2019-01-11 20:37:23 +01:00
<!-- 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 > Guess antibiotic column — guess_ab_col • 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" / >
2019-10-13 09:31:58 +02:00
2019-01-11 20:37:23 +01:00
<!-- jquery -->
2020-04-13 21:09:56 +02:00
< script src = "https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity = "sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin = "anonymous" > < / script >
2019-01-11 20:37:23 +01:00
<!-- Bootstrap -->
2020-04-13 21:09:56 +02:00
< link href = "https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel = "stylesheet" crossorigin = "anonymous" / >
2019-01-11 20:37:23 +01:00
2019-10-13 09:31:58 +02:00
2020-04-13 21:09:56 +02:00
< 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 >
2019-01-11 20:37:23 +01:00
2020-04-17 19:16:30 +02:00
<!-- bootstrap - toc -->
< link rel = "stylesheet" href = "../bootstrap-toc.css" >
< script src = "../bootstrap-toc.js" > < / script >
2019-01-11 20:37:23 +01:00
<!-- Font Awesome icons -->
2020-04-17 19:16:30 +02:00
< 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" / >
2019-01-11 20:37:23 +01:00
<!-- clipboard.js -->
2020-04-17 19:16:30 +02:00
< script src = "https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity = "sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin = "anonymous" > < / script >
2019-01-11 20:37:23 +01:00
2019-10-13 09:31:58 +02:00
<!-- headroom.js -->
2020-04-17 19:16:30 +02:00
< 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 >
2019-01-11 20:37:23 +01:00
<!-- pkgdown -->
< link href = "../pkgdown.css" rel = "stylesheet" >
< script src = "../pkgdown.js" > < / script >
< link href = "../extra.css" rel = "stylesheet" >
< script src = "../extra.js" > < / script >
2019-10-13 09:31:58 +02:00
< meta property = "og:title" content = "Guess antibiotic column — guess_ab_col" / >
2019-05-31 14:40:15 +02:00
< meta property = "og:description" content = "This tries to find a column name in a data set based on information from the antibiotics data set. Also supports WHONET abbreviations." / >
2020-07-08 14:48:06 +02:00
< meta property = "og:image" content = "https://msberends.github.io/AMR/logo.svg" / >
2019-01-11 20:37:23 +01:00
2019-10-13 09:31:58 +02:00
2019-01-11 20:37:23 +01:00
<!-- 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]-->
2019-10-13 09:31:58 +02:00
2019-01-11 20:37:23 +01:00
< / head >
2020-04-17 19:16:30 +02:00
< body data-spy = "scroll" data-target = "#toc" >
2019-01-11 20:37:23 +01:00
< 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 >
2020-07-22 10:24:23 +02:00
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Latest development version" > 1.2.0.9035< / span >
2019-01-11 20:37:23 +01:00
< / 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 >
2019-02-14 10:23:51 +01:00
< a href = "../articles/resistance_predict.html" >
2019-01-11 20:37:23 +01:00
< span class = "fa fa-dice" > < / span >
Predict antimicrobial resistance
< / a >
< / li >
2020-04-13 21:09:56 +02:00
< li >
< a href = "../articles/PCA.html" >
< span class = "fa fa-compress" > < / span >
Conduct principal component analysis for AMR
< / a >
< / li >
2019-05-28 16:50:40 +02:00
< li >
< a href = "../articles/MDR.html" >
< span class = "fa fa-skull-crossbones" > < / span >
Determine multi-drug resistance (MDR)
< / a >
< / li >
2019-01-29 00:06:50 +01:00
< li >
< a href = "../articles/WHONET.html" >
< span class = "fa fa-globe-americas" > < / span >
Work with WHONET data
< / a >
< / li >
2019-02-14 15:18:17 +01:00
< li >
< a href = "../articles/SPSS.html" >
< span class = "fa fa-file-upload" > < / span >
Import data from SPSS/SAS/Stata
< / a >
< / li >
2019-01-11 20:37:23 +01:00
< li >
< a href = "../articles/EUCAST.html" >
< span class = "fa fa-exchange-alt" > < / span >
Apply EUCAST rules
< / a >
< / li >
< li >
2019-02-14 10:23:51 +01:00
< a href = "../reference/mo_property.html" >
2019-01-11 20:37:23 +01:00
< span class = "fa fa-bug" > < / span >
Get properties of a microorganism
< / a >
< / li >
< li >
2019-05-10 16:44:59 +02:00
