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 > EUCAST rules — eucast_rules • 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" / >
2019-10-07 14:32:06 +02:00
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
2019-10-07 14:32:06 +02:00
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 -->
2019-10-07 14:32:06 +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" / >
2018-12-23 21:26:21 +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 >
2019-10-07 14:32:06 +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 >
2018-12-23 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
<!-- 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
2019-10-07 14:32:06 +02:00
< meta property = "og:title" content = "EUCAST rules — eucast_rules" / >
2018-12-23 21:26:21 +01:00
< meta property = "og:description" content = "Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, http://eucast.org), see Source. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables." / >
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" / >
2019-10-07 14:32:06 +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]-->
2019-10-07 14:32:06 +02:00
2018-12-23 21:26:21 +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" >
2018-12-29 22:24:19 +01:00
< a class = "navbar-link" href = "../index.html" > AMR (for R)< / a >
2019-11-03 22:24:42 +01:00
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Latest development version" > 0.8.0.9008< / 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 >
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 >
2019-10-07 14:32:06 +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 >
2018-12-23 21:26:21 +01:00
< / div > <!-- /.nav - collapse -->
< / div > <!-- /.container -->
< / div > <!-- /.navbar -->
2019-10-07 14:32:06 +02:00
2018-12-23 21:26:21 +01:00
< / header >
< div class = "row" >
< div class = "col-md-9 contents" >
< div class = "page-header" >
< h1 > EUCAST rules< / h1 >
< div class = "hidden name" > < code > eucast_rules.Rd< / code > < / div >
< / div >
< div class = "ref-description" >
< p > Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, < a href = 'http://eucast.org' > http://eucast.org< / a > ), see < em > Source< / em > . This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.< / p >
< / div >
2019-10-07 14:32:06 +02:00
< pre class = "usage" > < span class = 'fu' > eucast_rules< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > col_mo< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > info< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > , < span class = 'kw' > rules< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/c.html' > c< / a > < / span > (< span class = 'st' > "breakpoints"< / span > ,
2019-06-01 20:40:49 +02:00
< span class = 'st' > "expert"< / span > , < span class = 'st' > "other"< / span > , < span class = 'st' > "all"< / span > ), < span class = 'kw' > verbose< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > , < span class = 'no' > ...< / span > )< / pre >
2019-10-07 14:32:06 +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 >
2019-04-05 18:47:39 +02:00
< th > x< / th >
2019-05-10 16:44:59 +02:00
< td > < p > data with antibiotic columns, like e.g. < code > AMX< / code > and < code > AMC< / code > < / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
< tr >
< th > col_mo< / th >
2019-08-27 22:41:09 +02:00
< 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 > 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 > info< / th >
< td > < p > print progress< / p > < / td >
< / tr >
< tr >
< th > rules< / th >
2019-10-07 14:32:06 +02:00
< td > < p > a character vector that specifies which rules should be applied - one or more of < code > < a href = 'https://rdrr.io/r/base/c.html' > c("breakpoints", "expert", "other", "all")< / a > < / code > < / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
< tr >
< th > verbose< / th >
2019-08-09 14:28:46 +02:00
< td > < p > a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
< tr >
< th > ...< / th >
2019-05-10 16:44:59 +02:00
< td > < p > column name of an antibiotic, see section Antibiotics< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
< / table >
2019-10-07 14:32:06 +02:00
2018-12-23 21:26:21 +01:00
< h2 class = "hasAnchor" id = "source" > < a class = "anchor" href = "#source" > < / a > Source< / h2 >
2019-10-07 14:32:06 +02:00
< ul >
2018-12-23 21:26:21 +01:00
< li > < p > EUCAST Expert Rules. Version 2.0, 2012. < br / >
Leclercq et al. < strong > EUCAST expert rules in antimicrobial susceptibility testing.< / strong > < em > Clin Microbiol Infect.< / em > 2013;19(2):141-60. < br / >
< a href = 'https://doi.org/10.1111/j.1469-0691.2011.03703.x' > https://doi.org/10.1111/j.1469-0691.2011.03703.x< / a > < / p > < / li >
< li > < p > EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. < br / >
< a href = 'http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf' > http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf< / a > < / p > < / li >
2019-01-08 16:23:45 +01:00
< li > < p > EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. < br / >
< a href = 'http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx' > http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx< / a > < / p > < / li >
2018-12-23 21:26:21 +01:00
< / ul >
2019-10-07 14:32:06 +02:00
2018-12-23 21:26:21 +01:00
< h2 class = "hasAnchor" id = "value" > < a class = "anchor" href = "#value" > < / a > Value< / h2 >
2019-05-23 16:58:59 +02:00
< p > The input of < code > x< / code > , possibly with edited values of antibiotics. Or, if < code > verbose = TRUE< / code > , a < code > data.frame< / code > with all original and new values of the affected bug-drug combinations.< / p >
2019-04-05 18:47:39 +02:00
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
2019-05-10 16:44:59 +02:00
