2020-06-17 01:39:30 +02:00
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
< html lang = "en" >
< head >
< meta charset = "utf-8" >
< meta http-equiv = "X-UA-Compatible" content = "IE=edge" >
< meta name = "viewport" content = "width=device-width, initial-scale=1.0" >
< title > Antibiotic class selectors — antibiotic_class_selectors • AMR (for R)< / title >
<!-- favicons -->
< link rel = "icon" type = "image/png" sizes = "16x16" href = "../favicon-16x16.png" >
< link rel = "icon" type = "image/png" sizes = "32x32" href = "../favicon-32x32.png" >
< link rel = "apple-touch-icon" type = "image/png" sizes = "180x180" href = "../apple-touch-icon.png" / >
< link rel = "apple-touch-icon" type = "image/png" sizes = "120x120" href = "../apple-touch-icon-120x120.png" / >
< link rel = "apple-touch-icon" type = "image/png" sizes = "76x76" href = "../apple-touch-icon-76x76.png" / >
< link rel = "apple-touch-icon" type = "image/png" sizes = "60x60" href = "../apple-touch-icon-60x60.png" / >
<!-- jquery -->
< script src = "https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity = "sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin = "anonymous" > < / script >
<!-- Bootstrap -->
< link href = "https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel = "stylesheet" crossorigin = "anonymous" / >
< 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 = "../bootstrap-toc.css" >
< script src = "../bootstrap-toc.js" > < / script >
<!-- Font Awesome icons -->
< link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity = "sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin = "anonymous" / >
< link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity = "sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin = "anonymous" / >
<!-- clipboard.js -->
< script src = "https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity = "sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin = "anonymous" > < / script >
<!-- headroom.js -->
< script src = "https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity = "sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin = "anonymous" > < / script >
< 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 = "../pkgdown.css" rel = "stylesheet" >
< script src = "../pkgdown.js" > < / script >
< link href = "../extra.css" rel = "stylesheet" >
< script src = "../extra.js" > < / script >
< meta property = "og:title" content = "Antibiotic class selectors — antibiotic_class_selectors" / >
< meta property = "og:description" content = "Use these selection helpers inside any function that allows Tidyverse selections, like dplyr::select() or tidyr::pivot_longer(). 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." / >
2020-07-09 14:12:11 +02:00
< meta property = "og:image" content = "https://msberends.github.io/AMR/logo.svg" / >
2020-06-17 01:39:30 +02:00
<!-- 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 >
<![endif]-->
< / head >
< body data-spy = "scroll" data-target = "#toc" >
< div class = "container template-reference-topic" >
< header >
< div class = "navbar navbar-default navbar-fixed-top" role = "navigation" >
< div class = "container" >
< div class = "navbar-header" >
< button type = "button" class = "navbar-toggle collapsed" data-toggle = "collapse" data-target = "#navbar" aria-expanded = "false" >
< span class = "sr-only" > Toggle navigation< / span >
< span class = "icon-bar" > < / span >
< span class = "icon-bar" > < / span >
< span class = "icon-bar" > < / span >
< / button >
< span class = "navbar-brand" >
< a class = "navbar-link" href = "../index.html" > AMR (for R)< / a >
2020-08-10 11:44:58 +02:00
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Latest development version" > 1.3.0.9000< / span >
2020-06-17 01:39:30 +02:00
< / span >
< / div >
< div id = "navbar" class = "navbar-collapse collapse" >
< ul class = "nav navbar-nav" >
< li >
< a href = "../index.html" >
< span class = "fa fa-home" > < / span >
Home
< / a >
< / li >
< li class = "dropdown" >
< a href = "#" class = "dropdown-toggle" data-toggle = "dropdown" role = "button" aria-expanded = "false" >
< span class = "fa fa-question-circle" > < / span >
How to
< span class = "caret" > < / span >
< / a >