< a href = "../reference/ab_property.html" >
2019-01-11 20:37:23 +01:00
< 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 >
< a href = "../reference/" >
< 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 >
< a href = "../news/" >
< span class = "far fa far fa-newspaper" > < / span >
Changelog
< / a >
< / li >
< / ul >
< ul class = "nav navbar-nav navbar-right" >
< li >
2020-07-08 14:48:06 +02:00
< a href = "https://github.com/msberends/AMR" >
< span class = "fab fa fab fa-github" > < / span >
2019-01-11 20:37:23 +01:00
Source Code
< / a >
< / li >
< li >
< a href = "../LICENSE-text.html" >
< span class = "fa fa-book" > < / span >
Licence
< / a >
< / li >
< / ul >
< / div > <!-- /.nav - collapse -->
< / div > <!-- /.container -->
< / div > <!-- /.navbar -->
2019-10-13 09:31:58 +02:00
2019-01-11 20:37:23 +01:00
< / header >
< div class = "row" >
< div class = "col-md-9 contents" >
< div class = "page-header" >
< h1 > Guess antibiotic column< / h1 >
2020-07-08 14:48:06 +02:00
< small class = "dont-index" > Source: < a href = 'https://github.com/msberends/AMR/blob/master/R/guess_ab_col.R' > < code > R/guess_ab_col.R< / code > < / a > < / small >
2019-01-11 20:37:23 +01:00
< div class = "hidden name" > < code > guess_ab_col.Rd< / code > < / div >
< / div >
< div class = "ref-description" >
2019-11-28 22:32:17 +01:00
< p > This tries to find a column name in a data set based on information from the < a href = 'antibiotics.html' > antibiotics< / a > data set. Also supports WHONET abbreviations.< / p >
2019-01-11 20:37:23 +01:00
< / div >
2019-05-13 10:10:16 +02:00
< pre class = "usage" > < span class = 'fu' > guess_ab_col< / span > (< span class = 'kw' > x< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > search_string< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > verbose< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > )< / pre >
2019-10-13 09:31:58 +02:00
2019-01-11 20:37:23 +01:00
< 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 >
2019-05-13 10:10:16 +02:00
< th > x< / th >
2019-11-28 22:32:17 +01:00
< td > < p > a < code > < a href = 'https://rdrr.io/r/base/data.frame.html' > data.frame< / a > < / code > < / p > < / td >
2019-01-11 20:37:23 +01:00
< / tr >
< tr >
2019-05-13 10:10:16 +02:00
< th > search_string< / th >
2019-11-28 22:32:17 +01:00
< td > < p > a text to search < code > x< / code > for, will be checked with < code > < a href = 'as.ab.html' > as.ab()< / a > < / code > if this value is not a column in < code > x< / code > < / p > < / td >
2019-01-11 20:37:23 +01:00
< / tr >
< tr >
< th > verbose< / th >
< td > < p > a logical to indicate whether additional info should be printed< / p > < / td >
< / tr >
< / table >
2019-10-13 09:31:58 +02:00
2019-05-13 10:10:16 +02:00
< h2 class = "hasAnchor" id = "value" > < a class = "anchor" href = "#value" > < / a > Value< / h2 >
< p > A column name of < code > x< / code > , or < code > NULL< / code > when no result is found.< / p >
2019-05-31 14:40:15 +02:00
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
2019-11-28 22:32:17 +01:00
< p > You can look for an antibiotic (trade) name or abbreviation and it will search < code > x< / code > and the < a href = 'antibiotics.html' > antibiotics< / a > data set for any column containing a name or code of that antibiotic. < strong > Longer columns names take precendence over shorter column names.< / strong > < / p >
2020-01-05 17:22:09 +01:00
< h2 class = "hasAnchor" id = "maturing-lifecycle" > < a class = "anchor" href = "#maturing-lifecycle" > < / a > Maturing lifecycle< / h2 >
< p > < img src = 'figures/lifecycle_maturing.svg' style = margin-bottom:5px / > < br / >
2020-07-08 14:48:06 +02:00
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 >
2019-01-11 20:37:23 +01:00
< 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 >
2019-10-13 09:31:58 +02:00
2020-07-08 14:48:06 +02:00
< 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 >
2019-01-11 20:37:23 +01:00
< h2 class = "hasAnchor" id = "examples" > < a class = "anchor" href = "#examples" > < / a > Examples< / h2 >
