2018-12-23 21:26:21 +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" >
2021-01-18 16:57:56 +01:00
< title > Key Antibiotics for First (Weighted) Isolates — key_antibiotics • AMR (for R)< / title >
2018-12-29 22:24:19 +01:00
<!-- 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
2018-12-23 21:26:21 +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 >
2018-12-23 21:26:21 +01:00
<!-- Bootstrap -->
2020-12-27 00:07:00 +01:00
< link href = "https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel = "stylesheet" crossorigin = "anonymous" / >
2019-10-13 09:31:58 +02:00
2020-12-21 22:46:29 +01:00
2020-12-24 23:29:10 +01:00
< 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 >
2020-12-21 22:46:29 +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 >
2018-12-23 21:26:21 +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" / >
2018-12-23 21:26:21 +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 >
2018-12-23 21:26:21 +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 >
2018-12-23 21:26:21 +01:00
<!-- pkgdown -->
< link href = "../pkgdown.css" rel = "stylesheet" >
< script src = "../pkgdown.js" > < / script >
2018-12-29 22:24:19 +01:00
< link href = "../extra.css" rel = "stylesheet" >
< script src = "../extra.js" > < / script >
2018-12-23 21:26:21 +01:00
2021-01-18 16:57:56 +01:00
< meta property = "og:title" content = "Key Antibiotics for First (Weighted) Isolates — key_antibiotics" / >
< meta property = "og:description" content = "These function can be used to determine first isolates (see first_isolate()). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates can then be called first 'weighted' isolates." / >
2020-09-29 23:35:46 +02:00
< meta property = "og:image" content = "https://msberends.github.io/AMR/logo.png" / >
2018-12-23 21:26:21 +01:00
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +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
2018-12-23 21:26:21 +01:00
< / head >
2020-04-17 19:16:30 +02:00
< body data-spy = "scroll" data-target = "#toc" >
2018-12-23 21:26:21 +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" >
2018-12-29 22:24:19 +01:00
< a class = "navbar-link" href = "../index.html" > AMR (for R)< / a >
2021-04-20 10:46:17 +02:00
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Latest development version" > 1.6.0.9007< / span >
2018-12-23 21:26:21 +01:00
< / span >
< / div >
< div id = "navbar" class = "navbar-collapse collapse" >
< ul class = "nav navbar-nav" >
< li >
< a href = "../index.html" >
2020-12-21 22:46:29 +01:00
< span class = "fas fa-home" > < / span >
2018-12-29 22:24:19 +01:00
Home
< / a >
< / li >
2019-01-02 23:24:07 +01:00
< li class = "dropdown" >
< a href = "#" class = "dropdown-toggle" data-toggle = "dropdown" role = "button" aria-expanded = "false" >
2020-12-21 22:46:29 +01:00
< span class = "fas fa-question-circle" > < / span >
2019-01-02 23:24:07 +01:00
How to
2018-12-23 21:26:21 +01:00
2019-01-02 23:24:07 +01:00
< span class = "caret" > < / span >
2018-12-23 21:26:21 +01:00
< / a >
2019-01-02 23:24:07 +01:00
< ul class = "dropdown-menu" role = "menu" >
< li >
< a href = "../articles/AMR.html" >
2020-12-21 22:46:29 +01:00
< span class = "fas fa-directions" > < / span >
2019-01-02 23:24:07 +01:00
Conduct AMR analysis
< / a >
< / li >
< li >
2019-02-14 10:23:51 +01:00
< a href = "../articles/resistance_predict.html" >
2020-12-21 22:46:29 +01:00
< span class = "fas fa-dice" > < / span >
2019-01-02 23:24:07 +01:00
Predict antimicrobial resistance
< / a >
< / li >
2020-08-21 11:40:13 +02:00
< li >
< a href = "../articles/datasets.html" >
2020-12-21 22:46:29 +01:00
< span class = "fas fa-database" > < / span >
2020-08-21 11:40:13 +02:00
2020-09-03 20:59:21 +02:00
Data sets for download / own use
