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AMR
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(v1.2.0.9026) move to github

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dr. M.S. (Matthijs) Berends 2020-07-08 14:48:06 +02:00
parent 2134fc76e2
commit 76fc8e1b14
211 changed files with 1090 additions and 1748 deletions
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1
.Rbuildignore
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@ -12,6 +12,7 @@
^codecov\.yml$
^cran-comments\.md$
^CRAN-RELEASE$
^\.github$
^doc$
^docs$
^git_.*\.sh$

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.github/workflows/R-CMD-check.yaml vendored Normal file
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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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 more info: https://msberends.github.io/AMR. #
# ==================================================================== #
on:
push:
branches:
- premaster
- master
pull_request:
branches:
- master
name: R-CMD-check
jobs:
R-CMD-check:
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
strategy:
fail-fast: false
matrix:
config:
- {os: windows-latest, r: 'release'}
- {os: macOS-latest, r: 'release'}
- {os: ubuntu-16.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: windows-latest, r: 'oldrel'}
- {os: macOS-latest, r: 'oldrel'}
- {os: ubuntu-16.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: windows-latest, r: 'devel'}
- {os: macOS-latest, r: 'devel'}
- {os: ubuntu-16.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
# - {os: windows-latest, r: '3.6'}
# - {os: ubuntu-16.04, r: '3.5', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
# - {os: ubuntu-16.04, r: '3.4', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
# - {os: ubuntu-16.04, r: '3.3', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }}
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- uses: actions/checkout@v2
- uses: r-lib/actions/setup-r@master
with:
r-version: ${{ matrix.config.r }}
- uses: r-lib/actions/setup-pandoc@master
- name: Query dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
shell: Rscript {0}
- name: Cache R packages
if: runner.os != 'Windows'
uses: actions/cache@v1
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-
- name: Install system dependencies
if: runner.os == 'Linux'
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 dependencies
run: |
remotes::install_deps(dependencies = TRUE)
remotes::install_cran("rcmdcheck")
shell: Rscript {0}
- name: Session info
run: |
options(width = 100)
pkgs <- installed.packages()[, "Package"]
sessioninfo::session_info(pkgs, include_base = TRUE)
shell: Rscript {0}
- name: Check
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: Show testthat output
if: always()
run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
shell: bash
- name: Upload check results
if: failure()
uses: actions/upload-artifact@master
with:
name: ${{ runner.os }}-r${{ matrix.config.r }}-results
path: check

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.github/workflows/codecovr.yaml vendored Normal file
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@ -0,0 +1,68 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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 more info: https://msberends.github.io/AMR. #
# ==================================================================== #
on:
push:
branches:
- premaster
- master
pull_request:
branches:
- master
name: test-coverage
jobs:
test-coverage:
runs-on: macOS-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- uses: actions/checkout@v2
- uses: r-lib/actions/setup-r@master
- uses: r-lib/actions/setup-pandoc@master
- name: Query dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
shell: Rscript {0}
- name: Cache R packages
uses: actions/cache@v1
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-
- name: Install dependencies
run: |
install.packages(c("remotes"))
remotes::install_deps(dependencies = TRUE)
remotes::install_cran("covr")
shell: Rscript {0}
- name: Test coverage
run: covr::codecov()
shell: Rscript {0}

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.github/workflows/lintr.yaml vendored Normal file
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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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 more info: https://msberends.github.io/AMR. #
# ==================================================================== #
on:
push:
branches:
- premaster
- master
pull_request:
branches:
- master
name: lint
jobs:
lint:
runs-on: macOS-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- uses: actions/checkout@v2
- uses: r-lib/actions/setup-r@master
- name: Query dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
shell: Rscript {0}
- name: Cache R packages
uses: actions/cache@v1
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-
- name: Install dependencies
run: |
install.packages(c("remotes"))
remotes::install_deps(dependencies = TRUE)
remotes::install_cran("lintr")
shell: Rscript {0}
- name: Lint
run: lintr::lint_package()
shell: Rscript {0}

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.gitlab-ci.R
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@ -1,54 +0,0 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
install_if_needed <- function(pkg, repos, quiet) {
package_path <- find.package(pkg, quiet = quiet)
if (length(package_path) == 0) {
message("NOTE: pkg ", pkg, " missing, installing...")
install.packages(pkg, repos = repos, quiet = quiet)
}
}
gl_update_pkg_all <- function(repos = "https://cran.rstudio.com",
quiet = TRUE,
install_pkgdown = FALSE,
install_lintr = FALSE) {
# update existing
update.packages(ask = FALSE, repos = repos, quiet = quiet)
install_if_needed(pkg = "devtools", repos = repos, quiet = quiet)
if (install_pkgdown == TRUE) {
install_if_needed(pkg = "pkgdown", repos = repos, quiet = quiet)
}
if (install_lintr == TRUE) {
install_if_needed(pkg = "lintr", repos = repos, quiet = quiet)
}
install_if_needed(pkg = "cleaner", repos = repos, quiet = quiet)
devtools::install_dev_deps(repos = repos, quiet = quiet, upgrade = TRUE)
cat("INSTALLED:\n")
instld <- as.data.frame(installed.packages())
rownames(instld) <- NULL
print(instld[, c("Package", "Version")])
return(invisible(TRUE))
}

190
.gitlab-ci.yml
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@ -1,190 +0,0 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
# to do a full CRAN check with R-Hub:
# chck <- rhub::check(devtools::build(), platform = rhub::platforms()[!is.na(rhub::platforms()$`cran-name`), 'name'])
stages:
- test
- check
- lint
- website
- coverage
image: rocker/r-base
before_script:
- apt-get update -qq --allow-releaseinfo-change
# install dependencies for packages
- apt-get install -y wget locales libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev > /dev/null
# recent pandoc
- wget --quiet https://github.com/jgm/pandoc/releases/download/2.9.2.1/pandoc-2.9.2.1-1-amd64.deb
- dpkg -i pandoc*.deb
- rm pandoc*.deb
# set R system language
- echo "LC_ALL=en_US.UTF-8" >> /etc/environment
- echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
- echo "LANG=en_US.UTF-8" > /etc/locale.conf
- locale-gen
# cache R packages
- mkdir -p installed_deps
- echo 'R_LIBS="installed_deps"' > .Renviron
- echo 'R_LIBS_USER="installed_deps"' >> .Renviron
- echo 'R_LIBS_SITE="installed_deps"' >> .Renviron
# set language
- echo 'LANGUAGE="en_US.utf8"' >> .Renviron
- echo 'LANG="en_US.utf8"' >> .Renviron
- echo 'LANGUAGE="en_US.utf8"' > ~/.Renviron
# ---- TEST
R-release_test:
stage: test
when: always
allow_failure: false
script:
- Rscript -e 'sessionInfo()'
# install missing and outdated packages
- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE, install_lintr = TRUE)'
- Rscript -e 'devtools::test(stop_on_failure = FALSE)'
cache:
key: release
paths:
- installed_deps/
R-devel_test:
stage: test
when: always
image: rocker/r-devel
allow_failure: false
script:
- Rscriptdevel -e 'sessionInfo()'
# install missing and outdated packages
- Rscriptdevel -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE, install_lintr = TRUE)'
- Rscriptdevel -e 'devtools::test(stop_on_failure = FALSE)'
cache:
key: devel
paths:
- installed_deps/
# ---- CHECK
R-release:
stage: check
when: on_success
allow_failure: true
script:
- Rscript -e 'sessionInfo()'
# install missing and outdated packages
- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE, install_lintr = TRUE)'
# remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
- rm -rf vignettes
- Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'
# build package
- R CMD build . --no-build-vignettes --no-manual
- PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
- Rscript -e 'Sys.setenv(NOT_CRAN = "true")'
- R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran
artifacts:
when: always
paths:
- '*.Rcheck/*'
expire_in: '1 month'
cache:
key: release
paths:
- installed_deps/
R-devel:
stage: check
when: on_success
image: rocker/r-devel
allow_failure: true
script:
- Rscriptdevel -e 'sessionInfo()'
# install missing and outdated packages
- Rscriptdevel -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE)'
# remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
- rm -rf vignettes
- Rscriptdevel -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'
# build package
- Rdevel CMD build . --no-build-vignettes --no-manual
- PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
- Rscript -e 'Sys.setenv(NOT_CRAN = "true")'
- Rdevel CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran
artifacts:
when: always
paths:
- '*.Rcheck/*'
expire_in: '1 month'
cache:
key: devel
paths:
- installed_deps/
# ---- OTHER
lintr:
stage: lint
allow_failure: true
when: always
only:
- premaster
- master
script:
# check all syntax with lintr
- Rscript -e 'lintr::lint_package(exclusions = list("R/aa_helper_functions_dplyr.R"))'
cache:
key: release
paths:
- installed_deps/
policy: pull # no uploading after run
pages:
stage: website
allow_failure: true
when: always
only:
- master
script:
- mv docs public
artifacts:
paths:
- public
codecovr:
stage: coverage
allow_failure: true
when: always
only:
- premaster
- master
script:
- apt-get install --yes git
# codecov token is set in https://gitlab.com/msberends/AMR/settings/ci_cd
# Sys.setenv(NOT_CRAN = 'true'), because otherwise skip_on_cran() will be applied on Covr too, resulting in extremely low coverage percentages
- Rscript -e "Sys.setenv(NOT_CRAN = 'true'); cc <- covr::package_coverage(line_exclusions = list('R/atc_online.R', 'R/mo_history.R', 'R/mo_source.R', 'R/resistance_predict.R')); covr::codecov(coverage = cc, token = '$codecov'); cat('Code coverage:', covr::percent_coverage(cc))"
coverage: '/Code coverage: \d+\.\d+/'
cache:
key: release
paths:
- installed_deps/
policy: pull # no uploading after run

10
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.2.0.9025
Date: 2020-07-03
Version: 1.2.0.9026
Date: 2020-07-08
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),
@ -47,10 +47,10 @@ Suggests:
tidyr,
utils
VignetteBuilder: knitr,rmarkdown
URL: https://msberends.gitlab.io/AMR, https://gitlab.com/msberends/AMR
BugReports: https://gitlab.com/msberends/AMR/issues
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: 7.1.0
RoxygenNote: 7.1.1
Roxygen: list(markdown = TRUE)

6
NEWS.md
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@ -1,5 +1,5 @@
# AMR 1.2.0.9025
## <small>Last updated: 03-Jul-2020</small>
# AMR 1.2.0.9026
## <small>Last updated: 08-Jul-2020</small>
### New
* Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally
@ -22,7 +22,7 @@
* Improvements for `susceptibility()` and `resistance()` and all `count_*()`, `proportion_*()` functions:
* 95% speed improvement (!) by using other base R functions for calculation
* Using unexisting columns wil now return an error instead of dropping them silently
* Using variables for column names (as well as `dplyr::all_of()`) now works again
* Using variables for column names (as well as selectors like `dplyr::all_of()`) now works again
* Improvements for `as.ab()`:
* Dramatic improvement of the algorithm behind `as.ab()`, making many more input errors translatable, such as digitalised health care records, using too few or too many vowels or consonants and many more
* Added progress bar

22
R/aa_helper_functions.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
# functions from dplyr, will perhaps become poorman
@ -77,18 +77,22 @@ check_dataset_integrity <- function() {
"class", "order", "family", "genus",
"species", "subspecies", "rank",
"species_id", "source", "ref", "prevalence") %in% colnames(microorganisms),
na.rm = TRUE) & NROW(microorganisms) == NROW(MO_lookup)
na.rm = TRUE)
check_antibiotics <- all(c("ab", "atc", "cid", "name", "group",
"atc_group1", "atc_group2", "abbreviations",
"synonyms", "oral_ddd", "oral_units",
"iv_ddd", "iv_units", "loinc") %in% colnames(antibiotics),
na.rm = TRUE)
}, error = function(e)
stop('Please use the command \'library("AMR")\' before using this function, to load the required reference data.', call. = FALSE)
stop_('please use the command \'library("AMR")\' before using this function, to load the required reference data.', call = FALSE)
)
if (!check_microorganisms | !check_antibiotics) {
stop("Data set `microorganisms` or data set `antibiotics` is overwritten by your global environment and prevents the AMR package from working correctly. Please rename your object before using this function.", call. = FALSE)
}
data_in_pkg <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item"]
data_in_globalenv <- ls(envir = globalenv())
overwritten <- data_in_pkg[data_in_pkg %in% data_in_globalenv]
stop_if(length(overwritten) > 0,
"the following data set is overwritten by your global environment and prevents the AMR package from working correctly:\n",
paste0("'", overwritten, "'", collapse = ", "),
".\nPlease rename your object before using this function.", call = FALSE)
invisible(TRUE)
}
@ -198,7 +202,9 @@ stop_ifnot_installed <- function(package) {
import_fn <- function(name, pkg) {
stop_ifnot_installed(pkg)
get(name, envir = asNamespace(pkg))
tryCatch(
get(name, envir = asNamespace(pkg)),
error = function(e) stop_("an error occurred in import_fn() while using this function", call = FALSE))
}
stop_ <- function(..., call = TRUE) {

4
R/aa_helper_functions_dplyr.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
# ------------------------------------------------

4
R/ab.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Transform to antibiotic ID

4
R/ab_class_selectors.R
View File

@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Antibiotic class selectors

4
R/ab_from_text.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Retrieve antimicrobial drug names and doses from clinical text

4
R/ab_property.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Property of an antibiotic

4
R/age.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Age in years of individuals

8
R/amr.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' The `AMR` Package
@ -45,7 +45,7 @@
#' - Principal component analysis for AMR
#' @section Read more on our website!:
#' On our website <https://msberends.gitlab.io/AMR> you can find [a comprehensive tutorial](https://msberends.gitlab.io/AMR/articles/AMR.html) about how to conduct AMR analysis, the [complete documentation of all functions](https://msberends.gitlab.io/AMR/reference) (which reads a lot easier than here in R) and [an example analysis using WHONET data](https://msberends.gitlab.io/AMR/articles/WHONET.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 analysis, the [complete documentation of all functions](https://msberends.github.io/AMR/reference) (which reads a lot easier than here in R) 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:
#'
@ -59,7 +59,7 @@
#' The Netherlands
#'
#' If you have found a bug, please file a new issue at: \cr
#' <https://gitlab.com/msberends/AMR/issues>
#' <https://github.com/msberends/AMR/issues>
#' @name AMR
#' @rdname AMR
NULL

