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" >
2018-12-29 22:24:19 +01:00
< title > Key antibiotics for first < em > weighted< / em > isolates — key_antibiotics • 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" / >
2018-12-23 21:26:21 +01:00
<!-- jquery -->
< script src = "https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity = "sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin = "anonymous" > < / script >
<!-- Bootstrap -->
2018-12-29 22:24:19 +01:00
< link href = "https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel = "stylesheet" crossorigin = "anonymous" / >
2018-12-23 21:26:21 +01:00
< script src = "https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity = "sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin = "anonymous" > < / script >
<!-- Font Awesome icons -->
< link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity = "sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin = "anonymous" / >
<!-- clipboard.js -->
< script src = "https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity = "sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin = "anonymous" > < / script >
<!-- sticky kit -->
< script src = "https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity = "sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin = "anonymous" > < / script >
<!-- pkgdown -->
< link href = "../pkgdown.css" rel = "stylesheet" >
< script src = "../pkgdown.js" > < / script >
2018-12-29 22:24:19 +01:00
<!-- docsearch -->
< script src = "../docsearch.js" > < / script >
< link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity = "sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin = "anonymous" / >
< link href = "../docsearch.css" rel = "stylesheet" >
< script src = "https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity = "sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin = "anonymous" > < / script >
2018-12-23 21:26:21 +01:00
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
< meta property = "og:title" content = "Key antibiotics for first <em>weighted</em> 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 will then be called first weighted isolates." / >
2018-12-29 22:24:19 +01:00
2019-01-02 23:24:07 +01:00
< meta property = "og:image" content = "https://msberends.gitlab.io/AMR/logo.png" / >
2018-12-23 21:26:21 +01:00
< meta name = "twitter:card" content = "summary" / >
<!-- 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 >
< 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 >
2019-05-23 16:58:59 +02:00
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Released version" > 0.6.1.9035< / 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" >
2018-12-29 22:24:19 +01:00
< span class = "fa fa-home" > < / span >
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" >
< span class = "fa fa-question-circle" > < / span >
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" >
< 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" >
2019-01-02 23:24:07 +01:00
< span class = "fa fa-dice" > < / span >
Predict antimicrobial resistance
< / a >
< / li >
2019-05-23 16:58:59 +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 >
2019-01-02 23:24:07 +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" >
2019-01-02 23:24:07 +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" >
2019-01-02 23:24:07 +01:00
< span class = "fa fa-capsules" > < / span >
Get properties of an antibiotic
< / a >
< / li >
< li >
< a href = "../articles/freq.html" >
< span class = "fa fa-sort-amount-down" > < / span >
Create frequency tables
< / a >
< / li >
< li >
< a href = "../articles/G_test.html" >
< span class = "fa fa-clipboard-check" > < / span >
Use the G-test
< / a >
< / li >
2019-01-11 20:37:23 +01:00
< li >
< a href = "../articles/benchmarks.html" >
< span class = "fa fa-shipping-fast" > < / span >
Other: benchmarks
< / a >
< / li >
2019-01-02 23:24:07 +01:00
< / ul >
2018-12-23 21:26:21 +01:00
< / li >
< li >
2018-12-29 22:24:19 +01:00
< a href = "../reference/" >
< span class = "fa fa-book-open" > < / span >
Manual
< / a >
2018-12-23 21:26:21 +01:00
< / li >
< li >
2018-12-29 22:24:19 +01:00
< a href = "../authors.html" >
< span class = "fa fa-users" > < / span >
Authors
< / a >
2018-12-23 21:26:21 +01:00
< / li >
2018-12-29 22:24:19 +01:00
< li >
< a href = "../news/" >
< span class = "far fa 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 >
2018-12-29 22:24:19 +01:00
< a href = "https://gitlab.com/msberends/AMR" >
< span class = "fab fa fab fa-gitlab" > < / span >
Source Code
< / a >
2018-12-23 21:26:21 +01:00
< / li >
2019-01-02 23:24:07 +01:00
< li >
2018-12-29 22:24:19 +01:00
< a href = "../LICENSE-text.html" >
< span class = "fa fa-book" > < / span >
Licence
< / a >
< / li >
2018-12-23 21:26:21 +01:00
< / ul >
2018-12-29 22:24:19 +01:00
< form class = "navbar-form navbar-right" role = "search" >
< div class = "form-group" >
