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< h1 > Data set with bacterial intrinsic resistance< / h1 >
< 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 > intrinsic_resistant.Rd< / code > < / div >
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< p > Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.< / p >
< / div >
< pre class = "usage" > < span class = 'kw' > intrinsic_resistant< / span > < / pre >
< h2 class = "hasAnchor" id = "format" > < a class = "anchor" href = "#format" > < / a > Format< / h2 >
< p > A < code > < a href = 'https://rdrr.io/r/base/data.frame.html' > data.frame< / a > < / code > with 49,462 observations and 2 variables:< / p > < ul >
< li > < p > < code > microorganism< / code > < br / > Name of the microorganism< / p > < / li >
< li > < p > < code > antibiotic< / code > < br / > Name of the antibiotic drug< / p > < / li >
< / ul >
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
< p > The repository of this < code > AMR< / code > package contains a file comprising this exact data set: < a href = 'https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt' > https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt< / a > . This file < strong > allows for machine reading EUCAST guidelines about intrinsic resistance< / strong > , which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.< / p >
< p > This data set is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version 3.1, 2016.< / 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.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 > . As we would like to better understand the backgrounds and needs of our users, please < a href = 'https://msberends.github.io/AMR/survey.html' > participate in our survey< / a > !< / p >
< h2 class = "hasAnchor" id = "examples" > < a class = "anchor" href = "#examples" > < / a > Examples< / h2 >
< pre class = "examples" > < span class = 'co' > if< / span > (< span class = 'fu' > < a href = 'https://rdrr.io/r/base/library.html' > require< / a > < / span > (< span class = 'st' > < a href = 'https://dplyr.tidyverse.org' > "dplyr"< / a > < / span > )) {
< span class = 'kw' > intrinsic_resistant< / span > < span class = 'op' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/filter.html' > filter< / a > < / span > (< span class = 'kw' > antibiotic< / span > < span class = 'op' > ==< / span > < span class = 'st' > "Vancomycin"< / span > , < span class = 'kw' > microorganism< / span > < span class = 'op' > %like%< / span > < span class = 'st' > "Enterococcus"< / span > ) < span class = 'op' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/pull.html' > pull< / a > < / span > (< span class = 'kw' > microorganism< / span > )
< span class = 'co' > # [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"< / span >
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< p > Developed by < a href = 'https://www.rug.nl/staff/m.s.berends/' > Matthijs S. Berends< / a > , < a href = 'https://www.rug.nl/staff/c.f.luz/' > Christian F. Luz< / a > , < a href = 'https://www.rug.nl/staff/a.w.friedrich/' > Alexander W. Friedrich< / a > , < a href = 'https://www.rug.nl/staff/b.sinha/' > Bhanu N. M. Sinha< / a > , < a href = 'https://www.rug.nl/staff/c.j.albers/' > Casper J. Albers< / a > , < a href = 'https://www.rug.nl/staff/c.glasner/' > Corinna Glasner< / a > .< / p >
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