4
R/atc_online.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Get ATC properties from WHOCC website

4
R/availability.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Check availability of columns

4
R/bug_drug_combinations.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Determine bug-drug combinations

6
R/catalogue_of_life.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' The Catalogue of Life
@ -38,7 +38,7 @@
#'
#' 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://gitlab.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/master/data-raw/reproduction_of_microorganisms.R>.
#' @inheritSection AMR Read more on our website!
#' @name catalogue_of_life
#' @rdname catalogue_of_life

4
R/count.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Count available isolates

20
R/data.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Data sets with `r format(nrow(antibiotics) + nrow(antivirals), big.mark = ",")` antimicrobials
@ -56,13 +56,13 @@
#' ### Direct download
#' These data sets are available as 'flat files' for use even without R - you can find the files here:
#'
#' * <https://gitlab.com/msberends/AMR/raw/master/data-raw/antibiotics.txt>
#' * <https://gitlab.com/msberends/AMR/raw/master/data-raw/antivirals.txt>
#' * <https://github.com/msberends/AMR/raw/master/data-raw/antibiotics.txt>
#' * <https://github.com/msberends/AMR/raw/master/data-raw/antivirals.txt>
#'
#' Files in R format (with preserved data structure) can be found here:
#'
#' * <https://gitlab.com/msberends/AMR/raw/master/data/antibiotics.rda>
#' * <https://gitlab.com/msberends/AMR/raw/master/data/antivirals.rda>
#' * <https://github.com/msberends/AMR/raw/master/data/antibiotics.rda>
#' * <https://github.com/msberends/AMR/raw/master/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>
@ -102,11 +102,11 @@
#' ### Direct download
#' This data set is available as 'flat file' for use even without R - you can find the file here:
#'
#' * <https://gitlab.com/msberends/AMR/raw/master/data-raw/microorganisms.txt>
#' * <https://github.com/msberends/AMR/raw/master/data-raw/microorganisms.txt>
#'
#' The file in R format (with preserved data structure) can be found here:
#'
#' * <https://gitlab.com/msberends/AMR/raw/master/data/microorganisms.rda>
#' * <https://github.com/msberends/AMR/raw/master/data/microorganisms.rda>
#' @section About the records from DSMZ (see source):
#' Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists.
#'
@ -157,7 +157,7 @@ catalogue_of_life <- list(
#' Data set with `r format(nrow(example_isolates), big.mark = ",")` example isolates
#'
#' A data set containing `r format(nrow(example_isolates), big.mark = ",")` microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read [the tutorial on our website](https://msberends.gitlab.io/AMR/articles/AMR.html).
#' A data set containing `r format(nrow(example_isolates), big.mark = ",")` microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read [the tutorial on our website](https://msberends.github.io/AMR/articles/AMR.html).
#' @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
@ -231,6 +231,6 @@ catalogue_of_life <- list(
#' - `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://gitlab.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. This 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/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. This file is updated automatically.
#' @inheritSection AMR Read more on our website!
"rsi_translation"

4
R/deprecated.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Deprecated functions

4
R/disk.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Class 'disk'

6
R/eucast_rules.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
# global variables
@ -52,7 +52,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
#'
#' These rules are not applied at default, since they are not approved by EUCAST. To use these rules, please use `eucast_rules(..., rules = "all")`, or set the default behaviour of the `[eucast_rules()]` function with `options(AMR.eucast_rules = "all")` (or any other valid input value(s) to the `rules` parameter).
#'
#' The file containing all EUCAST rules is located here: <https://gitlab.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/master/data-raw/eucast_rules.tsv>.
#'
#' @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.

4
R/filter_ab_class.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Filter isolates on result in antimicrobial class

4
R/first_isolate.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Determine first (weighted) isolates

4
R/g.test.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' *G*-test for Count Data

4
R/ggplot_pca.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' PCA biplot with `ggplot2`

12
R/ggplot_rsi.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,12 +16,12 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' AMR plots with `ggplot2`
#'
#' Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal [ggplot2][ggplot2::ggplot()] functions.
#' Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on [ggplot2][ggplot2::ggplot()] functions.
#' @inheritSection lifecycle Maturing lifecycle
#' @param data a [`data.frame`] with column(s) of class [`rsi`] (see [as.rsi()])
#' @param position position adjustment of bars, either `"fill"`, `"stack"` or `"dodge"`
@ -49,13 +49,13 @@
#'
#' [facet_rsi()] creates 2d plots (at default based on S/I/R) using [ggplot2::facet_wrap()].
#'
#' [scale_y_percent()] transforms the y axis to a 0 to 100% range using [ggplot2::scale_continuous()].
#' [scale_y_percent()] transforms the y axis to a 0 to 100% range using [ggplot2::scale_y_continuous()].
#'
#' [scale_rsi_colours()] sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using [ggplot2::scale_brewer()].
#' [scale_rsi_colours()] sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using [ggplot2::scale_fill_manual()].
#'
#' [theme_rsi()] is a [ggplot2 theme][[ggplot2::theme()] with minimal distraction.
#'
#' [labels_rsi_count()] print datalabels on the bars with percentage and amount of isolates using [ggplot2::geom_text()]
#' [labels_rsi_count()] print datalabels on the bars with percentage and amount of isolates using [ggplot2::geom_text()].
#'
#' [ggplot_rsi()] is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (`%>%`). See Examples.
#' @rdname ggplot_rsi

4
R/globals.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
globalVariables(c(".",

4
R/guess_ab_col.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Guess antibiotic column

4
R/join_microorganisms.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Join [microorganisms] to a data set

4
R/key_antibiotics.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Key antibiotics for first *weighted* isolates

4
R/kurtosis.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Kurtosis of the sample

6
R/lifecycle.R
View File

@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
###############
@ -35,7 +35,7 @@
#' The [lifecycle][AMR::lifecycle] of this function is **experimental**. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this `AMR` package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
#' @section Maturing lifecycle:
#' \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
#' The [lifecycle][AMR::lifecycle] of this function is **maturing**. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome [to suggest changes at our repository](https://gitlab.com/msberends/AMR/-/issues) or [write us an email (see section 'Contact Us')][AMR::AMR].
#' The [lifecycle][AMR::lifecycle] of this function is **maturing**. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome [to suggest changes at our repository](https://github.com/msberends/AMR/issues) or [write us an email (see section 'Contact Us')][AMR::AMR].
#' @section Stable lifecycle:
#' \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.

4
R/like.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Pattern Matching

6
R/mdro.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Determine multidrug-resistant organisms (MDRO)
@ -46,7 +46,7 @@
#' - `guideline = "BRMO"`\cr
#' The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)" ([link](https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH))
#'
#' Please suggest your own (country-specific) guidelines by letting us know: <https://gitlab.com/msberends/AMR/issues/new>.
#' Please suggest your own (country-specific) guidelines by letting us know: <https://github.com/msberends/AMR/issues/new>.
#'
#' **Note:** Every test that involves the Enterobacteriaceae family, will internally be performed using its newly named order Enterobacterales, since the Enterobacteriaceae family has been taxonomically reclassified by Adeolu *et al.* in 2016. Before that, Enterobacteriaceae was the only family under the Enterobacteriales (with an i) order. All species under the old Enterobacteriaceae family are still under the new Enterobacterales (without an i) order, but divided into multiple families. The way tests are performed now by this [mdro()] function makes sure that results from before 2016 and after 2016 are identical.
#' @inheritSection as.rsi Interpretation of R and S/I

4
R/mic.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Class 'mic'

4
R/mo.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Transform to microorganism ID

4
R/mo_property.R
View File

@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Property of a microorganism

4
R/mo_source.R
View File

@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' User-defined reference data set for microorganisms

4
R/p_symbol.R
View File

@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Symbol of a p-value

4
R/pca.R
View File

@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Principal Component Analysis (for AMR)

4
R/proportion.R
View File

@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Calculate microbial resistance

4
R/resistance_predict.R
View File

@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Predict antimicrobial resistance

6
R/rsi.R
View File

@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Class 'rsi'
@ -37,7 +37,7 @@
#'
#' Supported guidelines to be used as input for the `guideline` parameter are: `r paste0('"', sort(unique(AMR::rsi_translation$guideline)), '"', collapse = ", ")`. Simply using `"CLSI"` or `"EUCAST"` for input will automatically select the latest version of that guideline.
#'
#' The repository of this package [contains a machine readable version](https://gitlab.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)**.
#' 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)**.
#'
#' After using [as.rsi()], you can use [eucast_rules()] to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
#'

4
R/rsi_calc.R
View File

@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
dots2vars <- function(...) {

4
R/rsi_df.R
View File

@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' @rdname proportion

4
R/skewness.R
View File

@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Skewness of the sample

16
R/translate.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,18 +16,18 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Translate strings from AMR package
#'
#' 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://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv>.
#' @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>.
#'
#' Currently supported languages are (besides English): `r paste(sort(gsub(";.*", "", ISOcodes::ISO_639_2[which(ISOcodes::ISO_639_2$Alpha_2 %in% unique(AMR:::translations_file$lang)), "Name"])), collapse = ", ")`. Not all these languages currently have translations available for all antimicrobial agents and colloquial microorganism names.
#' Currently supported languages are (besides English): `r paste(sort(gsub(";.*", "", ISOcodes::ISO_639_2[which(ISOcodes::ISO_639_2$Alpha_2 %in% unique(AMR:::translations_file$lang)), "Name"])), collapse = ", ")`. Please note that currently not 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://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation\%20suggestion).
#' Please suggest your own translations [by creating a new issue on our repository](https://github.com/msberends/AMR/issues/new?title=Translations).
#'
#' This file will be read by all functions where a translated output can be desired, like all [mo_property()] functions ([mo_name()], [mo_gramstain()], [mo_type()], etc.).
#'
@ -113,9 +113,9 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
paste0("'", sort(unique(df_trans$lang)), "'", collapse = ", "),
call = FALSE)
df_trans <- df_trans %>% subset(lang == language)
df_trans <- subset(df_trans, lang == language)
if (only_unknown == TRUE) {
df_trans <- df_trans %>% subset(pattern %like% "unknown")
df_trans <- subset(df_trans, pattern %like% "unknown")
}
# default case sensitive if value if 'ignore.case' is missing:
@ -126,7 +126,7 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
# check if text to look for is in one of the patterns
any_form_in_patterns <- tryCatch(any(from %like% paste0("(", paste(df_trans$pattern, collapse = "|"), ")")),
error = function(e) {
warning("Translation not possible. Please open an issue on GitLab (https://gitlab.com/msberends/AMR/issues) or GitHub (https://github.com/msberends/AMR/issues).", call. = FALSE)
warning("Translation not possible. Please open an issue on GitLab (https://github.com/msberends/AMR/issues) or GitHub (https://github.com/msberends/AMR/issues).", call. = FALSE)
return(FALSE)
})
if (NROW(df_trans) == 0 | !any_form_in_patterns) {

4
R/whocc.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' WHOCC: WHO Collaborating Centre for Drug Statistics Methodology

4
R/zzz.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
.onLoad <- function(libname, pkgname) {

6
README.md
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@ -3,12 +3,12 @@
# `AMR` (for R)
<img src="man/figures/logo.png" align="right" height="120px" />
This is the development source of the `AMR` package for R. Not a developer? Then please visit our website [https://msberends.gitlab.io/AMR](https://msberends.gitlab.io/AMR) to read about this package.
This is the development source of the `AMR` package for R. Not a developer? Then please visit our website [https://msberends.github.io/AMR](https://msberends.github.io/AMR) to read about this package.
*NOTE: this source code is on GitLab (https://gitlab.com/msberends/AMR) and GitHub (https://github.com/msberends/AMR).*
*NOTE: this source code is on GitHub (https://github.com/msberends/AMR) and GitLab (https://gitlab.com/msberends/AMR).*
### How to get this package
Please see [our website](https://msberends.gitlab.io/AMR/#get-this-package).
Please see [our website](https://msberends.github.io/AMR/#get-this-package).
### Copyright

10
_pkgdown.yml
View File

@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,11 +16,11 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
title: "AMR (for R)"
url: "https://msberends.gitlab.io/AMR"
url: "https://msberends.github.io/AMR"
development:
mode: "release" # improves indexing by search engines
@ -79,8 +79,8 @@ navbar:
href: "news/"
right:
- text: "Source Code"
icon: "fab fa-gitlab"
href: "https://gitlab.com/msberends/AMR"
icon: "fab fa-github"
href: "https://github.com/msberends/AMR"
- text: "Licence"
icon: "fa-book"
href: "LICENSE-text.html"

81
appveyor.yml
View File

@ -1,81 +0,0 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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 more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
# Download script file from this GitLab repo
init:
ps: |
$ErrorActionPreference = "Stop"
Invoke-WebRequest https://gitlab.com/msberends/AMR/raw/premaster/tests/appveyor/appveyor_tool.ps1 -OutFile "..\appveyor-tool.ps1"
Import-Module '..\appveyor-tool.ps1'
install:
ps: Bootstrap
cache:
- C:\RLibrary
# Adapt as necessary starting from here
environment:
R_ARCH: x64
GCC_PATH: mingw_64
WARNINGS_ARE_ERRORS: 1
PKGTYPE: both
USE_RTOOLS: true
matrix:
- R_VERSION: oldrel
- R_VERSION: release
- R_VERSION: devel
matrix:
allow_failures:
- R_VERSION: "devel"
build_script:
# - travis_tool.sh clean_library # turn off for caching, turn on for release of new R versions
- travis-tool.sh install_deps
test_script:
- travis-tool.sh run_tests
on_failure:
- 7z a failure.zip *.Rcheck\*
- appveyor PushArtifact failure.zip
artifacts:
- path: '*.Rcheck\**\*.log'
name: Logs
- path: '*.Rcheck\**\*.out'
name: Logs
- path: '*.Rcheck\**\*.fail'
name: Logs
- path: '*.Rcheck\**\*.Rout'
name: Logs
- path: '\*_*.tar.gz'
name: Bits
- path: '\*_*.zip'
name: Bits

4
codecov.yml
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
codecov:

2
cran-comments.md
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@ -1,3 +1,3 @@
* For this specific version, nothing to mention.
* Since version 0.3.0, CHECK returns a NOTE for having a data directory over 3 MB. This is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package.
* Since version 0.3.0 (2018-08-14), CHECK returns a NOTE for having a data directory over 3 MB. This is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package.

