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data-raw
inst
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AMR-deprecated.Rd
AMR-options.Rd
AMR.Rd
WHOCC.Rd
WHONET.Rd
ab_from_text.Rd
ab_property.Rd
add_custom_antimicrobials.Rd
add_custom_microorganisms.Rd
age.Rd
age_groups.Rd
antibiogram.Rd
antimicrobial_selectors.Rd
antimicrobials.Rd
as.ab.Rd
as.av.Rd
as.disk.Rd
as.mic.Rd
as.mo.Rd
as.sir.Rd
atc_online.Rd
av_from_text.Rd
av_property.Rd
availability.Rd
bug_drug_combinations.Rd
clinical_breakpoints.Rd
count.Rd
custom_eucast_rules.Rd
dosage.Rd
eucast_rules.Rd
example_isolates.Rd
example_isolates_unclean.Rd
export_ncbi_biosample.Rd
first_isolate.Rd
g.test.Rd
get_episode.Rd
ggplot_pca.Rd
ggplot_sir.Rd
guess_ab_col.Rd
intrinsic_resistant.Rd
italicise_taxonomy.Rd
join.Rd
key_antimicrobials.Rd
kurtosis.Rd
like.Rd
mdro.Rd
mean_amr_distance.Rd
microorganisms.Rd
microorganisms.codes.Rd
microorganisms.groups.Rd
mo_matching_score.Rd
mo_property.Rd
mo_source.Rd
pca.Rd
plot.Rd
proportion.Rd
random.Rd
resistance_predict.Rd
skewness.Rd
top_n_microorganisms.Rd
translate.Rd
pkgdown
tests
vignettes
.Rbuildignore
.gitignore
AMR.Rproj
CRAN-SUBMISSION
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
README.Rmd
README.md
_pkgdown.yml
codecov.yml
cran-comments.md
index.Rmd
index.md
logo.svg
42 lines
2.0 KiB
R
42 lines
2.0 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/data.R
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\docType{data}
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\name{intrinsic_resistant}
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\alias{intrinsic_resistant}
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\title{Data Set Denoting Bacterial Intrinsic Resistance}
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\format{
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A \link[tibble:tibble]{tibble} with 271 905 observations and 2 variables:
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\itemize{
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\item \code{mo}\cr Microorganism ID which occurs in \code{\link[=microorganisms]{microorganisms$mo}}. Names can be retrieved using \code{\link[=mo_name]{mo_name()}}.
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\item \code{ab}\cr Antimicrobial ID which occurs in \code{\link[=antimicrobials]{antimicrobials$ab}}. Names can be retrieved using \code{\link[=ab_name]{ab_name()}}.
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}
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}
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\usage{
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intrinsic_resistant
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}
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\description{
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Data set containing 'EUCAST Expected Resistant Phenotypes' of \emph{all} bug-drug combinations between the \link{microorganisms} and \link{antimicrobials} data sets.
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}
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\details{
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This data set is currently based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023).
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This data set is internally used by:
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\itemize{
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\item \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} (an \link[=antimicrobial_selectors]{antimicrobial selector})
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\item \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}}
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}
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}
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\section{Download Our Reference Data}{
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All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
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For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
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Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw/datasets}{our GitHub repository}.
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}
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\examples{
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intrinsic_resistant
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}
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\keyword{datasets}
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