2020-08-21 11:40:13 +02:00
< / a >
< / li >
2020-04-13 21:09:56 +02:00
< li >
< a href = "../articles/PCA.html" >
2020-12-21 22:46:29 +01:00
< span class = "fas fa-compress" > < / span >
2020-04-13 21:09:56 +02:00
Conduct principal component analysis for AMR
< / a >
< / li >
2019-05-23 16:58:59 +02:00
< li >
< a href = "../articles/MDR.html" >
2020-12-21 22:46:29 +01:00
< span class = "fas fa-skull-crossbones" > < / span >
2019-05-23 16:58:59 +02:00
Determine multi-drug resistance (MDR)
< / a >
< / li >
2019-01-29 00:06:50 +01:00
< li >
< a href = "../articles/WHONET.html" >
2020-12-21 22:46:29 +01:00
< span class = "fas fa-globe-americas" > < / span >
2019-01-29 00:06:50 +01:00
Work with WHONET data
< / a >
< / li >
2019-02-14 15:18:17 +01:00
< li >
< a href = "../articles/SPSS.html" >
2020-12-21 22:46:29 +01:00
< span class = "fas fa-file-upload" > < / span >
2019-02-14 15:18:17 +01:00
Import data from SPSS/SAS/Stata
< / a >
< / li >
2019-01-02 23:24:07 +01:00
< li >
< a href = "../articles/EUCAST.html" >
2020-12-21 22:46:29 +01:00
< span class = "fas fa-exchange-alt" > < / span >
2019-01-02 23:24:07 +01:00
Apply EUCAST rules
< / a >
< / li >
< li >
2019-02-14 10:23:51 +01:00
< a href = "../reference/mo_property.html" >
2020-12-21 22:46:29 +01:00
< span class = "fas fa-bug" > < / span >
2019-01-02 23:24:07 +01:00
Get properties of a microorganism
< / a >
< / li >
< li >
2019-05-10 16:44:59 +02:00
< a href = "../reference/ab_property.html" >
2020-12-21 22:46:29 +01:00
< span class = "fas fa-capsules" > < / span >
2019-01-02 23:24:07 +01:00
Get properties of an antibiotic
< / a >
< / li >
2019-01-11 20:37:23 +01:00
< li >
< a href = "../articles/benchmarks.html" >
2020-12-21 22:46:29 +01:00
< span class = "fas fa-shipping-fast" > < / span >
2019-01-11 20:37:23 +01:00
Other: benchmarks
< / a >
< / li >
2019-01-02 23:24:07 +01:00
< / ul >
2018-12-23 21:26:21 +01:00
< / li >
< li >
2020-07-28 18:39:57 +02:00
< a href = "../reference/index.html" >
2020-12-21 22:46:29 +01:00
< span class = "fas fa-book-open" > < / span >
2018-12-29 22:24:19 +01:00
Manual
< / a >
2018-12-23 21:26:21 +01:00
< / li >
< li >
2018-12-29 22:24:19 +01:00
< a href = "../authors.html" >
2020-12-21 22:46:29 +01:00
< span class = "fas fa-users" > < / span >
2018-12-29 22:24:19 +01:00
Authors
< / a >
2018-12-23 21:26:21 +01:00
< / li >
2018-12-29 22:24:19 +01:00
< li >
2020-07-28 18:39:57 +02:00
< a href = "../news/index.html" >
2020-12-21 22:46:29 +01:00
< span class = "far fa-newspaper" > < / span >
2018-12-23 21:26:21 +01:00
2018-12-29 22:24:19 +01:00
Changelog
2018-12-23 21:26:21 +01:00
< / a >
< / li >
2019-01-02 23:24:07 +01:00
< / ul >
< ul class = "nav navbar-nav navbar-right" >
< li >
2020-07-08 14:48:06 +02:00
< a href = "https://github.com/msberends/AMR" >
2020-12-21 22:46:29 +01:00
< span class = "fab fa-github" > < / span >
2018-12-29 22:24:19 +01:00
Source Code
< / a >
2018-12-23 21:26:21 +01:00
< / li >
2019-01-02 23:24:07 +01:00
< li >
2020-07-28 18:39:57 +02:00
< a href = "../survey.html" >
2020-12-21 22:46:29 +01:00
< span class = "fas fa-clipboard-list" > < / span >
2018-12-29 22:24:19 +01:00
2020-07-28 18:39:57 +02:00
Survey
2018-12-29 22:24:19 +01:00
< / a >
< / li >
2018-12-23 21:26:21 +01:00
< / ul >
< / div > <!-- /.nav - collapse -->
< / div > <!-- /.container -->
< / div > <!-- /.navbar -->
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +01:00
< / header >
< div class = "row" >
< div class = "col-md-9 contents" >
< div class = "page-header" >
2021-01-18 16:57:56 +01:00
< h1 > Key Antibiotics for First (Weighted) Isolates< / h1 >
2020-07-08 14:48:06 +02:00
< small class = "dont-index" > Source: < a href = 'https://github.com/msberends/AMR/blob/master/R/key_antibiotics.R' > < code > R/key_antibiotics.R< / code > < / a > < / small >