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data-raw/microorganisms.txt
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@ -736,6 +736,7 @@
"B_ACNTB_JUNI" "Acinetobacter junii" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Moraxellaceae" "Acinetobacter" "junii" "" "species" "Bouvet et al., 1986" "29130b9324716febfdbce7179b01e9bd" "CoL" 1 "13879009"
"B_ACNTB_KOOK" "Acinetobacter kookii" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Moraxellaceae" "Acinetobacter" "kookii" "" "species" "Choi et al., 2013" "791314" "DSMZ" 1
"B_ACNTB_LCTC" "Acinetobacter lactucae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Moraxellaceae" "Acinetobacter" "lactucae" "" "species" "Rooney et al., 2016" "794598" "DSMZ" 1
"B_ACNTB_LARV" "Acinetobacter larvae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Moraxellaceae" "Acinetobacter" "larvae" "" "species" "Liu et al., 2017" "795207" "DSMZ" 1
"B_ACNTB_LWFF" "Acinetobacter lwoffii" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Moraxellaceae" "Acinetobacter" "lwoffii" "" "species" "Brisou et al., 1986" "6e3b1ed9854282e9bafce3b2f7df00f9" "CoL" 1
"B_ACNTB_MDST" "Acinetobacter modestus" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Moraxellaceae" "Acinetobacter" "modestus" "" "species" "Nemec et al., 2016" "794039" "DSMZ" 1
"B_ACNTB_NCTR" "Acinetobacter nectaris" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Moraxellaceae" "Acinetobacter" "nectaris" "" "species" "Alvarez-Perez et al., 2013" "790645" "DSMZ" 1 "723323008"
@ -2430,6 +2431,7 @@
"B_[FAM]_AEROCCCC" "Aerococcaceae" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Aerococcaceae" "" "" "" "family" "" "057fddc497f1546f26951ef092e02b87" "CoL" 2
"B_AERCC" "Aerococcus" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Aerococcaceae" "Aerococcus" "" "" "genus" "" "0fc66055ad0db611f60c4f0396421d51" "CoL" 2 "9008009"
"B_AERCC_CHRS" "Aerococcus christensenii" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Aerococcaceae" "Aerococcus" "christensenii" "" "species" "Collins et al., 1999" "2ab13ae827b3c1ddd29fe7b60049a9ac" "CoL" 2 "409818008"
"B_AERCC_SNGC" "Aerococcus sanguicola" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Aerococcaceae" "Aerococcus" "sanguicola" "" "species" "Lawson et al., 2001" "783326" "DSMZ" 2
"B_AERCC_SNGN" "Aerococcus sanguinicola" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Aerococcaceae" "Aerococcus" "sanguinicola" "" "species" "Lawson et al., 2001" "796ff281ab493638185da69319259393" "CoL" 2 "427222006"
"B_AERCC_SUIS" "Aerococcus suis" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Aerococcaceae" "Aerococcus" "suis" "" "species" "Vela et al., 2007" "17a074a54acf7f23420e046afd54c05f" "CoL" 2
"B_AERCC_URIN" "Aerococcus urinae" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Aerococcaceae" "Aerococcus" "urinae" "" "species" "Aguirre et al., 1992" "7e2ead8d8cb690684800b35f8e80dfcd" "CoL" 2 "243230001"
@ -8417,6 +8419,9 @@
"B_BCTRD_GRMN" "Bacteroides graminisolvens" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Bacteroidaceae" "Bacteroides" "graminisolvens" "" "species" "Nishiyama et al., 2009" "0189b31b513fe80ea7ca818c9ff43192" "CoL" 2
"B_BCTRD_HLCG" "Bacteroides helcogenes" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Bacteroidaceae" "Bacteroides" "helcogenes" "" "species" "Benno et al., 1983" "761d72b47ca1a82a5996af2572135739" "CoL" 2
"B_BCTRD_INTS" "Bacteroides intestinalis" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Bacteroidaceae" "Bacteroides" "intestinalis" "" "species" "Bakir et al., 2006" "0bfac827879b8d5e224f7758a3d2d8f1" "CoL" 2 "712915005"
"B_BCTRD_KRNS" "Bacteroides koreensis" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Bacteroidaceae" "Bacteroides" "koreensis" "" "species" "Shin et al., 2017" "796142" "DSMZ" 2
"B_BCTRD_KRBB" "Bacteroides kribbi" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Bacteroidaceae" "Bacteroides" "kribbi" "" "species" "Shin et al., 2017" "796143" "DSMZ" 2
"B_BCTRD_LNTS" "Bacteroides lentus" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Bacteroidaceae" "Bacteroides" "lentus" "" "species" "Eggerth, 1935" "798327" "DSMZ" 2
"B_BCTRD_LUTI" "Bacteroides luti" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Bacteroidaceae" "Bacteroides" "luti" "" "species" "Hatamoto et al., 2014" "791844" "DSMZ" 2
"B_BCTRD_MSSL" "Bacteroides massiliensis" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Bacteroidaceae" "Bacteroides" "massiliensis" "" "species" "Fenner et al., 2005" "d214505a60093319e1a8e3ba61fe630f" "CoL" 2 "708567004"
"B_BCTRD_NORD" "Bacteroides nordii" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Bacteroidaceae" "Bacteroides" "nordii" "" "species" "Song et al., 2005" "7d1b475a13de2624a212b7cf1eb7e132" "CoL" 2
@ -8435,6 +8440,7 @@
"B_BCTRD_SRTR" "Bacteroides sartorii" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Bacteroidaceae" "Bacteroides" "sartorii" "" "species" "Clavel et al., 2012" "4f637ad6f3332fec71d795edf297f0c7" "CoL" 2
"B_BCTRD_STRC" "Bacteroides stercorirosoris" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Bacteroidaceae" "Bacteroides" "stercorirosoris" "" "species" "Kitahara et al., 2012" "ee122c4c95090744a6bdf633fd9d5e00" "CoL" 2
"B_BCTRD_RCRS" "Bacteroides stercoris" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Bacteroidaceae" "Bacteroides" "stercoris" "" "species" "Johnson et al., 1986" "daeebd5ec8bba7b76d45e1460db471c1" "CoL" 2 "163009"
"B_BCTRD_TCTM" "Bacteroides tectum" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Bacteroidaceae" "Bacteroides" "tectum" "" "species" "Love et al., 1986" "783467" "DSMZ" 2
"B_BCTRD_THTT" "Bacteroides thetaiotaomicron" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Bacteroidaceae" "Bacteroides" "thetaiotaomicron" "" "species" "Castellani et al., 1919" "c4bd13e2054f15c834480d57a8577020" "CoL" 2 "34236001"
"B_BCTRD_UNFR" "Bacteroides uniformis" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Bacteroidaceae" "Bacteroides" "uniformis" "" "species" "Eggerth et al., 1933" "032345ae9e1b73dadb9b137d024b20bf" "CoL" 2 "59604009"
"B_BCTRD_VLGT" "Bacteroides vulgatus" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Bacteroidaceae" "Bacteroides" "vulgatus" "" "species" "Eggerth et al., 1933" "f973c61c6d0a4e15928dbdc436b13c0f" "CoL" 2 "52798008"
@ -10965,6 +10971,7 @@
"B_CMPYL_COLI" "Campylobacter coli" "Bacteria" "Proteobacteria" "Epsilonproteobacteria" "Campylobacterales" "Campylobacteraceae" "Campylobacter" "coli" "" "species" "Veron et al., 1973" "6c569c28a8b120282d777d2b1f98554e" "CoL" 2 "40614002"
"B_CMPYL_CNCS" "Campylobacter concisus" "Bacteria" "Proteobacteria" "Epsilonproteobacteria" "Campylobacterales" "Campylobacteraceae" "Campylobacter" "concisus" "" "species" "Tanner et al., 1981" "6a7472de918950d9ea3fb4da6accbade" "CoL" 2 "9892000"
"B_CMPYL_CRCG" "Campylobacter corcagiensis" "Bacteria" "Proteobacteria" "Epsilonproteobacteria" "Campylobacterales" "Campylobacteraceae" "Campylobacter" "corcagiensis" "" "species" "Koziel et al., 2014" "792068" "DSMZ" 2
"B_CMPYL_CRYR" "Campylobacter cryaerophila" "Bacteria" "Proteobacteria" "Epsilonproteobacteria" "Campylobacterales" "Campylobacteraceae" "Campylobacter" "cryaerophila" "" "species" "Neill et al., 1985" "783584" "DSMZ" 2
"B_CMPYL_CNCL" "Campylobacter cuniculorum" "Bacteria" "Proteobacteria" "Epsilonproteobacteria" "Campylobacterales" "Campylobacteraceae" "Campylobacter" "cuniculorum" "" "species" "Zanoni et al., 2009" "3231356e94ded6c8ed9225a8174c2247" "CoL" 2
"B_CMPYL_CRVS" "Campylobacter curvus" "Bacteria" "Proteobacteria" "Epsilonproteobacteria" "Campylobacterales" "Campylobacteraceae" "Campylobacter" "curvus" "" "species" "Vandamme et al., 1991" "877e011524cf683cc924bc2afa2f4f1e" "CoL" 2 "116037008"
"B_CMPYL_FETS" "Campylobacter fetus" "Bacteria" "Proteobacteria" "Epsilonproteobacteria" "Campylobacterales" "Campylobacteraceae" "Campylobacter" "fetus" "" "species" "Sebald et al., 1963" "409ceefcdb679efc37676cadffb3e3e7" "CoL" 2 "84210007"
@ -15554,6 +15561,7 @@
"B_CRYNB_AMMN" "Corynebacterium ammoniagenes" "Bacteria" "Actinobacteria" "(unknown class)" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "ammoniagenes" "" "species" "Collins, 1987" "83d6f101baca47719776d6daa091dd17" "CoL" 2 "113607008"
"B_CRYNB_AMYC" "Corynebacterium amycolatum" "Bacteria" "Actinobacteria" "(unknown class)" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "amycolatum" "" "species" "Collins et al., 1988" "2697fc1a982784c82efbbe6d48d1ed64" "CoL" 2 "113611002"
"B_CRYNB_APPN" "Corynebacterium appendicis" "Bacteria" "Actinobacteria" "(unknown class)" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "appendicis" "" "species" "Yassin et al., 2002" "a6749ae107d7955240ae4bacca4a3b53" "CoL" 2 "423659000"
"B_CRYNB_AQTC" "Corynebacterium aquaticum" "Bacteria" "Actinobacteria" "" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "aquaticum" "" "species" "Leifson, 1962" "775153" "DSMZ" 2
"B_CRYNB_AQTM" "Corynebacterium aquatimens" "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "aquatimens" "" "species" "Aravena-Roman et al., 2012" "790174" "DSMZ" 2
"B_CRYNB_AQUL" "Corynebacterium aquilae" "Bacteria" "Actinobacteria" "(unknown class)" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "aquilae" "" "species" "Fernandez-Garayzabal et al., 2003" "eb89e2b18e8cf702deae686db631959a" "CoL" 2 "424012003"
"B_CRYNB_ARGN" "Corynebacterium argentoratense" "Bacteria" "Actinobacteria" "(unknown class)" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "argentoratense" "" "species" "Riegel et al., 1995" "248437e186f079f9098b51d7eab9a104" "CoL" 2 "417499006"
@ -15583,6 +15591,7 @@
"B_CRYNB_DURM" "Corynebacterium durum" "Bacteria" "Actinobacteria" "(unknown class)" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "durum" "" "species" "Riegel et al., 1997" "188914f51441fcf66e9dbdd6fa419ca5" "CoL" 2 "413926004"
"B_CRYNB_EFFC" "Corynebacterium efficiens" "Bacteria" "Actinobacteria" "(unknown class)" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "efficiens" "" "species" "Fudou et al., 2002" "100e54272c41242bd210c760dc3d49da" "CoL" 2 "423379003"
"B_CRYNB_EPDR" "Corynebacterium epidermidicanis" "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "epidermidicanis" "" "species" "Frischmann et al., 2018" "790130" "DSMZ" 2
"B_CRYNB_FACL" "Corynebacterium faecale" "Bacteria" "Actinobacteria" "" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "faecale" "" "species" "Chen et al., 2016" "794251" "DSMZ" 2
"B_CRYNB_FLSN" "Corynebacterium falsenii" "Bacteria" "Actinobacteria" "(unknown class)" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "falsenii" "" "species" "Sjoden et al., 1998" "a4b0881333077324ba938902ef33b158" "CoL" 2 "116389005"
"B_CRYNB_FLNM" "Corynebacterium felinum" "Bacteria" "Actinobacteria" "(unknown class)" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "felinum" "" "species" "Collins et al., 2001" "633a1e897b7623235da9235464dcd67c" "CoL" 2 "423568009"
"B_CRYNB_FLVS" "Corynebacterium flavescens" "Bacteria" "Actinobacteria" "(unknown class)" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "flavescens" "" "species" "Barksdale et al., 1979" "2aa053a0af38954875cb97011cb29443" "CoL" 2 "47802009"
@ -15609,6 +15618,7 @@
"B_CRYNB_KTSC" "Corynebacterium kutscheri" "Bacteria" "Actinobacteria" "(unknown class)" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "kutscheri" "" "species" "Bergey et al., 1925" "8ea3128da9bfa7cfc5ab4fb8c83e35fc" "CoL" 2 "88575000"
"B_CRYNB_LCTS" "Corynebacterium lactis" "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "lactis" "" "species" "Wiertz et al., 2018" "791337" "DSMZ" 2
"B_CRYNB_LPPH" "Corynebacterium lipophiloflavum" "Bacteria" "Actinobacteria" "(unknown class)" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "lipophiloflavum" "" "species" "Funke et al., 1997" "da6181226ddbe16d620eb7fbd0d50b3f" "CoL" 2 "416863001"
"B_CRYNB_LQFC" "Corynebacterium liquefaciens" "Bacteria" "Actinobacteria" "" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "liquefaciens" "" "species" "Laneelle et al., 1980" "798138" "DSMZ" 2
"B_CRYNB_LOWI" "Corynebacterium lowii" "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "lowii" "" "species" "Bernard et al., 2016" "794320" "DSMZ" 2
