2018-12-29 22:24:19 +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 > Determine first (weighted) isolates — first_isolate • 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" / >
2019-10-11 17:21:02 +02:00
2018-12-29 22:24:19 +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 -->
< link href = "https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel = "stylesheet" crossorigin = "anonymous" / >
2019-10-11 17:21:02 +02:00
2018-12-29 22:24:19 +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 -->
2019-10-11 17:21:02 +02:00
< link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity = "sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin = "anonymous" / >
< link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity = "sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin = "anonymous" / >
2018-12-29 22:24:19 +01:00
<!-- 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 >
2019-10-11 17:21:02 +02:00
<!-- headroom.js -->
< script src = "https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity = "sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin = "anonymous" > < / script >
< script src = "https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity = "sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin = "anonymous" > < / script >
2018-12-29 22:24:19 +01:00
<!-- pkgdown -->
< link href = "../pkgdown.css" rel = "stylesheet" >
< script src = "../pkgdown.js" > < / script >
<!-- 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 >
< link href = "../extra.css" rel = "stylesheet" >
< script src = "../extra.js" > < / script >
2019-10-11 17:21:02 +02:00
< meta property = "og:title" content = "Determine first (weighted) isolates — first_isolate" / >
2018-12-29 22:24:19 +01:00
< meta property = "og:description" content = "Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type." / >
2019-01-02 23:24:07 +01:00
< meta property = "og:image" content = "https://msberends.gitlab.io/AMR/logo.png" / >
2018-12-29 22:24:19 +01:00
< meta name = "twitter:card" content = "summary" / >
2019-10-11 17:21:02 +02:00
2018-12-29 22:24:19 +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]-->
2019-10-11 17:21:02 +02:00
2018-12-29 22:24:19 +01:00
< / 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" >
< a class = "navbar-link" href = "../index.html" > AMR (for R)< / a >
2019-11-29 19:43:23 +01:00
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Latest development version" > 0.9.0< / span >
2018-12-29 22:24:19 +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 >
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
2018-12-29 22:24:19 +01:00
2019-01-02 23:24:07 +01:00
< span class = "caret" > < / span >
2018-12-29 22:24:19 +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 >
2019-05-28 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 >
2019-01-02 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 >
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 >
2018-12-29 22:24:19 +01:00
< / 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 >
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 >
< / 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 >
< / ul >
2019-10-11 17:21:02 +02:00
< form class = "navbar-form navbar-right hidden-xs hidden-sm" role = "search" >
2018-12-29 22:24:19 +01:00
< 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 >
< / div > <!-- /.nav - collapse -->
< / div > <!-- /.container -->
< / div > <!-- /.navbar -->
2019-10-11 17:21:02 +02:00
2018-12-29 22:24:19 +01:00
< / header >
< div class = "row" >
< div class = "col-md-9 contents" >
< div class = "page-header" >
< h1 > Determine first (weighted) isolates< / h1 >
< div class = "hidden name" > < code > first_isolate.Rd< / code > < / div >
< / div >
< div class = "ref-description" >
< p > Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type.< / p >
< / div >
2019-11-28 22:32:17 +01:00
< pre class = "usage" > < span class = 'fu' > first_isolate< / span > (
< span class = 'no' > x< / span > ,
< span class = 'kw' > col_date< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > ,
< span class = 'kw' > col_patient_id< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > ,