< input type = "search" class = "form-control" name = "search-input" id = "search-input" placeholder = "Search..." aria-label = "Search for..." autocomplete = "off" >
< / div >
< / form >
2018-12-23 21:26:21 +01:00
< / div > <!-- /.nav - collapse -->
< / div > <!-- /.container -->
< / div > <!-- /.navbar -->
< / header >
< div class = "row" >
< div class = "col-md-9 contents" >
< div class = "page-header" >
< h1 > Key antibiotics for first < em > weighted< / em > isolates< / h1 >
< div class = "hidden name" > < code > key_antibiotics.Rd< / code > < / div >
< / div >
< div class = "ref-description" >
2018-12-31 01:48:53 +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 will then be called first < em > weighted< / em > isolates.< / p >
2018-12-23 21:26:21 +01:00
< / div >
2019-05-23 16:58:59 +02:00
< pre class = "usage" > < span class = 'fu' > key_antibiotics< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > col_mo< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > universal_1< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "AMX"< / span > ),
< span class = 'kw' > universal_2< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "AMC"< / span > ), < span class = 'kw' > universal_3< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > ,
< span class = 'st' > "CXM"< / span > ), < span class = 'kw' > universal_4< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "TZP"< / span > ),
< span class = 'kw' > universal_5< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "CIP"< / span > ), < span class = 'kw' > universal_6< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > ,
< span class = 'st' > "SXT"< / span > ), < span class = 'kw' > GramPos_1< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "VAN"< / span > ),
< span class = 'kw' > GramPos_2< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "TEC"< / span > ), < span class = 'kw' > GramPos_3< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > ,
< span class = 'st' > "TCY"< / span > ), < span class = 'kw' > GramPos_4< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "ERY"< / span > ),
< span class = 'kw' > GramPos_5< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "OXA"< / span > ), < span class = 'kw' > GramPos_6< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > ,
< span class = 'st' > "RIF"< / span > ), < span class = 'kw' > GramNeg_1< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "GEN"< / span > ),
< span class = 'kw' > GramNeg_2< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "TOB"< / span > ), < span class = 'kw' > GramNeg_3< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > ,
< span class = 'st' > "COL"< / span > ), < span class = 'kw' > GramNeg_4< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "CTX"< / span > ),
< span class = 'kw' > GramNeg_5< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "CAZ"< / span > ), < span class = 'kw' > GramNeg_6< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > ,
< span class = 'st' > "MEM"< / span > ), < span class = 'kw' > warnings< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > , < span class = 'no' > ...< / span > )
2018-12-23 21:26:21 +01:00
< span class = 'fu' > key_antibiotics_equal< / span > (< span class = 'no' > x< / span > , < span class = 'no' > y< / span > , < span class = 'kw' > type< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/c' > c< / a > < / span > (< span class = 'st' > "keyantibiotics"< / span > , < span class = 'st' > "points"< / span > ),
< span class = 'kw' > ignore_I< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > , < span class = 'kw' > points_threshold< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 2< / span > , < span class = 'kw' > info< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > )< / pre >
< 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 >
< td > < p > table with antibiotics coloms, like < code > AMX< / code > or < code > amox< / code > < / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
< tr >
< th > col_mo< / th >
2018-12-31 01:48:53 +01:00
< td > < p > column name of the unique IDs of the microorganisms (see < code > < a href = 'as.mo.html' > mo< / a > < / code > ), defaults to the first column of class < code > mo< / 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 >
2019-01-11 20:37:23 +01:00
< td > < p > column names of < strong > broad-spectrum< / strong > antibiotics, case-insensitive. At default, the columns containing these antibiotics will be 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 >
2019-01-11 20:37:23 +01:00
< td > < p > column names of antibiotics for < strong > Gram positives< / strong > , case-insensitive. At default, the columns containing these antibiotics will be 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 >
2019-01-11 20:37:23 +01:00
< td > < p > column names of antibiotics for < strong > Gram negatives< / strong > , case-insensitive. At default, the columns containing these antibiotics will be 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 >