2018-12-23 21:26:21 +01:00
< div class = "hidden name" > < code > key_antibiotics.Rd< / code > < / div >
< / div >
< div class = "ref-description" >
2021-01-18 16:57:56 +01:00
< p > These function can be used to determine first isolates (see < code > < a href = 'first_isolate.html' > first_isolate()< / a > < / code > ). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates can then be called first 'weighted' isolates.< / p >
2018-12-23 21:26:21 +01:00
< / div >
2020-10-15 09:46:41 +02:00
< pre class = "usage" > < span class = 'fu' > key_antibiotics< / span > < span class = 'op' > (< / span >
2021-02-08 14:18:42 +01:00
x < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
2020-10-15 09:46:41 +02:00
col_mo < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
universal_1 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "amoxicillin"< / span > < span class = 'op' > )< / span > ,
universal_2 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "amoxicillin/clavulanic acid"< / span > < span class = 'op' > )< / span > ,
universal_3 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "cefuroxime"< / span > < span class = 'op' > )< / span > ,
universal_4 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "piperacillin/tazobactam"< / span > < span class = 'op' > )< / span > ,
universal_5 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "ciprofloxacin"< / span > < span class = 'op' > )< / span > ,
universal_6 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "trimethoprim/sulfamethoxazole"< / span > < span class = 'op' > )< / span > ,
GramPos_1 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "vancomycin"< / span > < span class = 'op' > )< / span > ,
GramPos_2 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "teicoplanin"< / span > < span class = 'op' > )< / span > ,
GramPos_3 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "tetracycline"< / span > < span class = 'op' > )< / span > ,
GramPos_4 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "erythromycin"< / span > < span class = 'op' > )< / span > ,
GramPos_5 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "oxacillin"< / span > < span class = 'op' > )< / span > ,
GramPos_6 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "rifampin"< / span > < span class = 'op' > )< / span > ,
GramNeg_1 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "gentamicin"< / span > < span class = 'op' > )< / span > ,
GramNeg_2 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "tobramycin"< / span > < span class = 'op' > )< / span > ,
GramNeg_3 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "colistin"< / span > < span class = 'op' > )< / span > ,
GramNeg_4 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "cefotaxime"< / span > < span class = 'op' > )< / span > ,
GramNeg_5 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "ceftazidime"< / span > < span class = 'op' > )< / span > ,
GramNeg_6 < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , < span class = 'st' > "meropenem"< / span > < span class = 'op' > )< / span > ,
warnings < span class = 'op' > =< / span > < span class = 'cn' > TRUE< / span > ,
< span class = 'va' > ...< / span >
< span class = 'op' > )< / span >
< span class = 'fu' > key_antibiotics_equal< / span > < span class = 'op' > (< / span >
< span class = 'va' > y< / span > ,
< span class = 'va' > z< / span > ,
type < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/c.html' > c< / a > < / span > < span class = 'op' > (< / span > < span class = 'st' > "keyantibiotics"< / span > , < span class = 'st' > "points"< / span > < span class = 'op' > )< / span > ,
ignore_I < span class = 'op' > =< / span > < span class = 'cn' > TRUE< / span > ,