< span class = 'kw' > col_mo< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > ,
< span class = 'kw' > col_testcode< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > ,
< span class = 'kw' > col_specimen< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > ,
< span class = 'kw' > col_icu< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > ,
< span class = 'kw' > col_keyantibiotics< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > ,
< span class = 'kw' > episode_days< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 365< / span > ,
< span class = 'kw' > testcodes_exclude< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > ,
< span class = 'kw' > icu_exclude< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > ,
< span class = 'kw' > specimen_group< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > ,
< span class = 'kw' > type< / span > < span class = 'kw' > =< / span > < span class = 'st' > "keyantibiotics"< / 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' > TRUE< / span > ,
< span class = 'kw' > include_unknown< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > ,
< span class = 'no' > ...< / span >
)
< span class = 'fu' > filter_first_isolate< / span > (
< span class = 'no' > x< / span > ,
< span class = 'kw' > col_date< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > ,
< span class = 'kw' > col_patient_id< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > ,
< span class = 'kw' > col_mo< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > ,
< span class = 'no' > ...< / span >
)
< span class = 'fu' > filter_first_weighted_isolate< / span > (
< span class = 'no' > x< / span > ,
< span class = 'kw' > col_date< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > ,
< span class = 'kw' > col_patient_id< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > ,
< span class = 'kw' > col_mo< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > ,
< span class = 'kw' > col_keyantibiotics< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > ,
< span class = 'no' > ...< / span >
)< / pre >
2019-10-11 17:21:02 +02:00
2018-12-29 22:24:19 +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 14:56:23 +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 > containing isolates.< / p > < / td >
2018-12-29 22:24:19 +01:00
< / tr >
< tr >
< th > col_date< / th >
2019-01-15 12:45:24 +01:00
< td > < p > column name of the result date (or date that is was received on the lab), defaults to the first column of with a date class< / p > < / td >
2018-12-29 22:24:19 +01:00
< / tr >
< tr >
< th > col_patient_id< / th >
< td > < p > column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive)< / p > < / td >
< / 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 >
2018-12-29 22:24:19 +01:00
< / tr >
< tr >
< th > col_testcode< / th >
< td > < p > column name of the test codes. Use < code > col_testcode = NULL< / code > to < strong > not< / strong > exclude certain test codes (like test codes for screening). In that case < code > testcodes_exclude< / code > will be ignored.< / p > < / td >
< / tr >
< tr >
< th > col_specimen< / th >
< td > < p > column name of the specimen type or group< / p > < / td >
< / tr >
< tr >
< th > col_icu< / th >
< td > < p > column name of the logicals (< code > TRUE< / code > /< code > FALSE< / code > ) whether a ward or department is an Intensive Care Unit (ICU)< / p > < / td >
< / tr >
< tr >
< th > col_keyantibiotics< / th >
2019-11-28 22:32:17 +01:00
< td > < p > column name of the key antibiotics to determine first < em > weighted< / em > isolates, see < code > < a href = 'key_antibiotics.html' > key_antibiotics()< / a > < / code > . Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' (case insensitive). Use < code > col_keyantibiotics = FALSE< / code > to prevent this.< / p > < / td >
2018-12-29 22:24:19 +01:00
< / tr >
< tr >
< th > episode_days< / th >
2019-08-08 22:39:42 +02:00
< td > < p > episode in days after which a genus/species combination will be determined as 'first isolate' again. The default of 365 days is based on the guideline by CLSI, see Source.< / p > < / td >