< td > < p > give warning about missing antibiotic columns, they will anyway be ignored< / p > < / td >
< / tr >
< tr >
< th > ...< / th >
< td > < p > other parameters passed on to function< / p > < / td >
< / tr >
< tr >
< th > type< / th >
< td > < p > type to determine weighed isolates; can be < code > "keyantibiotics"< / code > or < code > "points"< / code > , see Details< / p > < / td >
< / tr >
< tr >
< th > ignore_I< / th >
< td > < p > logical to determine whether antibiotic interpretations with < code > "I"< / code > will be ignored when < code > type = "keyantibiotics"< / code > , see Details< / p > < / td >
< / tr >
< tr >
< th > points_threshold< / th >
< td > < p > points until the comparison of key antibiotics will lead to inclusion of an isolate when < code > type = "points"< / code > , see Details< / p > < / td >
< / tr >
< tr >
< th > info< / th >
< td > < p > print progress< / p > < / td >
< / tr >
2019-05-23 16:58:59 +02:00
< tr >
< th > x, y< / th >
< td > < p > characters to compare< / p > < / td >
< / tr >
2018-12-23 21:26:21 +01:00
< / table >
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
2019-01-11 20:37:23 +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 > ). 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, an MRSA will be included after a susceptible < em > S. aureus< / em > (MSSA) found within the same episode (see < code > episode< / code > parameter of < code > < a href = 'first_isolate.html' > first_isolate< / a > < / code > ). Without key antibiotic comparison it would not.< / p >
2018-12-23 21:26:21 +01:00
< p > At default, the antibiotics that are used for < strong > Gram positive bacteria< / strong > are (colum names): < br / >
< code > "amox"< / code > , < code > "amcl"< / code > , < code > "cfur"< / code > , < code > "pita"< / code > , < code > "cipr"< / code > , < code > "trsu"< / code > (until here is universal), < code > "vanc"< / code > , < code > "teic"< / code > , < code > "tetr"< / code > , < code > "eryt"< / code > , < code > "oxac"< / code > , < code > "rifa"< / code > .< / p >
< p > At default, the antibiotics that are used for < strong > Gram negative bacteria< / strong > are (colum names): < br / >
< code > "amox"< / code > , < code > "amcl"< / code > , < code > "cfur"< / code > , < code > "pita"< / code > , < code > "cipr"< / code > , < code > "trsu"< / code > (until here is universal), < code > "gent"< / code > , < code > "tobr"< / code > , < code > "coli"< / code > , < code > "cfot"< / code > , < code > "cfta"< / code > , < code > "mero"< / code > .< / p >
< p > The function < code > key_antibiotics_equal< / code > checks the characters returned by < code > key_antibiotics< / code > for equality, and returns a logical vector.< / p >
< h2 class = "hasAnchor" id = "key-antibiotics" > < a class = "anchor" href = "#key-antibiotics" > < / a > Key antibiotics< / h2 >
< p > There are two ways to determine whether isolates can be included as first < em > weighted< / em > isolates which will give generally the same results: < br / > < / p >
< p > < strong > 1. Using< / strong > < code > type = "keyantibiotics"< / code > < strong > and parameter< / strong > < code > ignore_I< / code > < br / >
2019-04-09 14:59:17 +02:00
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. < br / > < / p >
2018-12-23 21:26:21 +01:00
< p > < strong > 2. Using< / strong > < code > type = "points"< / code > < strong > and parameter< / strong > < code > points_threshold< / code > < br / >
2019-04-09 14:59:17 +02:00
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 default to < code > 2< / code > , an isolate will be (re)selected as a first weighted isolate.< / p >
2018-12-23 21:26:21 +01:00
2019-01-02 23:24:07 +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 >
2019-02-21 18:55:52 +01:00
< p > On our website < a href = 'https://msberends.gitlab.io/AMR' > https://msberends.gitlab.io/AMR< / a > you can find < a href = 'https://msberends.gitlab.io/AMR/articles/AMR.html' > a comprehensive tutorial< / a > about how to conduct AMR analysis, the < a href = 'https://msberends.gitlab.io/AMR/reference' > complete documentation of all functions< / a > (which reads a lot easier than here in R) and < a href = 'https://msberends.gitlab.io/AMR/articles/WHONET.html' > an example analysis using WHONET data< / a > .< / p >
2019-01-02 23:24:07 +01:00
2018-12-23 21:26:21 +01:00
< h2 class = "hasAnchor" id = "see-also" > < a class = "anchor" href = "#see-also" > < / a > See also< / h2 >
2018-12-31 01:48:53 +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 >
2019-01-02 23:24:07 +01:00
< pre class = "examples" > < span class = 'co' > # NOT RUN {< / span >
< span class = 'co' > # septic_patients is a dataset available in the AMR package< / span >
?< span class = 'no' > septic_patients< / span >
< span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/library' > library< / a > < / span > (< span class = 'no' > dplyr< / span > )