"B_CRYNB_LBRC" "Corynebacterium lubricantis" "Bacteria" "Actinobacteria" "(unknown class)" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "lubricantis" "" "species" "Kampfer et al., 2009" "b1b838e48e5f986bdebfce12e92b819b" "CoL" 2
"B_CRYNB_MCGN" "Corynebacterium macginleyi" "Bacteria" "Actinobacteria" "(unknown class)" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "macginleyi" "" "species" "Riegel et al., 1995" "f061871344574f355ac6ac89f02a0aaf" "CoL" 2 "363772007"
@ -15661,7 +15671,9 @@
"B_CRYNB_URPY" "Corynebacterium uropygiale" "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "uropygiale" "" "species" "Braun et al., 2016" "794126" "DSMZ" 2
"B_CRYNB_UTRQ" "Corynebacterium uterequi" "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "uterequi" "" "species" "Hoyles et al., 2018" "791215" "DSMZ" 2
"B_CRYNB_VRBL" "Corynebacterium variabile" "Bacteria" "Actinobacteria" "(unknown class)" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "variabile" "" "species" "Collins, 1987" "9c6d95c70bfb58c350f5295d423094bc" "CoL" 2 "11575001"
"B_CRYNB_RBLS" "Corynebacterium variabilis" "Bacteria" "Actinobacteria" "" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "variabilis" "" "species" "Collins, 1987" "783701" "DSMZ" 2
"B_CRYNB_VTRM" "Corynebacterium vitaeruminis" "Bacteria" "Actinobacteria" "(unknown class)" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "vitaeruminis" "" "species" "Laneelle et al., 1980" "81f6de6271113a7a1d61a141786c78fe" "CoL" 2 "116390001"
"B_CRYNB_TRMN" "Corynebacterium vitarumen" "Bacteria" "Actinobacteria" "" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "vitarumen" "" "species" "Laneelle et al., 1980" "783702" "DSMZ" 2
"B_CRYNB_XRSS" "Corynebacterium xerosis" "Bacteria" "Actinobacteria" "(unknown class)" "Actinomycetales" "Corynebacteriaceae" "Corynebacterium" "xerosis" "" "species" "Lehmann et al., 1899" "eda368b36b3b5f8557b8fc25bb3d87f6" "CoL" 2 "27101006"
"C_CRYNP" "Corynophrya" "Chromista" "Ciliophora" "Kinetofragminophora" "Suctorida" "Corynophryidae" "Corynophrya" "" "" "genus" "" "30fbc7bc50db56001cfd44dcf07a5fc7" "CoL" 3
"C_CRYNP_ABYS" "Corynophrya abyssalis" "Chromista" "Ciliophora" "Kinetofragminophora" "Suctorida" "Corynophryidae" "Corynophrya" "abyssalis" "" "species" "Bartsch et al., 2010" "a18401393d14ee783e73e8be3c73a884" "CoL" 3
@ -17842,6 +17854,7 @@
"C_DNTST_ENPL" "Dentostomina enoplostoma" "Chromista" "Foraminifera" "Tubothalamea" "Miliolida" "Hauerinidae" "Dentostomina" "enoplostoma" "" "species" "DOrbigny, 1839" "0c50c5a83074677bc408c07de08fb8aa" "CoL" 3
"B_DRMBC" "Dermabacter" "Bacteria" "Actinobacteria" "(unknown class)" "Actinomycetales" "Dermabacteraceae" "Dermabacter" "" "" "genus" "" "c254973d79329a9a81babca22bf7aa51" "CoL" 2 "413976002"
"B_DRMBC_HMNS" "Dermabacter hominis" "Bacteria" "Actinobacteria" "(unknown class)" "Actinomycetales" "Dermabacteraceae" "Dermabacter" "hominis" "" "species" "Jones et al., 1989" "4d3ef12bee5e2d1e0093af5e6a738b0f" "CoL" 2 "413977006"
"B_DRMBC_JNJN" "Dermabacter jinjuensis" "Bacteria" "Actinobacteria" "" "Actinomycetales" "Dermabacteraceae" "Dermabacter" "jinjuensis" "" "species" "Park et al., 2016" "794255" "DSMZ" 2
"B_DRMBC_VGNL" "Dermabacter vaginalis" "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales" "Dermabacteraceae" "Dermabacter" "vaginalis" "" "species" "Chang et al., 2016" "794030" "DSMZ" 2
"B_[FAM]_DRMBCTRC" "Dermabacteraceae" "Bacteria" "Actinobacteria" "(unknown class)" "Actinomycetales" "Dermabacteraceae" "" "" "" "family" "" "0f21d57e4b28d96773e1081bad008181" "CoL" 2
"B_[FAM]_DERMCCCC" "Dermacoccaceae" "Bacteria" "Actinobacteria" "(unknown class)" "Actinomycetales" "Dermacoccaceae" "" "" "" "family" "" "d822dbf47675fbd561fcabd9388b58b4" "CoL" 2
@ -23874,6 +23887,8 @@
"C_FCHRA_ULRN" "Fuscheria ulurensis" "Chromista" "Ciliophora" "Gymnostomatea" "Haptorida" "Fuscheriidae" "Fuscheria" "ulurensis" "" "species" "Foissner et al., 2009" "eab418d60de109c70adebdcfadd38393" "CoL" 3
"C_[FAM]_FUSCHERD" "Fuscheriidae" "Chromista" "Ciliophora" "Gymnostomatea" "Haptorida" "Fuscheriidae" "" "" "" "family" "" "c142b58b7df6153f2b251f1fe35e1fcb" "CoL" 2
"B_FSBCT" "Fusibacter" "Bacteria" "Firmicutes" "Clostridia" "Clostridiales" "(unknown family)" "Fusibacter" "" "" "genus" "" "2ef1cc64021e41234ccb81337243e326" "CoL" 2
"B_FSBCT_BZRT" "Fusibacter bizertensis" "Bacteria" "Firmicutes" "Clostridia" "Clostridiales" "" "Fusibacter" "bizertensis" "" "species" "Smii et al., 2015" "792439" "DSMZ" 2
"B_FSBCT_FNTS" "Fusibacter fontis" "Bacteria" "Firmicutes" "Clostridia" "Clostridiales" "" "Fusibacter" "fontis" "" "species" "Fadhlaoui et al., 2015" "793321" "DSMZ" 2
"B_FSBCT_PCVR" "Fusibacter paucivorans" "Bacteria" "Firmicutes" "Clostridia" "Clostridiales" "(unknown family)" "Fusibacter" "paucivorans" "" "species" "Ravot et al., 1999" "e377365519fc9048e61ebe12b0acc6da" "CoL" 2
"B_FSBCT_TNSN" "Fusibacter tunisiensis" "Bacteria" "Firmicutes" "Clostridia" "Clostridiales" "(unknown family)" "Fusibacter" "tunisiensis" "" "species" "Ben Hania et al., 2012" "fc23fa7985bcce14cb779cfdd5e8c24a" "CoL" 2
"B_FSCTN" "Fusicatenibacter" "Bacteria" "Firmicutes" "Clostridia" "Clostridiales" "Lachnospiraceae" "Fusicatenibacter" "" "" "genus" "" "DSMZ" 2
@ -24127,7 +24142,9 @@
"B_GEMLL_HMLY" "Gemella haemolysans" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "(unknown family)" "Gemella" "haemolysans" "" "species" "Berger, 1960" "cb12ee9348456944da1452c2ee07f711" "CoL" 2 "37511002"
"B_GEMLL_MRBL" "Gemella morbillorum" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "(unknown family)" "Gemella" "morbillorum" "" "species" "Kilpper-Balz et al., 1988" "2cf1ae502c0bf7d053d9520f7bc12d1e" "CoL" 2 "113765006"
"B_GEMLL_PLTC" "Gemella palaticanis" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "(unknown family)" "Gemella" "palaticanis" "" "species" "Collins et al., 1999" "0413b4f5665e096d10b0dd2c59f07646" "CoL" 2
"B_GEMLL_PRHM" "Gemella parahaemolysans" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "" "Gemella" "parahaemolysans" "" "species" "Hung et al., 2014" "791874" "DSMZ" 2
"B_GEMLL_SNGN" "Gemella sanguinis" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "(unknown family)" "Gemella" "sanguinis" "" "species" "Collins et al., 1999" "2c5a8f12014c650dfe5f55accde88084" "CoL" 2 "125038007"
"B_GEMLL_TWNN" "Gemella taiwanensis" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "" "Gemella" "taiwanensis" "" "species" "Hung et al., 2014" "791875" "DSMZ" 2
"B_GMNCC" "Geminicoccus" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "(unknown order)" "(unknown family)" "Geminicoccus" "" "" "genus" "" "3791b89a357dd7b75651125e72e5a27e" "CoL" 2
"B_GMNCC_ROSS" "Geminicoccus roseus" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "(unknown order)" "(unknown family)" "Geminicoccus" "roseus" "" "species" "Foesel et al., 2008" "ab4e9af2a2755d93be9d56dd1536c1e6" "CoL" 2
"C_GMNLL" "Geminiella" "Chromista" "Foraminifera" "(unknown class)" "Lagenida" "Ellipsolagenidae" "Geminiella" "" "" "genus" "" "163b7468129f33c2476fc3f18bfd8c88" "CoL" 3
@ -30007,10 +30024,13 @@
"B_LCTBC_RDNT" "Lactobacillus rodentium" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "rodentium" "" "species" "Killer et al., 2014" "791838" "DSMZ" 2
"B_LCTBC_ROGS" "Lactobacillus rogosae" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "rogosae" "" "species" "Holdeman et al., 1974" "1c971bb2a729c6604e6e5686fd92559f" "CoL" 2
"B_LCTBC_ROSS" "Lactobacillus rossiae" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "rossiae" "" "species" "Corsetti et al., 2005" "bb0621ab2aabb15f4880b9a92c698b2a" "CoL" 2 "432194007"
"B_LCTBC_RSSI" "Lactobacillus rossii" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "rossii" "" "species" "Corsetti et al., 2005" "784068" "DSMZ" 2
"B_LCTBC_RMNS" "Lactobacillus ruminis" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "ruminis" "" "species" "Sharpe et al., 1973" "227f53c5db4073601a8da25c2aa823a0" "CoL" 2 "84370002"
"B_LCTBC_SRMN" "Lactobacillus saerimneri" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "saerimneri" "" "species" "Pedersen et al., 2004" "48fdd7d3958b20a80de0f6aa37215fe2" "CoL" 2 "432191004"
"B_LCTBC_SAKE_SAKE" "Lactobacillus sake sake" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "sake" "sake" "species" "Torriani et al., 1996" "784071" "DSMZ" 2
"B_LCTBC_SAKE" "Lactobacillus sakei" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "sakei" "" "species" "Katagiri et al., 1996" "539147a998aca4d1b21139df1c19da17" "CoL" 2 "39861009"
"B_LCTBC_SAKE_CRNS" "Lactobacillus sakei carnosus" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "sakei" "carnosus" "infraspecies" "Torriani et al., 1996" "dde7319e76c9247eb5ad732536eb07c8" "CoL" 2
"B_LCTBC_SKEI_SAKE" "Lactobacillus sakei sake" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "sakei" "sake" "species" "Torriani et al., 1996" "798356" "DSMZ" 2
"B_LCTBC_SLTL" "Lactobacillus salitolerans" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "salitolerans" "" "species" "Tohno et al., 2019" "800710" "DSMZ" 2
"B_LCTBC_SLVR" "Lactobacillus salivarius" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "salivarius" "" "species" "Rogosa et al., 2006" "ac34ff01c9afe0de2ab69bfd339704b6" "CoL" 2 "37809002"
"B_LCTBC_SNFR" "Lactobacillus sanfranciscensis" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "sanfranciscensis" "" "species" "Weiss et al., 1984" "4211a00b19dfc4632b868fe123b0d1b8" "CoL" 2 "432195008"
@ -39308,6 +39328,7 @@
"B_NESSR_CANS" "Neisseria canis" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Neisseriales" "Neisseriaceae" "Neisseria" "canis" "" "species" "Berger, 1962" "f588178a6f811167d2a08e5d7b2a7310" "CoL" 2 "54978009"
"B_NESSR_CINR" "Neisseria cinerea" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Neisseriales" "Neisseriaceae" "Neisseria" "cinerea" "" "species" "Murray, 1939" "80fa1e21c2efa5f0c00ca26a5c190c1d" "CoL" 2 "69312007"
"B_NESSR_DENT" "Neisseria dentiae" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Neisseriales" "Neisseriaceae" "Neisseria" "dentiae" "" "species" "Sneath et al., 1997" "e6428b38ccc3818fb21e2146b9b9da01" "CoL" 2
"B_NESSR_DMSN" "Neisseria dumasiana" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Neisseriales" "Neisseriaceae" "Neisseria" "dumasiana" "" "species" "Wroblewski et al., 2017" "796193" "DSMZ" 2
"B_NESSR_ELNG" "Neisseria elongata" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Neisseriales" "Neisseriaceae" "Neisseria" "elongata" "" "species" "Bovre et al., 1970" "4fd583a67fe0f765137e4902de5cf11e" "CoL" 2 "12638001"
"B_NESSR_ELNG_GLYC" "Neisseria elongata glycolytica" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Neisseriales" "Neisseriaceae" "Neisseria" "elongata" "glycolytica" "infraspecies" "Henriksen et al., 1976" "53eb476c001de688a708c637afc447d1" "CoL" 2 "35693009"
"B_NESSR_ELNG_NTRR" "Neisseria elongata nitroreducens" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Neisseriales" "Neisseriaceae" "Neisseria" "elongata" "nitroreducens" "infraspecies" "Grant et al., 1991" "017d680b532a5e4033a40ef0dd780905" "CoL" 2
@ -42653,10 +42674,12 @@
"B_[FAM]_PANBCLLC" "Paenibacillaceae" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "" "" "" "family" "" "06f43a6ef8ac500d8120040e50675f88" "CoL" 2
"B_PNBCL" "Paenibacillus" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "" "" "genus" "" "d778edb5225cb28bd7344ed5dbd083e1" "CoL" 2 "114086007"
"B_PNBCL_ABYS" "Paenibacillus abyssi" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "abyssi" "" "species" "Huang et al., 2015" "792663" "DSMZ" 2
"B_PNBCL_ACRS" "Paenibacillus aceris" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "aceris" "" "species" "Hwang et al., 2017" "795204" "DSMZ" 2
"B_PNBCL_ACET" "Paenibacillus aceti" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "aceti" "" "species" "Li et al., 2016" "794569" "DSMZ" 2
"B_PNBCL_AEST" "Paenibacillus aestuarii" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "aestuarii" "" "species" "Bae et al., 2010" "2eaeee843908dc72f01599c01d1d7824" "CoL" 2