2018-12-29 22:24:19 +01:00
< / tr >
< tr >
< th > testcodes_exclude< / th >
< td > < p > character vector with test codes that should be excluded (case-insensitive)< / p > < / td >
< / tr >
< tr >
< th > icu_exclude< / th >
< td > < p > logical whether ICU isolates should be excluded (rows with value < code > TRUE< / code > in column < code > col_icu< / code > )< / p > < / td >
< / tr >
< tr >
< th > specimen_group< / th >
< td > < p > value in column < code > col_specimen< / code > to filter on< / 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 >
2019-08-08 22:39:42 +02:00
< tr >
< th > include_unknown< / th >
2019-08-09 14:28:46 +02:00
< td > < p > logical to determine whether 'unknown' microorganisms should be included too, i.e. microbial code < code > "UNKNOWN"< / code > , which defaults to < code > FALSE< / code > . For WHONET users, this means that all records with organism code < code > "con"< / code > (< em > contamination< / em > ) will be excluded at default. Isolates with a microbial ID of < code > NA< / code > will always be excluded as first isolate.< / p > < / td >
2019-08-08 22:39:42 +02:00
< / tr >
2018-12-29 22:24:19 +01:00
< tr >
< th > ...< / th >
2019-11-28 22:32:17 +01:00
< td > < p > parameters passed on to the < code > first_isolate()< / code > function< / p > < / td >
2018-12-29 22:24:19 +01:00
< / tr >
< / table >
2019-10-11 17:21:02 +02:00
2018-12-29 22:24:19 +01:00
< h2 class = "hasAnchor" id = "source" > < a class = "anchor" href = "#source" > < / a > Source< / h2 >
2019-11-28 22:32:17 +01:00
< p > Methodology of this function is based on:< / p >
< p > < strong > M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition< / strong > , 2014, < em > Clinical and Laboratory Standards Institute (CLSI)< / em > . < a href = 'https://clsi.org/standards/products/microbiology/documents/m39/' > https://clsi.org/standards/products/microbiology/documents/m39/< / a > .< / p >
2018-12-29 22:24:19 +01:00
< h2 class = "hasAnchor" id = "value" > < a class = "anchor" href = "#value" > < / a > Value< / h2 >
2019-11-28 22:32:17 +01:00
< p > A < code > < a href = 'https://rdrr.io/r/base/logical.html' > logical< / a > < / code > vector< / p >
2018-12-29 22:24:19 +01:00
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
< p > < strong > WHY THIS IS SO IMPORTANT< / strong > < br / >
2019-11-28 23:00:37 +01:00
To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode < a href = 'https://www.ncbi.nlm.nih.gov/pubmed/17304462' > (ref)< / a > . If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all < em > S. aureus< / em > isolates would be overestimated, because you included this MRSA more than once. It would be < a href = 'https://en.wikipedia.org/wiki/Selection_bias' > selection bias< / a > .< / p >
2019-08-09 14:28:46 +02:00
< p > All isolates with a microbial ID of < code > NA< / code > will be excluded as first isolate.< / p >
2019-11-28 22:32:17 +01:00
< p > The functions < code > filter_first_isolate()< / code > and < code > filter_first_weighted_isolate()< / code > are helper functions to quickly filter on first isolates. The function < code > filter_first_isolate()< / code > is essentially equal to:< / p > < pre > x %> %
2019-05-13 14:56:23 +02:00
mutate(only_firsts = first_isolate(x, ...)) %> %
2018-12-29 22:24:19 +01:00
filter(only_firsts == TRUE) %> %
select(-only_firsts)
2019-11-28 22:32:17 +01:00
< / pre >
< p > The function < code > filter_first_weighted_isolate()< / code > is essentially equal to:< / p > < pre > x %> %
2018-12-29 22:24:19 +01:00
mutate(keyab = key_antibiotics(.)) %> %
2019-05-13 14:56:23 +02:00
mutate(only_weighted_firsts = first_isolate(x,
2018-12-29 22:24:19 +01:00
col_keyantibiotics = "keyab", ...)) %> %
filter(only_weighted_firsts == TRUE) %> %
select(-only_weighted_firsts)
< / pre >
2019-10-11 17:21:02 +02:00
2018-12-29 22:24:19 +01:00
< h2 class = "hasAnchor" id = "key-antibiotics" > < a class = "anchor" href = "#key-antibiotics" > < / a > Key antibiotics< / h2 >
2019-10-11 17:21:02 +02:00
2019-11-28 22:32:17 +01:00
< 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:< / p > < ol >