points_threshold < span class = 'op' > =< / span > < span class = 'fl' > 2< / span > ,
info < span class = 'op' > =< / span > < span class = 'cn' > FALSE< / span >
< span class = 'op' > )< / span > < / pre >
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +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 >
2019-05-23 16:58:59 +02:00
< th > x< / th >
2021-01-24 14:48:56 +01:00
< td > < p > a < a href = 'https://rdrr.io/r/base/data.frame.html' > data.frame< / a > with antibiotics columns, like < code > AMX< / code > or < code > amox< / code > . Can be left blank to determine automatically< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
< tr >
< th > col_mo< / th >
2019-11-28 22:32:17 +01:00
< td > < p > column name of the IDs of the microorganisms (see < code > < a href = 'as.mo.html' > as.mo()< / a > < / code > ), defaults to the first column of class < code > < a href = 'as.mo.html' > mo< / a > < / code > . Values will be coerced using < code > < a href = 'as.mo.html' > as.mo()< / a > < / code > .< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
< tr >
< th > universal_1, universal_2, universal_3, universal_4, universal_5, universal_6< / th >
2020-10-19 17:09:19 +02:00
< td > < p > column names of < strong > broad-spectrum< / strong > antibiotics, case-insensitive. See details for which antibiotics will be used at default (which are guessed with < code > < a href = 'guess_ab_col.html' > guess_ab_col()< / a > < / code > ).< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
< tr >
< th > GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6< / th >
2020-10-19 17:09:19 +02:00
< td > < p > column names of antibiotics for < strong > Gram-positives< / strong > , case-insensitive. See details for which antibiotics will be used at default (which are guessed with < code > < a href = 'guess_ab_col.html' > guess_ab_col()< / a > < / code > ).< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
< tr >
< th > GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6< / th >
2020-10-19 17:09:19 +02:00
< td > < p > column names of antibiotics for < strong > Gram-negatives< / strong > , case-insensitive. See details for which antibiotics will be used at default (which are guessed with < code > < a href = 'guess_ab_col.html' > guess_ab_col()< / a > < / code > ).< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
< tr >
< th > warnings< / th >
2020-10-19 17:09:19 +02:00
< td > < p > give a warning about missing antibiotic columns (they will be ignored)< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
< tr >
< th > ...< / th >
2020-12-22 00:51:17 +01:00
< td > < p > other arguments passed on to functions< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
2019-05-23 17:35:58 +02:00
< tr >
< th > y, z< / th >
2020-10-19 17:09:19 +02:00
< td > < p > character vectors to compare< / p > < / td >
2019-05-23 17:35:58 +02:00
< / tr >
2018-12-23 21:26:21 +01:00
< tr >
< th > type< / th >
2021-01-18 16:57:56 +01:00
< td > < p > type to determine weighed isolates; can be < code > "keyantibiotics"< / code > or < code > "points"< / code > , see < em > Details< / em > < / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
< tr >
< th > ignore_I< / th >
2021-03-08 02:38:32 +01:00
< td > < p > logical to indicate whether antibiotic interpretations with < code > "I"< / code > will be ignored when < code > type = "keyantibiotics"< / code > , see < em > Details< / em > < / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
< tr >
< th > points_threshold< / th >
2021-01-18 16:57:56 +01:00
< td > < p > points until the comparison of key antibiotics will lead to inclusion of an isolate when < code > type = "points"< / code > , see < em > Details< / em > < / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