"B_PNBCL_AGRX" "Paenibacillus agarexedens" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "agarexedens" "" "species" "Uetanabaro et al., 2003" "34f7325ea04df422addf6139f76227a4" "CoL" 2 "429906007"
"B_PNBCL_AGRD" "Paenibacillus agaridevorans" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "agaridevorans" "" "species" "Uetanabaro et al., 2003" "830aae21cbe86216066ba7af5f9c87cb" "CoL" 2 "429907003"
"B_PNBCL_ALBD" "Paenibacillus albidus" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "albidus" "" "species" "Zhuang et al., 2017" "796151" "DSMZ" 2
"B_PNBCL_ALGN" "Paenibacillus alginolyticus" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "alginolyticus" "" "species" "Shida et al., 1997" "bc3b26b031ae0349cad729c4a579522e" "CoL" 2 "114087003"
"B_PNBCL_ALGR" "Paenibacillus algorifonticola" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "algorifonticola" "" "species" "Tang et al., 2011" "29a27c78f5d93976913c98158bea624d" "CoL" 2
"B_PNBCL_ALKL" "Paenibacillus alkaliterrae" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "alkaliterrae" "" "species" "Yoon et al., 2005" "819caeb31dafeee45c8b67e01809e774" "CoL" 2
@ -42705,6 +42728,7 @@
"B_PNBCL_DNDR" "Paenibacillus dendritiformis" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "dendritiformis" "" "species" "Tcherpakov et al., 1999" "e98e22d6a5472c702d773f45208b8d3f" "CoL" 2 "430608007"
"B_PNBCL_DNGD" "Paenibacillus dongdonensis" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "dongdonensis" "" "species" "Son et al., 2014" "792042" "DSMZ" 2
"B_PNBCL_DSNN" "Paenibacillus doosanensis" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "doosanensis" "" "species" "Kim et al., 2014" "791705" "DSMZ" 2
"B_PNBCL_DURM" "Paenibacillus durum" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "durum" "" "species" "Collins et al., 1994" "784553" "DSMZ" 2
"B_PNBCL_DURS" "Paenibacillus durus" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "durus" "" "species" "Collins et al., 1994" "3d10d59aee2784ef5fff65f7538ac245" "CoL" 2 "114091008"
"B_PNBCL_EDPH" "Paenibacillus edaphicus" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "edaphicus" "" "species" "Hu et al., 2010" "55c35c5efb25e66c778cf6d60eac2e9a" "CoL" 2
"B_PNBCL_EHMN" "Paenibacillus ehimensis" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "ehimensis" "" "species" "Lee et al., 2004" "977994e73d0595da2d2fdeaa365eb6cd" "CoL" 2 "430609004"
@ -42752,6 +42776,7 @@
"B_PNBCL_KRBB" "Paenibacillus kribbensis" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "kribbensis" "" "species" "Yoon et al., 2003" "7990cce5493b343b4dd578b73c8da83e" "CoL" 2
"B_PNBCL_KYNG" "Paenibacillus kyungheensis" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "kyungheensis" "" "species" "Siddiqi et al., 2015" "793494" "DSMZ" 2
"B_PNBCL_LCTS" "Paenibacillus lactis" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "lactis" "" "species" "Scheldeman et al., 2004" "a8fa50353b31da34a322d9fca3881572" "CoL" 2 "430629003"
"B_PNBCL_LACS" "Paenibacillus lacus" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "lacus" "" "species" "Chen et al., 2017" "795288" "DSMZ" 2
"B_PNBCL_LARV" "Paenibacillus larvae" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "larvae" "" "species" "Ash et al., 2006" "9bfc05efd3eea0854db404760e482e1e" "CoL" 2 "114098002"
"B_PNBCL_LATS" "Paenibacillus lautus" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "lautus" "" "species" "Heyndrickx et al., 1996" "b73ba9f5e23a3f1ddd34fcb98a3a10f8" "CoL" 2 "114100002"
"B_PNBCL_LEMN" "Paenibacillus lemnae" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Paenibacillaceae" "Paenibacillus" "lemnae" "" "species" "Kittiwongwattana et al., 2015" "792440" "DSMZ" 2
@ -43113,6 +43138,7 @@
"B_PANTO" "Pantoea" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Erwiniaceae" "Pantoea" "" "" "genus" "" "5e1e7e2c2f3da486dfc2d89e6b75865e" "CoL" 1 "115013001"
"B_PANTO_AGGL" "Pantoea agglomerans" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Erwiniaceae" "Pantoea" "agglomerans" "" "species" "Gavini et al., 1989" "a0ec10fe69cbe44b829f9c387c6d5ebd" "CoL" 1 "115015008"
"B_PANTO_ALLI" "Pantoea allii" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Erwiniaceae" "Pantoea" "allii" "" "species" "Brady et al., 2011" "4dd07886be48e1ae6e8ed37d203c0f84" "CoL" 1
"B_PANTO_ANNS" "Pantoea ananas" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Erwiniaceae" "Pantoea" "ananas" "" "species" "Mergaert et al., 1993" "784563" "DSMZ" 1
"B_PANTO_ANNT" "Pantoea ananatis" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Erwiniaceae" "Pantoea" "ananatis" "" "species" "Mergaert et al., 1993" "2c54740884f84a1a71a5cd300a79d15a" "CoL" 1 "115014007"
"B_PANTO_ANTH" "Pantoea anthophila" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Erwiniaceae" "Pantoea" "anthophila" "" "species" "Brady et al., 2009" "e722c6d8bb737b44d817a317c8ef8013" "CoL" 1
"B_PANTO_BRNN" "Pantoea brenneri" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Erwiniaceae" "Pantoea" "brenneri" "" "species" "Brady et al., 2010" "4431f9b8fd978b73e96e06a1286006c5" "CoL" 1
@ -49833,6 +49859,7 @@
"C_PRTNN_RNHL" "Proteonina reinholdi" "Chromista" "Foraminifera" "Globothalamea" "Lituolida" "Hormosinidae" "Proteonina" "reinholdi" "" "species" "Ten Dam, 1947" "c05060e270f23cfba9b6e353efdb2769" "CoL" 3
"B_PROTS" "Proteus" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Morganellaceae" "Proteus" "" "" "genus" "" "0f62bf27dd2e0a29481695b9c7a55fa5" "CoL" 1 "50517009"
"B_PROTS_ALMN" "Proteus alimentorum" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Morganellaceae" "Proteus" "alimentorum" "" "species" "Dai et al., 2018" "797660" "DSMZ" 1
"B_PROTS_CBRS" "Proteus cibarius" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Morganellaceae" "Proteus" "cibarius" "" "species" "Hyun et al., 2016" "794180" "DSMZ" 1
"B_PROTS_CIBI" "Proteus cibi" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Morganellaceae" "Proteus" "cibi" "" "species" "Dai et al., 2019" "800142" "DSMZ" 1
"B_PROTS_CLMB" "Proteus columbae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Morganellaceae" "Proteus" "columbae" "" "species" "Dai et al., 2018" "797522" "DSMZ" 1
"B_PROTS_FACS" "Proteus faecis" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Morganellaceae" "Proteus" "faecis" "" "species" "Dai et al., 2019" "800143" "DSMZ" 1
@ -50641,6 +50668,7 @@
"B_PSDMN_BRSS_NRNT" "Pseudomonas brassicacearum neoaurantiaca" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Pseudomonadaceae" "Pseudomonas" "brassicacearum" "neoaurantiaca" "infraspecies" "Ivanova et al., 2009" "ec8927aacb91b3a6cc4ca4a685f3914b" "CoL" 1
"B_PSDMN_BRNN" "Pseudomonas brenneri" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Pseudomonadaceae" "Pseudomonas" "brenneri" "" "species" "Baida et al., 2002" "49c16df22b9794811ee11992e802fb75" "CoL" 1 "415188002"
"B_PSDMN_CAEN" "Pseudomonas caeni" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Pseudomonadaceae" "Pseudomonas" "caeni" "" "species" "Xiao et al., 2009" "aa17e9af46852075ef859e600004f3e7" "CoL" 1
"B_PSDMN_CNDN" "Pseudomonas canadensis" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Pseudomonadaceae" "Pseudomonas" "canadensis" "" "species" "Tambong et al., 2017" "795214" "DSMZ" 1
"B_PSDMN_CNNB" "Pseudomonas cannabina" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Pseudomonadaceae" "Pseudomonas" "cannabina" "" "species" "Gardan et al., 1999" "eca546200fc614d4abd73c834d001c3c" "CoL" 1
"B_PSDMN_CRBX" "Pseudomonas carboxydohydrogena" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Pseudomonadaceae" "Pseudomonas" "carboxydohydrogena" "" "species" "Meyer et al., 1980" "6b549eed20115e65b1a5a7551409e7a5" "CoL" 1
"B_PSDMN_CRCP" "Pseudomonas caricapapayae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Pseudomonadaceae" "Pseudomonas" "caricapapayae" "" "species" "Robbs, 1956" "b2197848de1e1c7c10e903a27ab04aba" "CoL" 1 "76278000"
@ -50791,6 +50819,7 @@
"B_PSDMN_TNNS" "Pseudomonas taeanensis" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Pseudomonadaceae" "Pseudomonas" "taeanensis" "" "species" "Lee et al., 2010" "db0759c67acd25a657bdd93c8a41869e" "CoL" 1
"B_PSDMN_TTRL" "Pseudomonas taetrolens" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Pseudomonadaceae" "Pseudomonas" "taetrolens" "" "species" "Haynes, 1957" "37765eb7414456ba397f87b02ab3965c" "CoL" 1 "73287000"
"B_PSDMN_TWNN" "Pseudomonas taiwanensis" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Pseudomonadaceae" "Pseudomonas" "taiwanensis" "" "species" "Wang et al., 2010" "8d20832d1ffec1d093791edab57c79df" "CoL" 1 "450372006"
"B_PSDMN_TRMN" "Pseudomonas tarimensis" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Pseudomonadaceae" "Pseudomonas" "tarimensis" "" "species" "Anwar et al., 2017" "796144" "DSMZ" 1
"B_PSDMN_THRM" "Pseudomonas thermotolerans" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Pseudomonadaceae" "Pseudomonas" "thermotolerans" "" "species" "Manaia et al., 2002" "05b82ed17c4615effe847440ec86dfd1" "CoL" 1 "438068005"
"B_PSDMN_THVR" "Pseudomonas thivervalensis" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Pseudomonadaceae" "Pseudomonas" "thivervalensis" "" "species" "Achouak et al., 2000" "78fb8ff185618bc7c11c117c2f1551f3" "CoL" 1 "438028006"
"B_PSDMN_TNJN" "Pseudomonas tianjinensis" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Pseudomonadaceae" "Pseudomonas" "tianjinensis" "" "species" "Chen et al., 2018" "797819" "DSMZ" 1
@ -56894,12 +56923,14 @@
"B_SPHNGB_ALKL" "Sphingobacterium alkalisoli" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "alkalisoli" "" "species" "Xu et al., 2017" "795403" "DSMZ" 3
"B_SPHNGB_ANHN" "Sphingobacterium anhuiense" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "anhuiense" "" "species" "Wei et al., 2008" "7639c737c663d05e1aee5fd3fed2b3c8" "CoL" 3
"B_SPHNGB_ANTR" "Sphingobacterium antarcticum" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "antarcticum" "" "species" "Shivaji et al., 1992" "e19db9fdbc0a7ab1bf11b50b7fa32deb" "CoL" 3
"B_SPHNGB_CTCS" "Sphingobacterium antarcticus" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "antarcticus" "" "species" "Shivaji et al., 1992" "784914" "DSMZ" 3
"B_SPHNGB_AREN" "Sphingobacterium arenae" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "arenae" "" "species" "Jiang et al., 2014" "791480" "DSMZ" 3
"B_SPHNGB_ATHY" "Sphingobacterium athyrii" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "athyrii" "" "species" "Cheng et al., 2019" "800119" "DSMZ" 3
"B_SPHNGB_BMBS" "Sphingobacterium bambusae" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "bambusae" "" "species" "Duan et al., 2010" "9d76b2529efee4d3b1965472384825b0" "CoL" 3
"B_SPHNGB_BVSG" "Sphingobacterium bovisgrunnientis" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "bovisgrunnientis" "" "species" "Kaur et al., 2018" "797534" "DSMZ" 3
"B_SPHNGB_CAEN" "Sphingobacterium caeni" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "caeni" "" "species" "Sun et al., 2013" "790835" "DSMZ" 3
"B_SPHNGB_CNDN" "Sphingobacterium canadense" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "canadense" "" "species" "Mehnaz et al., 2008" "e0dd9101ff5b891528b9c312f348d715" "CoL" 3
"B_SPHNGB_CLLL" "Sphingobacterium cellulitidis" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "cellulitidis" "" "species" "Huys et al., 2017" "795224" "DSMZ" 3
"B_SPHNGB_CHNG" "Sphingobacterium changzhouense" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "changzhouense" "" "species" "Liu et al., 2013" "791381" "DSMZ" 3
"B_SPHNGB_CHZH" "Sphingobacterium chuzhouense" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "chuzhouense" "" "species" "Wang et al., 2016" "794891" "DSMZ" 3
"B_SPHNGB_CIBI" "Sphingobacterium cibi" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "cibi" "" "species" "Lai et al., 2016" "794899" "DSMZ" 3
@ -56914,6 +56945,7 @@
"B_SPHNGB_GRSF" "Sphingobacterium griseoflavum" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "griseoflavum" "" "species" "Long et al., 2016" "794133" "DSMZ" 3
"B_SPHNGB_HLXY" "Sphingobacterium haloxyli" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "haloxyli" "" "species" "Liu et al., 2018" "797903" "DSMZ" 3