< li > < p > Using < code > type = "keyantibiotics"< / code > and parameter < code > ignore_I< / code > < / p >
< 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 > < a href = 'key_antibiotics.html' > key_antibiotics()< / a > < / code > function.< / p > < / li >
< li > < p > Using < code > type = "points"< / code > and parameter < code > points_threshold< / code > < / p >
< 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 default to < code > 2< / code > , an isolate will be (re)selected as a first weighted isolate.< / p > < / li >
< / ol >
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 >
2019-10-11 17:21:02 +02:00
< 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 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 >
2018-12-29 22:24:19 +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 = 'key_antibiotics.html' > key_antibiotics()< / a > < / code > < / p > < / div >
2018-12-29 22:24:19 +01:00
< h2 class = "hasAnchor" id = "examples" > < a class = "anchor" href = "#examples" > < / a > Examples< / h2 >
2019-10-11 17:21:02 +02:00
< pre class = "examples" > < span class = 'co' > # `example_isolates` is a dataset available in the AMR package.< / span >
2019-08-27 16:45:42 +02:00
< span class = 'co' > # See ?example_isolates.< / span >
2019-01-02 23:24:07 +01:00
2019-10-11 17:21:02 +02:00
< span class = 'fu' > < a href = 'https://rdrr.io/r/base/library.html' > library< / a > < / span > (< span class = 'no' > dplyr< / span > )
2018-12-29 22:24:19 +01:00
< span class = 'co' > # Filter on first isolates:< / span >
2019-08-27 16:45:42 +02:00
< span class = 'no' > example_isolates< / 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' > first_isolate< / span > < span class = 'kw' > =< / span > < span class = 'fu' > first_isolate< / span > (< span class = 'no' > .< / span > ,
2018-12-29 22:24:19 +01:00
< span class = 'kw' > col_date< / span > < span class = 'kw' > =< / span > < span class = 'st' > "date"< / span > ,
< span class = 'kw' > col_patient_id< / span > < span class = 'kw' > =< / span > < span class = 'st' > "patient_id"< / span > ,
< span class = 'kw' > col_mo< / span > < span class = 'kw' > =< / span > < span class = 'st' > "mo"< / span > )) < span class = 'kw' > %> %< / span >
2019-01-29 20:20:09 +01:00
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/filter.html' > filter< / a > < / span > (< span class = 'no' > first_isolate< / span > < span class = 'kw' > ==< / span > < span class = 'fl' > TRUE< / span > )
2019-01-02 23:24:07 +01:00
2018-12-29 22:24:19 +01:00
< span class = 'co' > # Which can be shortened to:< / span >
2019-08-27 16:45:42 +02:00
< span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span >
2019-01-02 23:24:07 +01:00
< span class = 'fu' > filter_first_isolate< / span > ()
< span class = 'co' > # or for first weighted isolates:< / span >
2019-08-27 16:45:42 +02:00
< span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span >
2019-01-02 23:24:07 +01:00
< span class = 'fu' > filter_first_weighted_isolate< / span > ()
2018-12-29 22:24:19 +01:00
< span class = 'co' > # Now let's see if first isolates matter:< / span >
2019-08-27 16:45:42 +02:00
< span class = 'no' > A< / span > < span class = 'kw' > < -< / span > < span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span >
2019-01-29 20:20:09 +01:00
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/group_by.html' > group_by< / a > < / span > (< span class = 'no' > hospital_id< / span > ) < span class = 'kw' > %> %< / span >
2019-05-10 16:44:59 +02:00
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/summarise.html' > summarise< / a > < / span > (< span class = 'kw' > count< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'count.html' > n_rsi< / a > < / span > (< span class = 'no' > GEN< / span > ), < span class = 'co' > # gentamicin availability< / span >
2019-11-10 13:17:20 +01:00
< span class = 'kw' > resistance< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'proportion.html' > resistance< / a > < / span > (< span class = 'no' > GEN< / span > )) < span class = 'co' > # gentamicin resistance< / span >
2018-12-29 22:24:19 +01:00
2019-08-27 16:45:42 +02:00