< tr >
< th > info< / th >
2021-04-20 10:46:17 +02:00
< td > < p > a < a href = 'https://rdrr.io/r/base/logical.html' > logical< / a > to indicate whether a progress bar should be printed, defaults to < code > TRUE< / code > only in interactive mode< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
< / table >
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +01:00
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
2021-01-24 14:48:56 +01:00
< p > The < code > key_antibiotics()< / code > function is context-aware. This means that then the < code > x< / code > argument can be left blank, see < em > Examples< / em > .< / p >
2020-12-07 16:06:42 +01:00
< p > The function < code > key_antibiotics()< / code > returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using < code > key_antibiotics_equal()< / code > , to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (< code > "."< / code > ) by < code > key_antibiotics()< / code > and ignored by < code > key_antibiotics_equal()< / code > .< / p >
2020-05-16 13:05:47 +02:00
< p > The < code > < a href = 'first_isolate.html' > first_isolate()< / a > < / code > function only uses this function on the same microbial species from the same patient. Using this, e.g. an MRSA will be included after a susceptible < em > S. aureus< / em > (MSSA) is found within the same patient episode. Without key antibiotic comparison it would not. See < code > < a href = 'first_isolate.html' > first_isolate()< / a > < / code > for more info.< / p >
2019-11-28 22:32:17 +01:00
< p > At default, the antibiotics that are used for < strong > Gram-positive bacteria< / strong > are:< / p > < ul >
< li > < p > Amoxicillin< / p > < / li >
< li > < p > Amoxicillin/clavulanic acid< / p > < / li >
< li > < p > Cefuroxime< / p > < / li >
< li > < p > Piperacillin/tazobactam< / p > < / li >
< li > < p > Ciprofloxacin< / p > < / li >
< li > < p > Trimethoprim/sulfamethoxazole< / p > < / li >
< li > < p > Vancomycin< / p > < / li >
< li > < p > Teicoplanin< / p > < / li >
< li > < p > Tetracycline< / p > < / li >
< li > < p > Erythromycin< / p > < / li >
< li > < p > Oxacillin< / p > < / li >
< li > < p > Rifampin< / p > < / li >
< / ul >
< p > At default the antibiotics that are used for < strong > Gram-negative bacteria< / strong > are:< / p > < ul >
< li > < p > Amoxicillin< / p > < / li >
< li > < p > Amoxicillin/clavulanic acid< / p > < / li >
< li > < p > Cefuroxime< / p > < / li >
< li > < p > Piperacillin/tazobactam< / p > < / li >
< li > < p > Ciprofloxacin< / p > < / li >
< li > < p > Trimethoprim/sulfamethoxazole< / p > < / li >
< li > < p > Gentamicin< / p > < / li >
< li > < p > Tobramycin< / p > < / li >
< li > < p > Colistin< / p > < / li >
< li > < p > Cefotaxime< / p > < / li >
< li > < p > Ceftazidime< / p > < / li >
< li > < p > Meropenem< / p > < / li >
< / ul >
< p > The function < code > key_antibiotics_equal()< / code > checks the characters returned by < code > key_antibiotics()< / code > for equality, and returns a < code > < a href = 'https://rdrr.io/r/base/logical.html' > logical< / a > < / code > vector.< / p >
2021-01-18 16:57:56 +01:00
< h2 class = "hasAnchor" id = "stable-lifecycle" > < a class = "anchor" href = "#stable-lifecycle" > < / a > Stable Lifecycle< / h2 >
2020-01-05 17:22:09 +01:00
< p > < img src = 'figures/lifecycle_stable.svg' style = margin-bottom:5px / > < br / >
2020-05-22 20:15:19 +02:00
The < a href = 'lifecycle.html' > lifecycle< / a > of this function is < strong > stable< / strong > . In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.< / p >
2020-12-22 00:51:17 +01:00
< p > If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.< / p >
