added in 11
|
||||
genus is Bacillus NOR R fluoroquinolones R Bacillus Breakpoints 11 added in 11
|
||||
order is Enterobacterales PEN, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
order is Enterobacterales PEN, glycopeptides_except_lipo, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Enterobacter cloacae aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
@@ -232,17 +232,17 @@ genus_species is Klebsiella aerogenes aminopenicillins, AMC, CZO, FOX R Table
|
||||
genus_species is Escherichia hermannii aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Hafnia alvei aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus is Klebsiella aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Morganella morganii aminopenicillins, AMC, CZO, tetracyclines, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Proteus mirabilis tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Proteus penneri aminopenicillins, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Proteus vulgaris aminopenicillins, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Providencia rettgeri aminopenicillins, AMC, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Providencia stuartii aminopenicillins, AMC, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Morganella morganii aminopenicillins, AMC, CZO, DOX, MNO, TCY, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Proteus mirabilis DOX, MNO, TCY, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Proteus penneri aminopenicillins, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Proteus vulgaris aminopenicillins, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Providencia rettgeri aminopenicillins, AMC, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Providencia stuartii aminopenicillins, AMC, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus is Raoultella aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Serratia marcescens aminopenicillins, AMC, CZO, FOX, CXM, DOX, TCY, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Yersinia enterocolitica aminopenicillins, AMC, TIC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Yersinia pseudotuberculosis PLB, COL R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, FOX, CXM, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, FOX, CXM, glycopeptides_except_lipo, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
genus_species is Acinetobacter baumannii aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
genus_species is Acinetobacter pittii aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
genus_species is Acinetobacter nosocomialis aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
@@ -250,10 +250,10 @@ genus_species is Acinetobacter calcoaceticus aminopenicillins, AMC, CZO, CTX,
|
||||
genus_species is Achromobacter xylosoxidans aminopenicillins, CZO, CTX, CRO, ETP R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
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, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, TIC, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
genus_species is Ochrobactrum anthropi aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, CZO, CTX, CRO, ETP, CHL, KAN, NEO, TMP, SXT, tetracyclines, TGC R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
genus_species is Brucella anthropi aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, CZO, CTX, CRO, ETP, CHL, KAN, NEO, TMP, SXT, DOX, MNO, TCY, TGC R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
genus_species is Stenotrophomonas maltophilia aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
genus one_of Haemophilus, Moraxella, Neisseria, Campylobacter glycopeptides, LIN, DAP, LNZ R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
|
||||
genus one_of Haemophilus, Moraxella, Neisseria, Campylobacter glycopeptides_except_lipo, LIN, DAP, LNZ R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
|
||||
genus_species is Haemophilus influenzae FUS, streptogramins R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
|
||||
genus_species is Moraxella catarrhalis TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
|
||||
genus is Neisseria TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
|
||||
@@ -279,8 +279,8 @@ genus_species is Enterococcus casseliflavus FUS, CAZ, cephalosporins_except_CA
|
||||
genus_species is Enterococcus faecium FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
|
||||
genus is Corynebacterium FOS R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
|
||||
genus_species is Listeria monocytogenes cephalosporins R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
|
||||
genus one_of Leuconostoc, Pediococcus glycopeptides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
|
||||
genus is Lactobacillus glycopeptides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
|
||||
genus one_of Leuconostoc, Pediococcus glycopeptides_except_lipo R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
|
||||
genus is Lactobacillus glycopeptides_except_lipo R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
|
||||
genus_species is Clostridium ramosum VAN R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
|
||||
genus_species is Clostridium innocuum VAN R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
|
||||
genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN S aminopenicillins, cephalosporins_except_CAZ, carbapenems S Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules 3.1
|
||||
@@ -298,23 +298,23 @@ genus is Staphylococcus MFX R fluoroquinolones R Table 13: Interpretive rules fo
|
||||
genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules 3.1
|
||||
order is Enterobacterales CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules 3.1
|
||||
genus_species is Neisseria gonorrhoeae CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules 3.1
|
||||
order is Enterobacterales PEN, glycopeptides, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
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 3.2
|
||||
fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
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
|
||||
genus_species is Leclercia adecarboxylata FOS R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Morganella morganii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
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 3.2
|
||||
genus_species is Plesiomonas shigelloides aminopenicillins, AMC, SAM R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Proteus mirabilis tetracyclines, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Proteus penneri aminopenicillins, CZO, CEP, LEX, CFR, CXM, tetracyclines, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Proteus vulgaris aminopenicillins, CZO, CEP, LEX, CFR, CXM, tetracyclines, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Providencia rettgeri aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Providencia stuartii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Proteus mirabilis DOX, MNO, TCY, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