"B_SPHNGB_HTNN" "Sphingobacterium hotanense" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "hotanense" "" "species" "Xiao et al., 2013" "790574" "DSMZ" 3
"B_SPHNGB_HUMI" "Sphingobacterium humi" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "humi" "" "species" "Lee et al., 2017" "796154" "DSMZ" 3
"B_SPHNGB_JJNS" "Sphingobacterium jejuense" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "jejuense" "" "species" "Siddiqi et al., 2016" "794795" "DSMZ" 3
"B_SPHNGB_KTHR" "Sphingobacterium kitahiroshimense" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "kitahiroshimense" "" "species" "Matsuyama et al., 2008" "1b487ae730993a033dd44f4ec3221d2a" "CoL" 3
"B_SPHNGB_KYNG" "Sphingobacterium kyonggiense" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "kyonggiense" "" "species" "Choi et al., 2012" "790272" "DSMZ" 3
@ -56933,6 +56965,7 @@
"B_SPHNGB_SOLI" "Sphingobacterium soli" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "soli" "" "species" "Fu et al., 2017" "795506" "DSMZ" 3
"B_SPHNGB_SPRT" "Sphingobacterium spiritivorum" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "spiritivorum" "" "species" "Yabuuchi et al., 1983" "7d4093a1793e9c443c9697c57b1b5011" "CoL" 3 "61675006"
"B_SPHNGB_SUAD" "Sphingobacterium suaedae" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "suaedae" "" "species" "Sun et al., 2015" "793626" "DSMZ" 3
"B_SPHNGB_TBCS" "Sphingobacterium tabacisoli" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "tabacisoli" "" "species" "Zhou et al., 2017" "796213" "DSMZ" 3
"B_SPHNGB_TERR" "Sphingobacterium terrae" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "terrae" "" "species" "Chaudhary et al., 2018" "797530" "DSMZ" 3
"B_SPHNGB_THLP" "Sphingobacterium thalpophilum" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "thalpophilum" "" "species" "Takeuchi et al., 1993" "f74e7f7b4ef1d3d157e02c43c944e41b" "CoL" 3 "113954009"
"B_SPHNGB_THRM" "Sphingobacterium thermophilum" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "thermophilum" "" "species" "Yabe et al., 2016" "790761" "DSMZ" 3
@ -57001,8 +57034,10 @@
"B_SNGMNS_AERL" "Sphingomonas aerolata" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "aerolata" "" "species" "Busse et al., 2003" "d71319c356a2c3522a7f29010b7d062d" "CoL" 2 "438982007"
"B_SNGMNS_AERP" "Sphingomonas aerophila" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "aerophila" "" "species" "Kim et al., 2014" "791661" "DSMZ" 2
"B_SNGMNS_AEST" "Sphingomonas aestuarii" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "aestuarii" "" "species" "Roh et al., 2009" "9ee9164ad23512c6aa68e8e68b1ad8b5" "CoL" 2
"B_SNGMNS_AGRI" "Sphingomonas agri" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "agri" "" "species" "Siddiqi et al., 2017" "796214" "DSMZ" 2
"B_SNGMNS_ALPN" "Sphingomonas alpina" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "alpina" "" "species" "Margesin et al., 2012" "790013" "DSMZ" 2
"B_SNGMNS_ANTR" "Sphingomonas antarctica" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "antarctica" "" "species" "Huang et al., 2017" "796054" "DSMZ" 2
"B_SNGMNS_AQTC" "Sphingomonas aquatica" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "aquatica" "" "species" "Choi et al., 2017" "795211" "DSMZ" 2
"B_SNGMNS_AQTL" "Sphingomonas aquatilis" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "aquatilis" "" "species" "Lee et al., 2001" "a0d00893c721d7c701437af6d0b68e37" "CoL" 2 "438983002"
"B_SNGMNS_ARNT" "Sphingomonas arantia" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "arantia" "" "species" "Jia et al., 2016" "793916" "DSMZ" 2
"B_SNGMNS_ASCC" "Sphingomonas asaccharolytica" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "asaccharolytica" "" "species" "Takeuchi et al., 1995" "d0f62018c7890604901ac6b83768877f" "CoL" 2 "439679006"
@ -57030,6 +57065,7 @@
"B_SNGMNS_FLAV" "Sphingomonas flava" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "flava" "" "species" "Corrig Du et al., 2015" "793390" "DSMZ" 2
"B_SNGMNS_FNTC" "Sphingomonas fonticola" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "fonticola" "" "species" "Sheu et al., 2015" "793605" "DSMZ" 2
"B_SNGMNS_FRMS" "Sphingomonas formosensis" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "formosensis" "" "species" "Lin et al., 2012" "790015" "DSMZ" 2
"B_SNGMNS_FRGD" "Sphingomonas frigidaeris" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "frigidaeris" "" "species" "Lee et al., 2017" "796111" "DSMZ" 2
"B_SNGMNS_GEI" "Sphingomonas gei" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "gei" "" "species" "Zhu et al., 2015" "792696" "DSMZ" 2
"B_SNGMNS_GMNS" "Sphingomonas gimensis" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "gimensis" "" "species" "Feng et al., 2014" "792286" "DSMZ" 2
"B_SNGMNS_GNSN" "Sphingomonas ginsengisoli" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "ginsengisoli" "" "species" "An et al., 2013" "777083" "DSMZ" 2
@ -57062,6 +57098,7 @@
"B_SNGMNS_MALI" "Sphingomonas mali" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "mali" "" "species" "Takeuchi et al., 1995" "14d21127ff1cd6290f9e142244dc243d" "CoL" 2 "438538007"
"B_SNGMNS_MLNS" "Sphingomonas melonis" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "melonis" "" "species" "Buonaurio et al., 2002" "5862b2dca76ce845bc6a61e42730d25b" "CoL" 2 "437985007"
"B_SNGMNS_MSPH" "Sphingomonas mesophila" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "mesophila" "" "species" "Li et al., 2019" "800696" "DSMZ" 2
"B_SNGMNS_MTLL" "Sphingomonas metalli" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "metalli" "" "species" "Feng et al., 2016" "794142" "DSMZ" 2
"B_SNGMNS_MLLS" "Sphingomonas molluscorum" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "molluscorum" "" "species" "Romanenko et al., 2007" "faae3d7c0df29170b19eda034247ace1" "CoL" 2 "709300006"
"B_SNGMNS_MNTN" "Sphingomonas montana" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "montana" "" "species" "Manandhar et al., 2018" "796387" "DSMZ" 2
"B_SNGMNS_MNTS" "Sphingomonas montis" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Sphingomonadaceae" "Sphingomonas" "montis" "" "species" "Chaudhary et al., 2019" "798059" "DSMZ" 2
@ -58149,6 +58186,7 @@
"B_STPHY_CAEL" "Staphylococcus caeli" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Staphylococcaceae" "Staphylococcus" "caeli" "" "species" "MacFadyen et al., 2019" "798096" "DSMZ" 1
"B_STPHY_CPTS" "Staphylococcus capitis" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Staphylococcaceae" "Staphylococcus" "capitis" "" "species" "Kloos et al., 1975" "1193b8010f095b3f414b0b4a7e61d941" "CoL" 1 "40347003"
"B_STPHY_CPTS_URLY" "Staphylococcus capitis urealyticus" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Staphylococcaceae" "Staphylococcus" "capitis" "urealyticus" "infraspecies" "Bannerman et al., 1991" "ce0c0335b06f21a72ac55f8b284d52f1" "CoL" 1 "103492009"
"B_STPHY_CPTS_YTCS" "Staphylococcus capitis ureolyticus" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Staphylococcaceae" "Staphylococcus" "capitis" "ureolyticus" "species" "Bannerman et al., 1991" "784963" "DSMZ" 1
"B_STPHY_CAPR" "Staphylococcus caprae" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Staphylococcaceae" "Staphylococcus" "caprae" "" "species" "Devriese et al., 1998" "bbe445567c16e696e54dc109ba6bc9b8" "CoL" 1 "76969000"
"B_STPHY_CRNS" "Staphylococcus carnosus" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Staphylococcaceae" "Staphylococcus" "carnosus" "" "species" "Schleifer et al., 1982" "6e3a53da19778d9db3bef31a02cab1c8" "CoL" 1 "9784002"
"B_STPHY_CRNS_UTLS" "Staphylococcus carnosus utilis" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Staphylococcaceae" "Staphylococcus" "carnosus" "utilis" "infraspecies" "Probst et al., 1998" "4f69c1cb6be4cb74200fdab137ff0acc" "CoL" 1 "438733001"
@ -58201,6 +58239,7 @@
"B_STPHY_SCCN" "Staphylococcus succinus" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Staphylococcaceae" "Staphylococcus" "succinus" "" "species" "Lambert et al., 1998" "97b472391b6336adfbe3f99fa8b10469" "CoL" 1 "438729008"
"B_STPHY_SCCN_CASE" "Staphylococcus succinus casei" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Staphylococcaceae" "Staphylococcus" "succinus" "casei" "infraspecies" "Place et al., 2003" "0926b1c776f856ed9a9f9c1a9fad60f2" "CoL" 1 "440815004"
"B_STPHY_VTLN" "Staphylococcus vitulinus" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Staphylococcaceae" "Staphylococcus" "vitulinus" "" "species" "Webster et al., 2004" "9caa058a9ea00c6454065dd426548abe" "CoL" 1 "440569005"
"B_STPHY_VTLS" "Staphylococcus vitulus" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Staphylococcaceae" "Staphylococcus" "vitulus" "" "species" "Webster et al., 2004" "784968" "DSMZ" 1
"B_STPHY_WRNR" "Staphylococcus warneri" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Staphylococcaceae" "Staphylococcus" "warneri" "" "species" "Kloos et al., 1975" "7ea86b655238a5c4ef000deada350eca" "CoL" 1 "63550006"
"B_STPHY_XYLS" "Staphylococcus xylosus" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Staphylococcaceae" "Staphylococcus" "xylosus" "" "species" "Schleifer et al., 1975" "117a3247c6aff3f937e16f4efe1eb22c" "CoL" 1 "32737005"
"B_STPHYL" "Staphylospora" "Bacteria" "Firmicutes" "Bacilli" "Bacillales" "Thermoactinomycetaceae" "Staphylospora" "" "" "genus" "" "DSMZ" 2
@ -58916,7 +58955,9 @@
"B_STRPT_CAML" "Streptococcus cameli" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "cameli" "" "species" "Kadri et al., 2015" "792771" "DSMZ" 1
"B_STRPT_CANS" "Streptococcus canis" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "canis" "" "species" "Devriese et al., 1986" "0849b426bc0abdfe28d40c1495f1fd5e" "CoL" 1 "88231003"
"B_STRPT_CAPR" "Streptococcus caprae" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "caprae" "" "species" "Vela et al., 2016" "793751" "DSMZ" 1
"B_STRPT_CSSL" "Streptococcus casseliflavus" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "casseliflavus" "" "species" "Vaughan et al., 1979" "781304" "DSMZ" 1
"B_STRPT_CSTR" "Streptococcus castoreus" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "castoreus" "" "species" "Lawson et al., 2005" "2a64aa1e506cfff4215fc3ad53922a79" "CoL" 1
"B_STRPT_CAVI" "Streptococcus caviae" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "caviae" "" "species" "Palakawong Na Ayudthaya et al., 2017" "795284" "DSMZ" 1
"B_STRPT_CHNJ" "Streptococcus chenjunshii" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "chenjunshii" "" "species" "Tian et al., 2019" "800708" "DSMZ" 1
"B_STRPT_CNST_PHRY" "Streptococcus constellatus pharyngis" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "constellatus" "pharyngis" "infraspecies" "Whiley et al., 1999" "ac1ecd4578b7331814b44a98c2f733a0" "CoL" 1 "415602002"
"B_STRPT_CNST_VBRG" "Streptococcus constellatus viborgensis" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "constellatus" "viborgensis" "species" "Jensen et al., 2013" "790923" "DSMZ" 1
@ -58986,6 +59027,7 @@
"B_STRPT_ORSR" "Streptococcus orisratti" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "orisratti" "" "species" "Zhu et al., 2000" "6ee21abee87a261ed1b1efb79085d113" "CoL" 1 "438034004"
"B_STRPT_RSIS" "Streptococcus orisuis" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "orisuis" "" "species" "Takada et al., 2007" "3fbb34ad017368789bbad1056730542c" "CoL" 1
"B_STRPT_OVIS" "Streptococcus ovis" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "ovis" "" "species" "Collins et al., 2001" "1fcad4cd3f156ca858b302d38971ee5e" "CoL" 1 "438035003"
"B_STRPT_OVBR" "Streptococcus ovuberis" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "ovuberis" "" "species" "Zamora et al., 2017" "796216" "DSMZ" 1
"B_STRPT_PNDN" "Streptococcus panodentis" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "panodentis" "" "species" "Okamoto et al., 2016" "793690" "DSMZ" 1
"B_STRPT_PNTH" "Streptococcus pantholopis" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "pantholopis" "" "species" "Bai et al., 2016" "794568" "DSMZ" 1
"B_STRPT_PRSN" "Streptococcus parasanguinis" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "parasanguinis" "" "species" "Whiley et al., 1990" "cb634a0af53fb79b57a68cf461079c04" "CoL" 1 "113990002"