< ul class = "dropdown-menu" role = "menu" >
< li >
< a href = "../articles/AMR.html" >
< span class = "fa fa-directions" > < / span >
Conduct AMR analysis
< / a >
< / li >
< li >
< a href = "../articles/resistance_predict.html" >
< span class = "fa fa-dice" > < / span >
Predict antimicrobial resistance
< / a >
< / li >
< li >
< a href = "../articles/PCA.html" >
< span class = "fa fa-compress" > < / span >
Conduct principal component analysis for AMR
< / a >
< / li >
< li >
< a href = "../articles/MDR.html" >
< span class = "fa fa-skull-crossbones" > < / span >
Determine multi-drug resistance (MDR)
< / a >
< / li >
< li >
< a href = "../articles/WHONET.html" >
< span class = "fa fa-globe-americas" > < / span >
Work with WHONET data
< / a >
< / li >
< li >
< a href = "../articles/SPSS.html" >
< span class = "fa fa-file-upload" > < / span >
Import data from SPSS/SAS/Stata
< / a >
< / li >
< li >
< a href = "../articles/EUCAST.html" >
< span class = "fa fa-exchange-alt" > < / span >
Apply EUCAST rules
< / a >
< / li >
< li >
< a href = "../reference/mo_property.html" >
< span class = "fa fa-bug" > < / span >
Get properties of a microorganism
< / a >
< / li >
< li >
< a href = "../reference/ab_property.html" >
< span class = "fa fa-capsules" > < / span >
Get properties of an antibiotic
< / a >
< / li >
< li >
< a href = "../articles/benchmarks.html" >
< span class = "fa fa-shipping-fast" > < / span >
Other: benchmarks
< / a >
< / li >
< / ul >
< / li >
< li >
2020-07-28 18:39:57 +02:00
< a href = "../reference/index.html" >
2020-06-17 01:39:30 +02:00
< span class = "fa fa-book-open" > < / span >
Manual
< / a >
< / li >
< li >
< a href = "../authors.html" >
< span class = "fa fa-users" > < / span >
Authors
< / a >
< / li >
< li >
2020-07-28 18:39:57 +02:00
< a href = "../news/index.html" >
2020-06-17 01:39:30 +02:00
< span class = "far fa far fa-newspaper" > < / span >
Changelog
< / a >
< / li >
< / ul >
< ul class = "nav navbar-nav navbar-right" >
< li >
2020-07-09 14:12:11 +02:00
< a href = "https://github.com/msberends/AMR" >
< span class = "fab fa fab fa-github" > < / span >
2020-06-17 01:39:30 +02:00
Source Code
< / a >
< / li >
< li >
2020-07-28 18:39:57 +02:00
< a href = "../survey.html" >
< span class = "fa fa-clipboard-list" > < / span >
2020-06-17 01:39:30 +02:00
2020-07-28 18:39:57 +02:00
Survey
2020-06-17 01:39:30 +02:00
< / a >
< / li >
< / ul >
< / div > <!-- /.nav - collapse -->
< / div > <!-- /.container -->
< / div > <!-- /.navbar -->
< / header >
< div class = "row" >
< div class = "col-md-9 contents" >
< div class = "page-header" >
< h1 > Antibiotic class selectors< / h1 >
2020-07-09 14:12:11 +02:00
< 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 >
2020-06-17 01:39:30 +02:00
< 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 >
2020-06-17 15:14:37 +02:00
< pre class = "usage" > < span class = 'fu' > ab_class< / span > (< span class = 'no' > ab_class< / span > )
< span class = 'fu' > aminoglycosides< / span > ()
2020-06-17 01:39:30 +02:00
< 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 >
2020-06-17 15:14:37 +02:00
< 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 >
2020-06-17 01:39:30 +02:00
< 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 >
2020-07-31 10:50:08 +02:00
< pre class = "examples" > < span class = 'kw' > if< / span > (< span class = 'fl' > FALSE< / span > ) {
< span class = 'fu' > < a href = 'https://rdrr.io/r/base/library.html' > library< / a > < / span > (< span class = 'no' > dplyr< / span > )
2020-06-17 01:39:30 +02:00
< 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 > ())
2020-06-17 15:14:37 +02:00
< 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 > ()
2020-06-17 01:39:30 +02:00
< 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 >
}< / pre >
< / div >
< div class = "col-md-3 hidden-xs hidden-sm" id = "pkgdown-sidebar" >
< nav id = "toc" data-toggle = "toc" class = "sticky-top" >
< h2 data-toc-skip > Contents< / h2 >
< / nav >
< / div >
< / div >
< footer >
< div class = "copyright" >
< 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 >
< / div >
< div class = "pkgdown" >
< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.5.1.< / p >
< / div >
< / footer >
< / div >
< / body >
< / html >