< p > < strong > Note:< / strong > This function does not translate MIC values to RSI values. Use < code > < a href = 'as.rsi.html' > as.rsi< / a > < / code > for that. < br / >
< strong > Note:< / strong > When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.< / p >
2019-06-01 20:40:49 +02:00
< p > The file containing all EUCAST rules is located here: < a href = 'https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv' > https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv< / a > .< / p >
2018-12-23 21:26:21 +01:00
< h2 class = "hasAnchor" id = "antibiotics" > < a class = "anchor" href = "#antibiotics" > < / a > Antibiotics< / h2 >
2019-10-07 14:32:06 +02:00
< p > To define antibiotics column names, leave as it is to determine it automatically with < code > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / code > or input a text (case-insensitive), or use < code > NULL< / code > to skip a column (e.g. < code > TIC = NULL< / code > to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.< / p >
< p > The following antibiotics are used for the functions < code > eucast_rules< / code > and < code > < a href = 'mdro.html' > mdro< / a > < / code > . These are shown below in the format '< strong > antimicrobial ID< / strong > : name (< a href = 'https://www.whocc.no/atc/structure_and_principles/' > ATC code< / a > )', sorted by name:< / p >
2019-05-29 19:56:17 +02:00
< p > < strong > AMK< / strong > : amikacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB06' > J01GB06< / a > ),
2019-05-10 16:44:59 +02:00
< strong > AMX< / strong > : amoxicillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA04' > J01CA04< / a > ),
2019-05-29 19:56:17 +02:00
< strong > AMC< / strong > : amoxicillin/clavulanic acid (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CR02' > J01CR02< / a > ),
2019-05-10 16:44:59 +02:00
< strong > AMP< / strong > : ampicillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA01' > J01CA01< / a > ),
2019-10-26 21:56:41 +02:00
< strong > SAM< / strong > : ampicillin/sulbactam (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CR01' > J01CR01< / a > ),
2019-05-10 16:44:59 +02:00
< strong > AZM< / strong > : azithromycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FA10' > J01FA10< / a > ),
< strong > AZL< / strong > : azlocillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA09' > J01CA09< / a > ),
< strong > ATM< / strong > : aztreonam (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DF01' > J01DF01< / a > ),
2019-05-29 19:56:17 +02:00
< strong > CAP< / strong > : capreomycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J04AB30' > J04AB30< / a > ),
2019-05-10 16:44:59 +02:00
< strong > RID< / strong > : cefaloridine (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DB02' > J01DB02< / a > ),
2019-05-29 19:56:17 +02:00
< strong > CZO< / strong > : cefazolin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DB04' > J01DB04< / a > ),
2019-05-10 16:44:59 +02:00
< strong > FEP< / strong > : cefepime (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DE01' > J01DE01< / a > ),
< strong > CTX< / strong > : cefotaxime (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DD01' > J01DD01< / a > ),
2019-10-26 21:56:41 +02:00
< strong > CTT< / strong > : cefotetan (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DC05' > J01DC05< / a > ),
2019-05-10 16:44:59 +02:00
< strong > FOX< / strong > : cefoxitin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DC01' > J01DC01< / a > ),
2019-10-26 21:56:41 +02:00
< strong > CPT< / strong > : ceftaroline (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DI02' > J01DI02< / a > ),
2019-05-10 16:44:59 +02:00
< strong > CAZ< / strong > : ceftazidime (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DD02' > J01DD02< / a > ),
< strong > CRO< / strong > : ceftriaxone (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DD04' > J01DD04< / a > ),
< strong > CXM< / strong > : cefuroxime (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DC02' > J01DC02< / a > ),
2019-10-26 21:56:41 +02:00
< strong > CED< / strong > : cephradine (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DB09' > J01DB09< / a > ),
2019-05-10 16:44:59 +02:00
< strong > CHL< / strong > : chloramphenicol (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01BA01' > J01BA01< / a > ),
< strong > CIP< / strong > : ciprofloxacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MA02' > J01MA02< / a > ),
< strong > CLR< / strong > : clarithromycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FA09' > J01FA09< / a > ),
< strong > CLI< / strong > : clindamycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FF01' > J01FF01< / a > ),
< strong > COL< / strong > : colistin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XB01' > J01XB01< / a > ),
< strong > DAP< / strong > : daptomycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XX09' > J01XX09< / a > ),
2019-10-26 21:56:41 +02:00
< strong > DOR< / strong > : doripenem (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DH04' > J01DH04< / a > ),
2019-05-10 16:44:59 +02:00
< strong > DOX< / strong > : doxycycline (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01AA02' > J01AA02< / a > ),
< strong > ETP< / strong > : ertapenem (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DH03' > J01DH03< / a > ),
< strong > ERY< / strong > : erythromycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FA01' > J01FA01< / a > ),
2019-05-29 19:56:17 +02:00
< strong > ETH< / strong > : ethambutol (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J04AK02' > J04AK02< / a > ),
< strong > FLC< / strong > : flucloxacillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CF05' > J01CF05< / a > ),
2019-05-10 16:44:59 +02:00
< strong > FOS< / strong > : fosfomycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XX01' > J01XX01< / a > ),