2021-01-18 16:57:56 +01:00
< h2 class = "hasAnchor" id = "key-antibiotics" > < a class = "anchor" href = "#key-antibiotics" > < / a > Key Antibiotics< / h2 >
2018-12-23 21:26:21 +01:00
2019-10-13 09:31:58 +02:00
2021-01-18 16:57:56 +01:00
< p > There are two ways to determine whether isolates can be included as first weighted isolates which will give generally the same results:< / p > < ol >
2020-12-22 00:51:17 +01:00
< li > < p > Using < code > type = "keyantibiotics"< / code > and argument < code > ignore_I< / code > < / p >
2019-11-28 22:32:17 +01:00
< p > Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With < code > ignore_I = FALSE< / code > , also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. Read more about this in the < code > key_antibiotics()< / code > function.< / p > < / li >
2020-12-22 00:51:17 +01:00
< li > < p > Using < code > type = "points"< / code > and argument < code > points_threshold< / code > < / p >
2021-02-08 14:18:42 +01:00
< p > A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds < code > points_threshold< / code > , which defaults to < code > 2< / code > , an isolate will be (re)selected as a first weighted isolate.< / p > < / li >
2019-11-28 22:32:17 +01:00
< / ol >
2021-01-18 16:57:56 +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 >
2019-01-02 23:24:07 +01:00
2019-10-13 09:31:58 +02:00
2021-02-02 23:57:35 +01:00
< 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 data analysis, the < a href = 'https://msberends.github.io/AMR/reference/' > complete documentation of all functions< / a > 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 >
2018-12-23 21:26:21 +01:00
< h2 class = "hasAnchor" id = "see-also" > < a class = "anchor" href = "#see-also" > < / a > See also< / h2 >
2019-11-28 22:32:17 +01:00
< div class = 'dont-index' > < p > < code > < a href = 'first_isolate.html' > first_isolate()< / a > < / code > < / p > < / div >
2018-12-23 21:26:21 +01:00
< h2 class = "hasAnchor" id = "examples" > < a class = "anchor" href = "#examples" > < / a > Examples< / h2 >
2021-01-24 14:48:56 +01:00
< pre class = "examples" > < span class = 'co' > # `example_isolates` is a data set available in the AMR package.< / span >
2019-08-27 16:45:42 +02:00
< span class = 'co' > # See ?example_isolates.< / span >
2019-06-11 14:18:25 +02:00
2020-12-07 16:06:42 +01:00
< span class = 'co' > # output of the `key_antibiotics()` function could be like this:< / span >
2020-10-15 09:46:41 +02:00
< span class = 'va' > strainA< / span > < span class = 'op' > < -< / span > < span class = 'st' > "SSSRR.S.R..S"< / span >
< span class = 'va' > strainB< / span > < span class = 'op' > < -< / span > < span class = 'st' > "SSSIRSSSRSSS"< / span >
2018-12-23 21:26:21 +01:00
2020-12-07 16:06:42 +01:00
< span class = 'co' > # those strings can be compared with:< / span >
2020-10-15 09:46:41 +02:00
< span class = 'fu' > key_antibiotics_equal< / span > < span class = 'op' > (< / span > < span class = 'va' > strainA< / span > , < span class = 'va' > strainB< / span > < span class = 'op' > )< / span >
2019-01-02 23:24:07 +01:00
< span class = 'co' > # TRUE, because I is ignored (as well as missing values)< / span >
2018-12-23 21:26:21 +01:00
2020-10-15 09:46:41 +02:00
< span class = 'fu' > key_antibiotics_equal< / span > < span class = 'op' > (< / span > < span class = 'va' > strainA< / span > , < span class = 'va' > strainB< / span > , ignore_I < span class = 'op' > =< / span > < span class = 'cn' > FALSE< / span > < span class = 'op' > )< / span >
2020-12-07 16:06:42 +01:00
< span class = 'co' > # FALSE, because I is not ignored and so the 4th character differs< / span >
2020-09-29 23:35:46 +02:00
< span class = 'co' > # \donttest{< / span >
2020-10-15 09:46:41 +02:00