12
data-raw/reproduction_of_microorganisms.R
View File

@ -821,6 +821,18 @@ sum(duplicated(MOs$mo))
sum(duplicated(MOs$fullname))
colnames(MOs)
# add the ones we would delete now, that have unexisting codes and names (also in the old names)
MOs <- MOs %>%
mutate(mo = as.character(mo)) %>%
bind_rows(
AMR::microorganisms %>%
mutate(mo = as.character(mo)) %>%
filter(genus %in% gen & !fullname %in% AMR::microorganisms$fullname &
!fullname %in% AMR::microorganisms.old$fullname &
!mo %in% microorganisms$mo) %>%
select(all_of(colnames(AMR::microorganisms)))
)
# here we welcome the new ones:
MOs %>% arrange(fullname) %>% filter(!fullname %in% AMR::microorganisms$fullname) %>% View()
MOs.old %>% arrange(fullname) %>% filter(!fullname %in% AMR::microorganisms.old$fullname) %>% View()

BIN
data/microorganisms.rda
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Binary file not shown.

34
docs/404.html
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@ -9,12 +9,12 @@
<title>Page not found (404) • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="https://msberends.gitlab.io/AMR/favicon-16x16.png">
<link rel="icon" type="image/png" sizes="32x32" href="https://msberends.gitlab.io/AMR/favicon-32x32.png">
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="https://msberends.gitlab.io/AMR/apple-touch-icon.png" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
@ -25,8 +25,8 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="https://msberends.gitlab.io/AMR/bootstrap-toc.css">
<script src="https://msberends.gitlab.io/AMR/bootstrap-toc.js"></script>
<link rel="stylesheet" href="https://msberends.github.io/AMR/bootstrap-toc.css">
<script src="https://msberends.github.io/AMR/bootstrap-toc.js"></script>
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
@ -40,16 +40,16 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="https://msberends.gitlab.io/AMR/pkgdown.css" rel="stylesheet">
<script src="https://msberends.gitlab.io/AMR/pkgdown.js"></script>
<link href="https://msberends.github.io/AMR/pkgdown.css" rel="stylesheet">
<script src="https://msberends.github.io/AMR/pkgdown.js"></script>
<link href="https://msberends.gitlab.io/AMR/extra.css" rel="stylesheet">
<script src="https://msberends.gitlab.io/AMR/extra.js"></script>
<link href="https://msberends.github.io/AMR/extra.css" rel="stylesheet">
<script src="https://msberends.github.io/AMR/extra.js"></script>
<meta property="og:title" content="Page not found (404)" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -80,8 +80,8 @@
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9025</span>
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -199,8 +199,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>

8
docs/LICENSE-text.html
View File

@ -49,7 +49,7 @@
<script src="extra.js"></script>
<meta property="og:title" content="License" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9025</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -199,8 +199,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>

8
docs/articles/index.html
View File

@ -49,7 +49,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Articles" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9025</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -199,8 +199,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>

10
docs/authors.html
View File

@ -49,7 +49,7 @@
<script src="extra.js"></script>
<meta property="og:title" content="Citation and Authors" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9025</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -199,8 +199,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -226,7 +226,7 @@
<div class="contents col-md-9">
<div class="page-header">
<h1>Citation</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/inst/CITATION'><code>inst/CITATION</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/inst/CITATION'><code>inst/CITATION</code></a></small>
</div>
<p>Berends MS, Luz CF et al. (2019). AMR - An R Package for Working with Antimicrobial Resistance Data. bioRxiv, https://doi.org/10.1101/810622</p>

4
docs/extra.css
View File

@ -4,7 +4,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -17,7 +17,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
*/

5
docs/extra.js
View File

@ -4,7 +4,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -17,7 +17,7 @@
# 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 more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
*/
@ -88,6 +88,7 @@ $( document ).ready(function() {
x = x.replace("Sofia", "Dr. Sofia");
x = x.replace("Dennis", "Dr. Dennis");
x = x.replace("Judith", "Dr. Judith");
x = x.replace("Gwen", "Dr. Gwen");
}
return(x);
}

16
docs/index.html
View File

@ -24,7 +24,7 @@
using evidence-based methods, like those defined by Leclercq et al. (2013)
&lt;doi:10.1111/j.1469-0691.2011.03703.x&gt; and the Clinical and Laboratory
Standards Institute (2014) &lt;isbn: 1-56238-899-1&gt;.">
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg">
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@ -43,7 +43,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9025</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -161,8 +161,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -199,8 +199,8 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
<a href="#what-is-amr-for-r" class="anchor"></a>What is <code>AMR</code> (for R)?</h3>
<p><em>(To find out how to conduct AMR analysis, please <a href="./articles/AMR.html">continue reading here to get started</a>.)</em></p>
<p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org">R package</a> 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. <strong>Our aim is to provide a standard</strong> for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~70,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~550 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>This package was created for both routine data analysis and academic research, at the Faculty of Medical Sciences of the University of Groningen, the Netherlands, and the Medical Microbiology &amp; Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is <a href="./news">actively maintained</a> and is free software (see <a href="#copyright">Copyright</a>). It is fully independent of any other R package, works with all versions of R since R-3.0.0 (April 2013) and has a total file size of only 5 MB. It was designed to work in any setting, including those with very limited resources.</p>
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~70,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~550 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>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). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl">Certe Medical Diagnostics and Advice</a> and <a href="https://www.umcg.nl">University Medical Center Groningen</a>. This R package is <a href="./news">actively maintained</a> and is free software (see <a href="#copyright">Copyright</a>).</p>
<div class="main-content">
<p>
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in more than 100 countries</strong><br> Since its first public release in early 2018, this package has been downloaded from more than 100 countries <small>(source: <a href="https://cran-logs.rstudio.com" target="_blank">CRAN logs</a>)</small>. Click the map to enlarge, to see the names of the countries.
@ -371,9 +371,9 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
<ul class="list-unstyled">
<li>Download from CRAN at <br><a href="https://cloud.r-project.org/package=AMR">https://​cloud.r-project.org/​package=AMR</a>
</li>
<li>Browse source code at <br><a href="https://gitlab.com/msberends/AMR/">https://​gitlab.com/​msberends/​AMR/​</a>
<li>Browse source code at <br><a href="https://github.com/msberends/AMR/">https://​github.com/​msberends/​AMR/​</a>
</li>
<li>Report a bug at <br><a href="https://gitlab.com/msberends/AMR/issues">https://​gitlab.com/​msberends/​AMR/​issues</a>
<li>Report a bug at <br><a href="https://github.com/msberends/AMR/issues">https://​github.com/​msberends/​AMR/​issues</a>
</li>
</ul>
</div>

22
docs/news/index.html
View File

@ -49,7 +49,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Changelog" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9025</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -199,8 +199,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -226,16 +226,16 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1 data-toc-skip>Changelog <small></small></h1>
<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1209025" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9025">
<a href="#amr-1209025" class="anchor"></a>AMR 1.2.0.9025<small> Unreleased </small>
<div id="amr-1209026" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9026">
<a href="#amr-1209026" class="anchor"></a>AMR 1.2.0.9026<small> Unreleased </small>
</h1>
<div id="last-updated-03-jul-2020" class="section level2">
<div id="last-updated-08-jul-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-03-jul-2020" class="anchor"></a><small>Last updated: 03-Jul-2020</small>
<a href="#last-updated-08-jul-2020" class="anchor"></a><small>Last updated: 08-Jul-2020</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
@ -266,7 +266,7 @@
<ul>
<li>95% speed improvement (!) by using other base R functions for calculation</li>
<li>Using unexisting columns wil now return an error instead of dropping them silently</li>
<li>Using variables for column names (as well as <code><a href="https://dplyr.tidyverse.org/reference/reexports.html">dplyr::all_of()</a></code>) now works again</li>
<li>Using variables for column names (as well as selectors like <code><a href="https://dplyr.tidyverse.org/reference/reexports.html">dplyr::all_of()</a></code>) now works again</li>
</ul>
</li>
<li>Improvements for <code><a href="../reference/as.ab.html">as.ab()</a></code>:

6
docs/pkgdown.yml
View File

@ -10,8 +10,8 @@ articles:
WHONET: WHONET.html
benchmarks: benchmarks.html
resistance_predict: resistance_predict.html
last_built: 2020-07-03T10:14Z
last_built: 2020-07-08T12:47Z
urls:
reference: https://msberends.gitlab.io/AMR/reference
article: https://msberends.gitlab.io/AMR/articles
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

12
docs/reference/AMR-deprecated.html
View File

@ -50,7 +50,7 @@
<meta property="og:title" content="Deprecated functions — AMR-deprecated" />
<meta property="og:description" content="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)." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Deprecated functions</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/deprecated.R'><code>R/deprecated.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/deprecated.R'><code>R/deprecated.R</code></a></small>
<div class="hidden name"><code>AMR-deprecated.Rd</code></div>
</div>
@ -258,7 +258,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

14
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@ -50,7 +50,7 @@
<meta property="og:title" content="The <code>AMR</code> Package — AMR" />
<meta property="og:description" content="Welcome to the AMR package." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>The <code>AMR</code> Package</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/amr.R'><code>R/amr.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/amr.R'><code>R/amr.R</code></a></small>
<div class="hidden name"><code>AMR.Rd</code></div>
</div>
@ -263,7 +263,7 @@
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="contact-us"><a class="anchor" href="#contact-us"></a>Contact Us</h2>
@ -278,7 +278,7 @@ Post Office Box 30001 <br />
9700 RB Groningen <br />
The Netherlands</p>
<p>If you have found a bug, please file a new issue at: <br />
<a href='https://gitlab.com/msberends/AMR/issues'>https://gitlab.com/msberends/AMR/issues</a></p>
<a href='https://github.com/msberends/AMR/issues'>https://github.com/msberends/AMR/issues</a></p>
</div>
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@ -50,7 +50,7 @@
<meta property="og:title" content="WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC" />
<meta property="og:description" content="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." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/whocc.R'><code>R/whocc.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/whocc.R'><code>R/whocc.R</code></a></small>
<div class="hidden name"><code>WHOCC.Rd</code></div>
</div>
@ -250,7 +250,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'><a href='as.ab.html'>as.ab</a></span>(<span class='st'>"meropenem"</span>)

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@ -50,7 +50,7 @@
<meta property="og:title" content="Data set with 500 isolates - WHONET example — WHONET" />
<meta property="og:description" content="This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The data itself was based on our example_isolates data set." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data set with 500 isolates - WHONET example</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>WHONET.Rd</code></div>
</div>
@ -273,7 +273,7 @@
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
</div>
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14
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@ -50,7 +50,7 @@
<meta property="og:title" content="Retrieve antimicrobial drug names and doses from clinical text — ab_from_text" />
<meta property="og:description" content="Use this function on e.g. clinical texts from health care records. It returns a list with all antimicrobial drugs, doses and forms of administration found in the texts." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Retrieve antimicrobial drug names and doses from clinical text</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ab_from_text.R'><code>R/ab_from_text.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ab_from_text.R'><code>R/ab_from_text.R</code></a></small>
<div class="hidden name"><code>ab_from_text.Rd</code></div>
</div>
@ -299,12 +299,12 @@
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># mind the bad spelling of amoxicillin in this line, </span>

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@ -50,7 +50,7 @@
<meta property="og:title" content="Property of an antibiotic — ab_property" />
<meta property="og:description" content="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()." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Property of an antibiotic</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ab_property.R'><code>R/ab_property.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ab_property.R'><code>R/ab_property.R</code></a></small>
<div class="hidden name"><code>ab_property.Rd</code></div>
</div>
@ -330,7 +330,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><a href='antibiotics.html'>antibiotics</a></p></div>

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@ -50,7 +50,7 @@
<meta property="og:title" content="Age in years of individuals — age" />
<meta property="og:description" content="Calculates age in years based on a reference date, which is the sytem date at default." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Age in years of individuals</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/age.R'><code>R/age.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/age.R'><code>R/age.R</code></a></small>
<div class="hidden name"><code>age.Rd</code></div>
</div>
@ -272,7 +272,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p>To split ages into groups, use the <code><a href='age_groups.html'>age_groups()</a></code> function.</p></div>

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@ -50,7 +50,7 @@
<meta property="og:title" content="Split ages into age groups — age_groups" />
<meta property="og:description" content="Split ages into age groups defined by the split parameter. This allows for easier demographic (antimicrobial resistance) analysis." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Split ages into age groups</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/age.R'><code>R/age.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/age.R'><code>R/age.R</code></a></small>
<div class="hidden name"><code>age_groups.Rd</code></div>
</div>
@ -281,7 +281,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p>To determine ages, based on one or more reference dates, use the <code><a href='age.html'>age()</a></code> function.</p></div>

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@ -50,7 +50,7 @@
<meta property="og:title" content="Data sets with 558 antimicrobials — antibiotics" />
<meta property="og:description" content="Two data sets containing all antibiotics/antimycotics and antivirals. Use as.ab() or one of the 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." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data sets with 558 antimicrobials</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>antibiotics.Rd</code></div>
</div>
@ -291,13 +291,13 @@
<p>These data sets are available as 'flat files' for use even without R - you can find the files here:</p><ul>
<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data-raw/antibiotics.txt'>https://gitlab.com/msberends/AMR/raw/master/data-raw/antibiotics.txt</a></p></li>
<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data-raw/antivirals.txt'>https://gitlab.com/msberends/AMR/raw/master/data-raw/antivirals.txt</a></p></li>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data-raw/antibiotics.txt'>https://github.com/msberends/AMR/raw/master/data-raw/antibiotics.txt</a></p></li>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data-raw/antivirals.txt'>https://github.com/msberends/AMR/raw/master/data-raw/antivirals.txt</a></p></li>
</ul>
<p>Files in R format (with preserved data structure) can be found here:</p><ul>
<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data/antibiotics.rda'>https://gitlab.com/msberends/AMR/raw/master/data/antibiotics.rda</a></p></li>
<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data/antivirals.rda'>https://gitlab.com/msberends/AMR/raw/master/data/antivirals.rda</a></p></li>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data/antibiotics.rda'>https://github.com/msberends/AMR/raw/master/data/antibiotics.rda</a></p></li>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data/antivirals.rda'>https://github.com/msberends/AMR/raw/master/data/antivirals.rda</a></p></li>
</ul>
@ -314,7 +314,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a></p></div>

14
docs/reference/as.ab.html
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@ -50,7 +50,7 @@
<meta property="og:title" content="Transform to antibiotic ID — as.ab" />
<meta property="og:description" content="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)." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Transform to antibiotic ID</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ab.R'><code>R/ab.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ab.R'><code>R/ab.R</code></a></small>
<div class="hidden name"><code>as.ab.Rd</code></div>
</div>
@ -282,7 +282,7 @@
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<h2 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</h2>
@ -296,7 +296,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'>

