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< h1 > Antibiotic class selectors< / h1 >
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< small class = "dont-index" > Source: < a href = 'https://github.com/msberends/AMR/blob/master/R/ab_class_selectors.R' > < code > R/ab_class_selectors.R< / code > < / a > < / small >
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< div class = "hidden name" > < code > antibiotic_class_selectors.Rd< / code > < / div >
< / div >
< div class = "ref-description" >
< p > Use these selection helpers inside any function that allows < a href = 'https://tidyselect.r-lib.org/reference/language.html' > Tidyverse selections< / a > , like < code > < a href = 'https://dplyr.tidyverse.org/reference/select.html' > dplyr::select()< / a > < / code > or < code > < a href = 'https://tidyr.tidyverse.org/reference/pivot_longer.html' > tidyr::pivot_longer()< / a > < / code > . They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.< / p >
< / div >
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< pre class = "usage" > < span class = 'fu' > ab_class< / span > (< span class = 'no' > ab_class< / span > )
< span class = 'fu' > aminoglycosides< / span > ()
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< span class = 'fu' > carbapenems< / span > ()
< span class = 'fu' > cephalosporins< / span > ()
< span class = 'fu' > cephalosporins_1st< / span > ()
< span class = 'fu' > cephalosporins_2nd< / span > ()
< span class = 'fu' > cephalosporins_3rd< / span > ()
< span class = 'fu' > cephalosporins_4th< / span > ()
< span class = 'fu' > cephalosporins_5th< / span > ()
< span class = 'fu' > fluoroquinolones< / span > ()
< span class = 'fu' > glycopeptides< / span > ()
< span class = 'fu' > macrolides< / span > ()
< span class = 'fu' > penicillins< / span > ()
< span class = 'fu' > tetracyclines< / span > ()< / pre >
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< h2 class = "hasAnchor" id = "arguments" > < a class = "anchor" href = "#arguments" > < / a > Arguments< / h2 >
< table class = "ref-arguments" >
< colgroup > < col class = "name" / > < col class = "desc" / > < / colgroup >
< tr >
< th > ab_class< / th >
< td > < p > an antimicrobial class, like < code > "carbapenems"< / code > . The columns < code > group< / code > , < code > atc_group1< / code > and < code > atc_group2< / code > of the < a href = 'antibiotics.html' > antibiotics< / a > data set will be searched (case-insensitive) for this value.< / p > < / td >
< / tr >
< / table >
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< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
< p > All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.). This means that a selector like e.g. < code > aminoglycosides()< / code > will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.< / p >
< p > These functions only work if the < code > tidyselect< / code > package is installed, that comes with the < code > dplyr< / code > package. An error will be thrown if < code > tidyselect< / code > package is not installed, or if the functions are used outside a function that allows Tidyverse selections like < code > < a href = 'https://dplyr.tidyverse.org/reference/select.html' > select()< / a > < / code > or < code > pivot_longer()< / code > .< / 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 = 'filter_ab_class.html' > filter_ab_class()< / a > < / code > for the < code > < a href = 'https://dplyr.tidyverse.org/reference/filter.html' > filter()< / a > < / code > equivalent.< / p > < / div >
< 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' > "dplyr"< / span > )) {
< span class = 'co' > # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):< / span >
< span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/select.html' > select< / a > < / span > (< span class = 'fu' > carbapenems< / span > ())
< span class = 'co' > # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':< / span >
< span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/select.html' > select< / a > < / span > (< span class = 'no' > mo< / span > , < span class = 'fu' > aminoglycosides< / span > ())
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< span class = 'co' > # this will select columns 'mo' and all antimycobacterial drugs ('RIF'):< / span >
< span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/select.html' > select< / a > < / span > (< span class = 'no' > mo< / span > , < span class = 'fu' > ab_class< / span > (< span class = 'st' > "mycobact"< / span > ))
< span class = 'co' > # get bug/drug combinations for only macrolides in Gram-positives:< / span >
< span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/filter.html' > filter< / a > < / span > (< span class = 'fu' > < a href = 'mo_property.html' > mo_gramstain< / a > < / span > (< span class = 'no' > mo< / span > ) < span class = 'kw' > %like%< / span > < span class = 'st' > "pos"< / span > ) < span class = 'kw' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/select.html' > select< / a > < / span > (< span class = 'no' > mo< / span > , < span class = 'fu' > macrolides< / span > ()) < span class = 'kw' > %> %< / span >
< span class = 'fu' > < a href = 'bug_drug_combinations.html' > bug_drug_combinations< / a > < / span > () < span class = 'kw' > %> %< / span >
< span class = 'fu' > < a href = 'https://rdrr.io/r/base/format.html' > format< / a > < / span > ()
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< span class = 'fu' > < a href = 'https://rdrr.io/r/base/data.frame.html' > data.frame< / a > < / span > (< span class = 'kw' > irrelevant< / span > < span class = 'kw' > =< / span > < span class = 'st' > "value"< / span > ,
< span class = 'kw' > J01CA01< / span > < span class = 'kw' > =< / span > < span class = 'st' > "S"< / span > ) < span class = 'kw' > %> %< / span > < span class = 'co' > # ATC code of ampicillin< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/select.html' > select< / a > < / span > (< span class = 'fu' > penicillins< / span > ()) < span class = 'co' > # so the 'J01CA01' column is selected< / 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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