2019-10-13 09:31:58 +02:00
< pre class = "examples" > < span class = 'no' > df< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/data.frame.html' > data.frame< / a > < / span > (< span class = 'kw' > amox< / span > < span class = 'kw' > =< / span > < span class = 'st' > "S"< / span > ,
2019-01-11 20:37:23 +01:00
< span class = 'kw' > tetr< / span > < span class = 'kw' > =< / span > < span class = 'st' > "R"< / span > )
< span class = 'fu' > guess_ab_col< / span > (< span class = 'no' > df< / span > , < span class = 'st' > "amoxicillin"< / span > )
< span class = 'co' > # [1] "amox"< / span >
2019-05-10 16:44:59 +02:00
< span class = 'fu' > guess_ab_col< / span > (< span class = 'no' > df< / span > , < span class = 'st' > "J01AA07"< / span > ) < span class = 'co' > # ATC code of tetracycline< / span >
2019-01-11 20:37:23 +01:00
< span class = 'co' > # [1] "tetr"< / span >
< span class = 'fu' > guess_ab_col< / span > (< span class = 'no' > df< / span > , < span class = 'st' > "J01AA07"< / span > , < span class = 'kw' > verbose< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > )
2020-07-22 10:24:23 +02:00
< span class = 'co' > # NOTE: Using column `tetr` as input for `J01AA07` (tetracycline).< / span >
2019-01-11 20:37:23 +01:00
< span class = 'co' > # [1] "tetr"< / span >
2019-01-29 00:06:50 +01:00
< span class = 'co' > # WHONET codes< / span >
2019-10-13 09:31:58 +02:00
< span class = 'no' > df< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/data.frame.html' > data.frame< / a > < / span > (< span class = 'kw' > AMP_ND10< / span > < span class = 'kw' > =< / span > < span class = 'st' > "R"< / span > ,
2019-01-29 00:06:50 +01:00
< span class = 'kw' > AMC_ED20< / span > < span class = 'kw' > =< / span > < span class = 'st' > "S"< / span > )
< span class = 'fu' > guess_ab_col< / span > (< span class = 'no' > df< / span > , < span class = 'st' > "ampicillin"< / span > )
< span class = 'co' > # [1] "AMP_ND10"< / span >
< span class = 'fu' > guess_ab_col< / span > (< span class = 'no' > df< / span > , < span class = 'st' > "J01CR02"< / span > )
< span class = 'co' > # [1] "AMC_ED20"< / span >
2019-05-10 16:44:59 +02:00
< span class = 'fu' > guess_ab_col< / span > (< span class = 'no' > df< / span > , < span class = 'fu' > < a href = 'as.ab.html' > as.ab< / a > < / span > (< span class = 'st' > "augmentin"< / span > ))
2019-01-29 00:06:50 +01:00
< span class = 'co' > # [1] "AMC_ED20"< / span >
2019-05-31 14:40:15 +02:00
< span class = 'co' > # Longer names take precendence:< / span >
2019-10-13 09:31:58 +02:00
< span class = 'no' > df< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/data.frame.html' > data.frame< / a > < / span > (< span class = 'kw' > AMP_ED2< / span > < span class = 'kw' > =< / span > < span class = 'st' > "S"< / span > ,
2019-05-31 14:40:15 +02:00
< span class = 'kw' > AMP_ED20< / span > < span class = 'kw' > =< / span > < span class = 'st' > "S"< / span > )
< span class = 'fu' > guess_ab_col< / span > (< span class = 'no' > df< / span > , < span class = 'st' > "ampicillin"< / span > )
2019-10-13 09:31:58 +02:00
< span class = 'co' > # [1] "AMP_ED20"< / span > < / pre >
2019-01-11 20:37:23 +01:00
< / div >
2020-04-13 21:09:56 +02:00
< div class = "col-md-3 hidden-xs hidden-sm" id = "pkgdown-sidebar" >
2020-04-17 19:16:30 +02:00
< nav id = "toc" data-toggle = "toc" class = "sticky-top" >
< h2 data-toc-skip > Contents< / h2 >
< / nav >
2019-01-11 20:37:23 +01:00
< / div >
< / div >
2019-10-13 09:31:58 +02:00
2019-01-11 20:37:23 +01:00
< footer >
< div class = "copyright" >
2020-01-26 20:38:54 +01:00
< 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 >
2019-01-11 20:37:23 +01:00
< / div >
< div class = "pkgdown" >
2020-05-22 20:15:19 +02:00
< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.5.1.< / p >
2019-01-11 20:37:23 +01:00
< / div >
2019-10-13 09:31:58 +02:00
2019-01-11 20:37:23 +01:00
< / footer >
< / div >
2019-10-13 09:31:58 +02:00
2019-01-11 20:37:23 +01:00
< / body >
< / html >
2019-10-13 09:31:58 +02:00