12
docs/reference/as.disk.html
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@ -50,7 +50,7 @@
<meta property="og:title" content="Class 'disk' — as.disk" />
<meta property="og:description" content="This transforms a vector to a new class disk, which is a growth zone size (around an antibiotic disk) in millimetres between 6 and 50." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Class 'disk'</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/disk.R'><code>R/disk.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/disk.R'><code>R/disk.R</code></a></small>
<div class="hidden name"><code>as.disk.Rd</code></div>
</div>
@ -269,7 +269,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>

12
docs/reference/as.mic.html
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@ -50,7 +50,7 @@
<meta property="og:title" content="Class 'mic' — as.mic" />
<meta property="og:description" content="This transforms a vector to a new class mic, which is an ordered factor with valid MIC values as levels. Invalid MIC values will be translated as NA with a warning." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Class 'mic'</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mic.R'><code>R/mic.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mic.R'><code>R/mic.R</code></a></small>
<div class="hidden name"><code>as.mic.Rd</code></div>
</div>
@ -269,7 +269,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>

12
docs/reference/as.mo.html
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@ -50,7 +50,7 @@
<meta property="og:title" content="Transform to microorganism ID — as.mo" />
<meta property="og:description" content="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 &quot;Staphylococcus aureus&quot;), an abbreviated name (like &quot;S. aureus&quot;), an abbreviation known in the field (like &quot;MRSA&quot;), or just a genus. Please see Examples." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Transform to microorganism ID</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/mo.R'><code>R/mo.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mo.R'><code>R/mo.R</code></a></small>
<div class="hidden name"><code>as.mo.Rd</code></div>
</div>
@ -378,7 +378,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a> for the <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> that is being used to determine ID's.</p>

14
docs/reference/as.rsi.html
View File

@ -50,7 +50,7 @@
<meta property="og:title" content="Class 'rsi' — as.rsi" />
<meta property="og:description" content="Interpret 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 &amp;lt; I &amp;lt; R. Invalid antimicrobial interpretations will be translated as NA with a warning." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Class 'rsi'</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/rsi.R'><code>R/rsi.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/rsi.R'><code>R/rsi.R</code></a></small>
<div class="hidden name"><code>as.rsi.Rd</code></div>
</div>
@ -308,7 +308,7 @@
<p>When using <code>as.rsi()</code> on untransformed data, the data will be cleaned to only contain values S, I and R. When using the function on data with class <code><a href='as.mic.html'>mic</a></code> (using <code><a href='as.mic.html'>as.mic()</a></code>) or class <code><a href='as.disk.html'>disk</a></code> (using <code><a href='as.disk.html'>as.disk()</a></code>), the data will be interpreted based on the guideline set with the <code>guideline</code> parameter.</p>
<p>Supported guidelines to be used as input for the <code>guideline</code> parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020". Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> for input will automatically select the latest version of that guideline.</p>
<p>The repository of this package <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine readable version</a> of all guidelines. This is a CSV file consisting of 18,964 rows and 10 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 <strong>allows for easy implementation of these rules in laboratory information systems (LIS)</strong>.</p>
<p>The repository of this package <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine readable version</a> of all guidelines. This is a CSV file consisting of 18,964 rows and 10 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 <strong>allows for easy implementation of these rules in laboratory information systems (LIS)</strong>.</p>
<p>After using <code>as.rsi()</code>, you can use <code><a href='eucast_rules.html'>eucast_rules()</a></code> to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
<p>The function <code>is.rsi.eligible()</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> parameter.</p>
<h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
@ -336,7 +336,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='as.mic.html'>as.mic()</a></code></p></div>

12
docs/reference/atc_online.html
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@ -51,7 +51,7 @@
<meta property="og:title" content="Get ATC properties from WHOCC website — atc_online_property" />
<meta property="og:description" content="Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit.
This function requires an internet connection." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -83,7 +83,7 @@ This function requires an internet connection." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -201,8 +201,8 @@ This function requires an internet connection." />
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -228,7 +228,7 @@ This function requires an internet connection." />
<div class="col-md-9 contents">
<div class="page-header">
<h1>Get ATC properties from WHOCC website</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/atc_online.R'><code>R/atc_online.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/atc_online.R'><code>R/atc_online.R</code></a></small>
<div class="hidden name"><code>atc_online.Rd</code></div>
</div>
@ -312,7 +312,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {

12
docs/reference/availability.html
View File

@ -50,7 +50,7 @@
<meta property="og:title" content="Check availability of columns — availability" />
<meta property="og:description" content="Easy check for data availability of all columns in a data set. This makes it easy to get an idea of which antimicrobial combinations can be used for calculation with e.g. susceptibility() and resistance()." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Check availability of columns</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/availability.R'><code>R/availability.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/availability.R'><code>R/availability.R</code></a></small>
<div class="hidden name"><code>availability.Rd</code></div>
</div>
@ -267,7 +267,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'>availability</span>(<span class='no'>example_isolates</span>)

12
docs/reference/bug_drug_combinations.html
View File

@ -50,7 +50,7 @@
<meta property="og:title" content="Determine bug-drug combinations — bug_drug_combinations" />
<meta property="og:description" content="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." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Determine bug-drug combinations</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/bug_drug_combinations.R'><code>R/bug_drug_combinations.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/bug_drug_combinations.R'><code>R/bug_drug_combinations.R</code></a></small>
<div class="hidden name"><code>bug_drug_combinations.Rd</code></div>
</div>
@ -333,7 +333,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># \donttest{</span>

14
docs/reference/catalogue_of_life.html
View File

@ -50,7 +50,7 @@
<meta property="og:title" content="The Catalogue of Life — catalogue_of_life" />
<meta property="og:description" content="This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>The Catalogue of Life</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
<div class="hidden name"><code>catalogue_of_life.Rd</code></div>
</div>
@ -258,12 +258,12 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</ul>
<p>The Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>) 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.</p>
<p>The syntax used to transform the original data to a cleansed R format, can be found here: <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R'>https://gitlab.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R</a>.</p>
<p>The syntax used to transform the original data to a cleansed R format, can be found here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R'>https://github.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R</a>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p>Data set <a href='microorganisms.html'>microorganisms</a> for the actual data. <br />

12
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View File

@ -50,7 +50,7 @@
<meta property="og:title" content="Version info of included Catalogue of Life — catalogue_of_life_version" />
<meta property="og:description" content="This function returns information about the included data from the Catalogue of Life." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Version info of included Catalogue of Life</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
<div class="hidden name"><code>catalogue_of_life_version.Rd</code></div>
</div>
@ -255,7 +255,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a></p></div>

12
docs/reference/count.html
View File

@ -51,7 +51,7 @@
<meta property="og:title" content="Count available isolates — count" />
<meta property="og:description" content="These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in summarise() from the dplyr package and also support grouped variables, please see Examples.
count_resistant() should be used to count resistant isolates, count_susceptible() should be used to count susceptible isolates." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9016</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -201,8 +201,8 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -228,7 +228,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<div class="col-md-9 contents">
<div class="page-header">
<h1>Count available isolates</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/count.R'><code>R/count.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/count.R'><code>R/count.R</code></a></small>
<div class="hidden name"><code>count.Rd</code></div>
</div>
@ -360,7 +360,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='proportion.html'>proportion_*</a></code> to calculate microbial resistance and susceptibility.</p></div>

16
docs/reference/eucast_rules.html
View File

@ -51,7 +51,7 @@
<meta property="og:title" content="Apply EUCAST rules — eucast_rules" />
<meta property="og:description" content="Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, http://eucast.org), see Source. This includes (1) expert rules and intrinsic resistance and (2) inferred resistance as defined in their breakpoint tables.
To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -201,8 +201,8 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -228,7 +228,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<div class="col-md-9 contents">
<div class="page-header">
<h1>Apply EUCAST rules</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/eucast_rules.R'><code>R/eucast_rules.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/eucast_rules.R'><code>R/eucast_rules.R</code></a></small>
<div class="hidden name"><code>eucast_rules.Rd</code></div>
</div>
@ -307,7 +307,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
</ul>
<p>These rules are not applied at default, since they are not approved by EUCAST. To use these rules, please use <code>eucast_rules(..., rules = "all")</code>, or set the default behaviour of the <code>[eucast_rules()]</code> function with <code><a href='https://rdrr.io/r/base/options.html'>options(AMR.eucast_rules = "all")</a></code> (or any other valid input value(s) to the <code>rules</code> parameter).</p>
<p>The file containing all EUCAST rules is located here: <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p>
<p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p>
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
@ -398,12 +398,12 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># \donttest{</span>

14
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@ -50,7 +50,7 @@
<meta property="og:title" content="Data set with 2,000 example isolates — example_isolates" />
<meta property="og:description" content="A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read the tutorial on our website." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,12 +227,12 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data set with 2,000 example isolates</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>example_isolates.Rd</code></div>
</div>
<div class="ref-description">
<p>A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>the tutorial on our website</a>.</p>
<p>A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read <a href='https://msberends.github.io/AMR/articles/AMR.html'>the tutorial on our website</a>.</p>
</div>
<pre class="usage"><span class='no'>example_isolates</span></pre>
@ -257,7 +257,7 @@
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

12
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@ -50,7 +50,7 @@
<meta property="og:title" content="Data set with unclean data — example_isolates_unclean" />
<meta property="og:description" content="A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR analysis. This data set can be used for practice." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data set with unclean data</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>example_isolates_unclean.Rd</code></div>
</div>
@ -252,7 +252,7 @@
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

10
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@ -50,7 +50,7 @@
<meta property="og:title" content="Filter isolates on result in antimicrobial class — filter_ab_class" />
<meta property="og:description" content="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." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Filter isolates on result in antimicrobial class</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/filter_ab_class.R'><code>R/filter_ab_class.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/filter_ab_class.R'><code>R/filter_ab_class.R</code></a></small>
<div class="hidden name"><code>filter_ab_class.Rd</code></div>
</div>

12
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@ -50,7 +50,7 @@
<meta property="og:title" content="Determine first (weighted) isolates — first_isolate" />
<meta property="og:description" content="Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Determine first (weighted) isolates</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/first_isolate.R'><code>R/first_isolate.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/first_isolate.R'><code>R/first_isolate.R</code></a></small>
<div class="hidden name"><code>first_isolate.Rd</code></div>
</div>
@ -393,7 +393,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='key_antibiotics.html'>key_antibiotics()</a></code></p></div>

12
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@ -50,7 +50,7 @@
<meta property="og:title" content="<em>G</em>-test for Count Data — g.test" />
<meta property="og:description" content="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)." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1><em>G</em>-test for Count Data</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/g.test.R'><code>R/g.test.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/g.test.R'><code>R/g.test.R</code></a></small>
<div class="hidden name"><code>g.test.Rd</code></div>
</div>
@ -334,7 +334,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>

12
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@ -50,7 +50,7 @@
<meta property="og:title" content="PCA biplot with <code>ggplot2</code> — ggplot_pca" />
<meta property="og:description" content="Produces a ggplot2 variant of a so-called biplot for PCA (principal component analysis), but is more flexible and more appealing than the base R biplot() function." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>PCA biplot with <code>ggplot2</code></h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ggplot_pca.R'><code>R/ggplot_pca.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ggplot_pca.R'><code>R/ggplot_pca.R</code></a></small>
<div class="hidden name"><code>ggplot_pca.Rd</code></div>
</div>
@ -376,7 +376,7 @@
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>

24
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@ -49,8 +49,8 @@
<script src="../extra.js"></script>
<meta property="og:title" content="AMR plots with <code>ggplot2</code> — ggplot_rsi" />
<meta property="og:description" content="Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal ggplot2 functions." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
<meta property="og:description" content="Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on ggplot2 functions." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9026</span>
</span>
</div>
@ -200,8 +200,8 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
@ -227,12 +227,12 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>AMR plots with <code>ggplot2</code></h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ggplot_rsi.R'><code>R/ggplot_rsi.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ggplot_rsi.R'><code>R/ggplot_rsi.R</code></a></small>
<div class="hidden name"><code>ggplot_rsi.Rd</code></div>
</div>
<div class="ref-description">
<p>Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal <a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot2</a> functions.</p>
<p>Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on <a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot2</a> functions.</p>
</div>
<pre class="usage"><span class='fu'>ggplot_rsi</span>(
@ -393,10 +393,10 @@
<p><code>geom_rsi()</code> will take any variable from the data that has an <code><a href='as.rsi.html'>rsi</a></code> class (created with <code><a href='as.rsi.html'>as.rsi()</a></code>) using <code><a href='proportion.html'>rsi_df()</a></code> and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.</p>
<p><code>facet_rsi()</code> creates 2d plots (at default based on S/I/R) using <code><a href='https://ggplot2.tidyverse.org/reference/facet_wrap.html'>ggplot2::facet_wrap()</a></code>.</p>
<p><code>scale_y_percent()</code> transforms the y axis to a 0 to 100% range using <code>ggplot2::scale_continuous()</code>.</p>
<p><code>scale_rsi_colours()</code> sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using <code>ggplot2::scale_brewer()</code>.</p>
<p><code>scale_y_percent()</code> transforms the y axis to a 0 to 100% range using <code><a href='https://ggplot2.tidyverse.org/reference/scale_continuous.html'>ggplot2::scale_y_continuous()</a></code>.</p>
<p><code>scale_rsi_colours()</code> sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using <code><a href='https://ggplot2.tidyverse.org/reference/scale_manual.html'>ggplot2::scale_fill_manual()</a></code>.</p>
<p><code>theme_rsi()</code> is a [ggplot2 theme][<code><a href='https://ggplot2.tidyverse.org/reference/theme.html'>ggplot2::theme()</a></code> with minimal distraction.</p>
<p><code>labels_rsi_count()</code> print datalabels on the bars with percentage and amount of isolates using <code><a href='https://ggplot2.tidyverse.org/reference/geom_text.html'>ggplot2::geom_text()</a></code></p>
<p><code>labels_rsi_count()</code> print datalabels on the bars with percentage and amount of isolates using <code><a href='https://ggplot2.tidyverse.org/reference/geom_text.html'>ggplot2::geom_text()</a></code>.</p>
<p><code>ggplot_rsi()</code> is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (<code>%&gt;%</code>). See Examples.</p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
@ -404,12 +404,12 @@
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"ggplot2"</span>) <span class='kw'>&amp;</span> <span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {

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