2018-12-23 21:26:21 +01:00
< span class = 'co' > # set key antibiotics to a new variable< / span >
< span class = 'no' > my_patients< / span > < span class = 'kw' > < -< / span > < span class = 'no' > septic_patients< / span > < span class = 'kw' > %> %< / span >
2019-01-29 20:20:09 +01:00
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/mutate.html' > mutate< / a > < / span > (< span class = 'kw' > keyab< / span > < span class = 'kw' > =< / span > < span class = 'fu' > key_antibiotics< / span > (< span class = 'no' > .< / span > )) < span class = 'kw' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/mutate.html' > mutate< / a > < / span > (
2018-12-23 21:26:21 +01:00
< span class = 'co' > # now calculate first isolates< / span >
2018-12-31 01:48:53 +01:00
< span class = 'kw' > first_regular< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'first_isolate.html' > first_isolate< / a > < / span > (< span class = 'no' > .< / span > , < span class = 'kw' > col_keyantibiotics< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > ),
2018-12-23 21:26:21 +01:00
< span class = 'co' > # and first WEIGHTED isolates< / span >
2018-12-31 01:48:53 +01:00
< span class = 'kw' > first_weighted< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'first_isolate.html' > first_isolate< / a > < / span > (< span class = 'no' > .< / span > , < span class = 'kw' > col_keyantibiotics< / span > < span class = 'kw' > =< / span > < span class = 'st' > "keyab"< / span > )
2019-01-02 23:24:07 +01:00
)
2018-12-23 21:26:21 +01:00
< span class = 'co' > # Check the difference, in this data set it results in 7% more isolates:< / span >
2019-01-02 23:24:07 +01:00
< span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/sum' > sum< / a > < / span > (< span class = 'no' > my_patients< / span > $< span class = 'no' > first_regular< / span > , < span class = 'kw' > na.rm< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > )
< span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/sum' > sum< / a > < / span > (< span class = 'no' > my_patients< / span > $< span class = 'no' > first_weighted< / span > , < span class = 'kw' > na.rm< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > )
2018-12-23 21:26:21 +01:00
< span class = 'co' > # output of the `key_antibiotics` function could be like this:< / span >
< span class = 'no' > strainA< / span > < span class = 'kw' > < -< / span > < span class = 'st' > "SSSRR.S.R..S"< / span >
< span class = 'no' > strainB< / span > < span class = 'kw' > < -< / span > < span class = 'st' > "SSSIRSSSRSSS"< / span >
2019-01-02 23:24:07 +01:00
< span class = 'fu' > key_antibiotics_equal< / span > (< span class = 'no' > strainA< / span > , < span class = 'no' > strainB< / span > )
< span class = 'co' > # TRUE, because I is ignored (as well as missing values)< / span >
2018-12-23 21:26:21 +01:00
2019-01-02 23:24:07 +01:00
< span class = 'fu' > key_antibiotics_equal< / span > (< span class = 'no' > strainA< / span > , < span class = 'no' > strainB< / span > , < span class = 'kw' > ignore_I< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > )
< span class = 'co' > # FALSE, because I is not ignored and so the 4th value differs< / span >
< span class = 'co' > # }< / span > < / pre >
2018-12-23 21:26:21 +01:00
< / div >
< div class = "col-md-3 hidden-xs hidden-sm" id = "sidebar" >
< h2 > Contents< / h2 >
< ul class = "nav nav-pills nav-stacked" >
< li > < a href = "#arguments" > Arguments< / a > < / li >
< li > < a href = "#details" > Details< / a > < / li >
< li > < a href = "#key-antibiotics" > Key antibiotics< / a > < / li >
2019-01-02 23:24:07 +01:00
< li > < a href = "#read-more-on-our-website-" > Read more on our website!< / a > < / li >
2018-12-23 21:26:21 +01:00
< li > < a href = "#see-also" > See also< / a > < / li >
< li > < a href = "#examples" > Examples< / a > < / li >
< / ul >
< / div >
< / div >
< footer >
< div class = "copyright" >
2018-12-29 22:24:19 +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/c.glasner/' > Corinna Glasner< / a > , < a href = 'https://www.rug.nl/staff/a.w.friedrich/' > Alex W. Friedrich< / a > , < a href = 'https://www.rug.nl/staff/b.sinha/' > Bhanu N. M. Sinha< / a > .< / p >
2018-12-23 21:26:21 +01:00
< / div >
< div class = "pkgdown" >
< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.3.0.< / p >
< / div >
< / footer >
< / div >
2018-12-29 22:24:19 +01:00
< script src = "https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity = "sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin = "anonymous" > < / script >
< script >
docsearch({
apiKey: 'f737050abfd4d726c63938e18f8c496e',
indexName: 'amr',
inputSelector: 'input#search-input.form-control',
transformData: function(hits) {
return hits.map(function (hit) {
hit.url = updateHitURL(hit);
return hit;
});
}
});
< / script >
2018-12-23 21:26:21 +01:00
< / body >
< / html >