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 3.2
|
||||
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 3.2
|
||||
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 3.2
|
||||
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 3.2
|
||||
genus is Raoultella aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
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 3.2
|
||||
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 3.2
|
||||
@@ -324,20 +324,20 @@ genus_species is Aeromonas veronii aminopenicillins, AMC, SAM, FOX R Table 1:
|
||||
genus_species is Aeromonas dhakensis aminopenicillins, AMC, SAM, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Aeromonas caviae aminopenicillins, AMC, SAM, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Aeromonas jandaei aminopenicillins, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, cephalosporins_1st, cephalosporins_2nd, glycopeptides, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
|
||||
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 3.2
|
||||
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 3.2 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 3.2 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus_species is Achromobacter xylosoxidans aminopenicillins, CRO, CTX, ETP R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 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 3.2 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, SAM, TIC, TCC, PIP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus_species is Ochrobactrum 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 3.2 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, tetracyclines, TGC R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 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 3.2 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 3.2 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 3.2 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus_species is Haemophilus influenzae FUS, streptogramins, glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
|
||||
genus_species is Moraxella catarrhalis TMP, glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
|
||||
genus is Neisseria TMP, glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
|
||||
genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL, glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
|
||||
fullname like ^Campylobacter (jejuni|coli) FUS, streptogramins, TMP, glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
|
||||
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 3.2
|
||||
genus_species is Moraxella catarrhalis TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
|
||||
genus is Neisseria TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
|
||||
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 3.2
|
||||
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 3.2
|
||||
gramstain is Gram-positive ATM, TEM, polymyxins, NAL R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
|
||||
genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
|
||||
genus_species is Staphylococcus cohnii CAZ, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
|
||||
@@ -367,13 +367,13 @@ 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
|
||||
genus is Salmonella PEF R CIP R Expert Rules on Salmonella Expert Rules 3.2
|
||||
genus_species is Staphylococcus aureus FOX1 R all_betalactams R Expert Rules on Staphylococcus Expert Rules 3.2
|
||||
genus_species is Staphylococcus aureus FOX1 S all_betalactams S Expert Rules on Staphylococcus Expert Rules 3.2
|
||||
genus_species is Staphylococcus aureus FOX1 R betalactams R Expert Rules on Staphylococcus Expert Rules 3.2
|
||||
genus_species is Staphylococcus aureus FOX1 S betalactams S Expert Rules on Staphylococcus Expert Rules 3.2
|
||||
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 3.2 all penicillins without beta-lactamse inhibitor
|
||||
genus is Staphylococcus ERY, CLI S macrolides, lincosamides S Expert Rules on Staphylococcus Expert Rules 3.2
|
||||
genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Expert Rules on Staphylococcus Expert Rules 3.2
|
||||
@@ -400,7 +400,7 @@ genus_species is Streptococcus pneumoniae TCY S DOX, MNO S Expert Rules on Strep
|
||||
genus_species is Streptococcus pneumoniae TCY R DOX, MNO R Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
|
||||
genus_species is Streptococcus pneumoniae VAN S lipoglycopeptides S Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
|
||||
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 3.2
|
||||
genus_species is Haemophilus influenzae PEN S all_betalactams S Expert Rules on Haemophilus influenzae Expert Rules 3.2
|
||||
genus_species is Haemophilus influenzae PEN S betalactams S Expert Rules on Haemophilus influenzae Expert Rules 3.2
|
||||
genus_species is Haemophilus influenzae NAL S fluoroquinolones S Expert Rules on Haemophilus influenzae Expert Rules 3.2
|
||||
genus_species is Haemophilus influenzae NAL R CIP, LVX, MFX R Expert Rules on Haemophilus influenzae Expert Rules 3.2
|
||||
genus_species is Haemophilus influenzae TCY S DOX, MNO S Expert Rules on Haemophilus influenzae 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
|
||||
|
||||
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+622
-622
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Load Diff
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@@ -1 +1 @@
|
||||
8338ff5f079f4519fa3c44f8c5bace64
|
||||
ee4434541c7b6529b391d2684748e28b
|
||||
|
||||
Binary file not shown.
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+417
-179
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+70753
-70019
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Load Diff
+1
-1
@@ -1 +1 @@
|
||||
82bd6236cf159569f6f5c99f48f92d86
|
||||
638a06636d8b547c2cb9d1ec243ecb7e
|
||||
|
||||
+21
-3
@@ -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)))
|
||||
}
|
||||
@@ -136,8 +136,8 @@ read_EUCAST <- function(sheet, file, guideline_name) {
|
||||
disk_R = ifelse(has_zone_diameters, G, NA_character_)) %>%
|
||||
filter(!is.na(drug),
|
||||
!(is.na(MIC_S) & is.na(MIC_R) & is.na(disk_S) & is.na(disk_R)),
|
||||
!MIC_S %like% "(MIC|S ≤|note)",
|
||||
!MIC_S %like% "^[-]",
|
||||
MIC_S %unlike% "(MIC|S ≤|note)",
|
||||
MIC_S %unlike% "^[-]",
|
||||
drug != MIC_S,) %>%
|
||||
mutate(administration = case_when(drug %like% "[( ]oral" ~ "oral",
|
||||
drug %like% "[( ]iv" ~ "iv",
|
||||
@@ -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)
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user