< span class = 'kw' > if< / span > < span class = 'op' > (< / span > < span class = 'kw' > < a href = 'https://rdrr.io/r/base/library.html' > require< / a > < / span > < span class = 'op' > (< / span > < span class = 'st' > < a href = 'https://dplyr.tidyverse.org' > "dplyr"< / a > < / span > < span class = 'op' > )< / span > < span class = 'op' > )< / span > < span class = 'op' > {< / span >
2020-09-29 23:35:46 +02:00
< span class = 'co' > # set key antibiotics to a new variable< / span >
2020-10-15 09:46:41 +02:00
< span class = 'va' > my_patients< / span > < span class = 'op' > < -< / span > < span class = 'va' > example_isolates< / span > < span class = 'op' > %> %< / span >
2020-12-07 16:06:42 +01:00
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/mutate.html' > mutate< / a > < / span > < span class = 'op' > (< / span > keyab < span class = 'op' > =< / span > < span class = 'fu' > key_antibiotics< / span > < span class = 'op' > (< / span > < span class = 'op' > )< / span > < span class = 'op' > )< / span > < span class = 'op' > %> %< / span > < span class = 'co' > # no need to define `x`< / span >
2020-10-15 09:46:41 +02:00
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/mutate.html' > mutate< / a > < / span > < span class = 'op' > (< / span >
2020-09-29 23:35:46 +02:00
< span class = 'co' > # now calculate first isolates< / span >
2020-12-07 16:06:42 +01:00
first_regular < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'first_isolate.html' > first_isolate< / a > < / span > < span class = 'op' > (< / span > col_keyantibiotics < span class = 'op' > =< / span > < span class = 'cn' > FALSE< / span > < span class = 'op' > )< / span > ,
2020-09-29 23:35:46 +02:00
< span class = 'co' > # and first WEIGHTED isolates< / span >
2020-12-07 16:06:42 +01:00
first_weighted < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'first_isolate.html' > first_isolate< / a > < / span > < span class = 'op' > (< / span > col_keyantibiotics < span class = 'op' > =< / span > < span class = 'st' > "keyab"< / span > < span class = 'op' > )< / span >
2020-10-15 09:46:41 +02:00
< span class = 'op' > )< / span >
2020-09-29 23:35:46 +02:00
2020-12-07 16:06:42 +01:00
< span class = 'co' > # Check the difference, in this data set it results in a lot more isolates:< / span >
2020-10-15 09:46:41 +02:00
< span class = 'fu' > < a href = 'https://rdrr.io/r/base/sum.html' > sum< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > my_patients< / span > < span class = 'op' > $< / span > < span class = 'va' > first_regular< / span > , na.rm < span class = 'op' > =< / span > < span class = 'cn' > TRUE< / span > < span class = 'op' > )< / span >
< span class = 'fu' > < a href = 'https://rdrr.io/r/base/sum.html' > sum< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > my_patients< / span > < span class = 'op' > $< / span > < span class = 'va' > first_weighted< / span > , na.rm < span class = 'op' > =< / span > < span class = 'cn' > TRUE< / span > < span class = 'op' > )< / span >
< span class = 'op' > }< / span >
2020-09-29 23:35:46 +02:00
< span class = 'co' > # }< / span >
< / pre >
2018-12-23 21:26:21 +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 >
2018-12-23 21:26:21 +01:00
< / div >
< / div >
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +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 >
2018-12-23 21:26:21 +01:00
< / div >
< div class = "pkgdown" >
2020-12-24 23:29:10 +01:00
< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.6.1.< / p >
2018-12-23 21:26:21 +01:00
< / div >
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +01:00
< / footer >
< / div >
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +01:00
< / body >
< / html >
2019-10-13 09:31:58 +02:00