< span class = 'no' > B< / span > < span class = 'kw' > < -< / span > < span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span >
2019-05-10 16:44:59 +02:00
< span class = 'fu' > filter_first_weighted_isolate< / span > () < span class = 'kw' > %> %< / span > < span class = 'co' > # the 1st isolate filter< / span >
2019-01-29 20:20:09 +01:00
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/group_by.html' > group_by< / a > < / span > (< span class = 'no' > hospital_id< / span > ) < span class = 'kw' > %> %< / span >
2019-05-10 16:44:59 +02:00
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/summarise.html' > summarise< / a > < / span > (< span class = 'kw' > count< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'count.html' > n_rsi< / a > < / span > (< span class = 'no' > GEN< / span > ), < span class = 'co' > # gentamicin availability< / span >
2019-11-10 13:17:20 +01:00
< span class = 'kw' > resistance< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'proportion.html' > resistance< / a > < / span > (< span class = 'no' > GEN< / span > )) < span class = 'co' > # gentamicin resistance< / span >
2018-12-29 22:24:19 +01:00
2019-01-02 23:24:07 +01:00
< span class = 'co' > # Have a look at A and B.< / span >
< span class = 'co' > # B is more reliable because every isolate is only counted once.< / span >
2019-04-09 14:59:17 +02:00
< span class = 'co' > # Gentamicin resitance in hospital D appears to be 3.1% higher than< / span >
< span class = 'co' > # when you (erroneously) would have used all isolates for analysis.< / span >
2018-12-29 22:24:19 +01:00
2019-01-02 23:24:07 +01:00
< span class = 'co' > ## OTHER EXAMPLES:< / span >
2019-10-11 17:21:02 +02:00
< span class = 'kw' > if< / span > (< span class = 'fl' > FALSE< / span > ) {
2018-12-29 22:24:19 +01:00
< span class = 'co' > # set key antibiotics to a new variable< / span >
2019-05-13 14:56:23 +02:00
< span class = 'no' > x< / span > $< span class = 'no' > keyab< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > < a href = 'key_antibiotics.html' > key_antibiotics< / a > < / span > (< span class = 'no' > x< / span > )
2018-12-29 22:24:19 +01:00
2019-10-11 17:21:02 +02:00
< span class = 'no' > x< / span > $< span class = 'no' > first_isolate< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > first_isolate< / span > (< span class = 'no' > x< / span > )
2018-12-29 22:24:19 +01:00
2019-10-11 17:21:02 +02:00
< span class = 'no' > x< / span > $< span class = 'no' > first_isolate_weighed< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > first_isolate< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > col_keyantibiotics< / span > < span class = 'kw' > =< / span > < span class = 'st' > 'keyab'< / span > )
2018-12-29 22:24:19 +01:00
2019-10-11 17:21:02 +02:00
< span class = 'no' > x< / span > $< span class = 'no' > first_blood_isolate< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > first_isolate< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > specimen_group< / span > < span class = 'kw' > =< / span > < span class = 'st' > "Blood"< / span > )
}< / pre >
2018-12-29 22:24:19 +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 = "#source" > Source< / a > < / li >
< li > < a href = "#value" > Value< / 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 >
2018-12-29 22:24:19 +01:00
< li > < a href = "#see-also" > See also< / a > < / li >
< li > < a href = "#examples" > Examples< / a > < / li >
< / ul >
< / div >
< / div >
2019-10-11 17:21:02 +02:00
2018-12-29 22:24:19 +01:00
< footer >
< div class = "copyright" >
2019-08-15 17:09:27 +02:00
< 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/' > Alex 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 >
2018-12-29 22:24:19 +01:00
< / div >
< div class = "pkgdown" >
2019-10-11 17:21:02 +02:00
< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.4.1.< / p >
2018-12-29 22:24:19 +01:00
< / div >
2019-10-11 17:21:02 +02:00
2018-12-29 22:24:19 +01:00
< / footer >
< / div >
< 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 >
2019-10-11 17:21:02 +02:00
2018-12-29 22:24:19 +01:00
< / body >
< / html >
2019-10-11 17:21:02 +02:00