< strong > FUS< / strong > : fusidic acid (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XC01' > J01XC01< / a > ),
2019-05-29 19:56:17 +02:00
< strong > GAT< / strong > : gatifloxacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MA16' > J01MA16< / a > ),
2019-05-10 16:44:59 +02:00
< strong > GEN< / strong > : gentamicin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB03' > J01GB03< / a > ),
2019-10-26 21:56:41 +02:00
< strong > GEH< / strong > : gentamicin-high (no ATC code),
2019-05-10 16:44:59 +02:00
< strong > IPM< / strong > : imipenem (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DH51' > J01DH51< / a > ),
2019-05-29 19:56:17 +02:00
< strong > INH< / strong > : isoniazid (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J04AC01' > J04AC01< / a > ),
2019-05-10 16:44:59 +02:00
< strong > KAN< / strong > : kanamycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB04' > J01GB04< / a > ),
< strong > LVX< / strong > : levofloxacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MA12' > J01MA12< / a > ),
< strong > LIN< / strong > : lincomycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FF02' > J01FF02< / a > ),
< strong > LNZ< / strong > : linezolid (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XX08' > J01XX08< / a > ),
< strong > MEM< / strong > : meropenem (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DH02' > J01DH02< / a > ),
2019-05-29 19:56:17 +02:00
< strong > MTR< / strong > : metronidazole (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XD01' > J01XD01< / a > ),
2019-05-10 16:44:59 +02:00
< strong > MEZ< / strong > : mezlocillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA10' > J01CA10< / a > ),
< strong > MNO< / strong > : minocycline (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01AA08' > J01AA08< / a > ),
< strong > MFX< / strong > : moxifloxacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MA14' > J01MA14< / a > ),
< strong > NAL< / strong > : nalidixic acid (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MB02' > J01MB02< / a > ),
< strong > NEO< / strong > : neomycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB05' > J01GB05< / a > ),
< strong > NET< / strong > : netilmicin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB07' > J01GB07< / a > ),
< strong > NIT< / strong > : nitrofurantoin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XE01' > J01XE01< / a > ),
< strong > NOR< / strong > : norfloxacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MA06' > J01MA06< / a > ),
2019-10-26 21:56:41 +02:00
< strong > NOV< / strong > : novobiocin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=QJ01XX95' > QJ01XX95< / a > ),
2019-05-10 16:44:59 +02:00
< strong > OFX< / strong > : ofloxacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MA01' > J01MA01< / a > ),
2019-05-29 19:56:17 +02:00
< strong > OXA< / strong > : oxacillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CF04' > J01CF04< / a > ),
2019-10-27 00:31:59 +02:00
< strong > PEN< / strong > : penicillin G (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CE01' > J01CE01< / a > ),
2019-05-10 16:44:59 +02:00
< strong > PIP< / strong > : piperacillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA12' > J01CA12< / a > ),
< strong > TZP< / strong > : piperacillin/tazobactam (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CR05' > J01CR05< / a > ),
< strong > PLB< / strong > : polymyxin B (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XB02' > J01XB02< / a > ),
< strong > PRI< / strong > : pristinamycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FG01' > J01FG01< / a > ),
2019-05-29 19:56:17 +02:00
< strong > PZA< / strong > : pyrazinamide (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J04AK01' > J04AK01< / a > ),
2019-05-10 16:44:59 +02:00
< strong > QDA< / strong > : quinupristin/dalfopristin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FG02' > J01FG02< / a > ),
2019-05-29 19:56:17 +02:00
< strong > RIB< / strong > : rifabutin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J04AB04' > J04AB04< / a > ),
2019-05-10 16:44:59 +02:00
< strong > RIF< / strong > : rifampicin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J04AB02' > J04AB02< / a > ),
2019-05-29 19:56:17 +02:00
< strong > RFP< / strong > : rifapentine (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J04AB05' > J04AB05< / a > ),
2019-10-27 00:31:59 +02:00
< strong > RXT< / strong > : roxithromycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FA06' > J01FA06< / a > ),
2019-05-10 16:44:59 +02:00
< strong > SIS< / strong > : sisomicin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB08' > J01GB08< / a > ),
2019-10-26 21:56:41 +02:00
< strong > STH< / strong > : streptomycin-high (no ATC code),
2019-05-10 16:44:59 +02:00
< strong > TEC< / strong > : teicoplanin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XA02' > J01XA02< / a > ),
2019-10-26 21:56:41 +02:00
< strong > TLV< / strong > : telavancin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XA03' > J01XA03< / a > ),
2019-05-10 16:44:59 +02:00
< strong > TCY< / strong > : tetracycline (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01AA07' > J01AA07< / a > ),
< strong > TIC< / strong > : ticarcillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA13' > J01CA13< / a > ),
2019-10-26 21:56:41 +02:00
< strong > TCC< / strong > : ticarcillin/clavulanic acid (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CR03' > J01CR03< / a > ),
2019-05-10 16:44:59 +02:00
< strong > TGC< / strong > : tigecycline (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01AA12' > J01AA12< / a > ),
< strong > TOB< / strong > : tobramycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB01' > J01GB01< / a > ),
< strong > TMP< / strong > : trimethoprim (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01EA01' > J01EA01< / a > ),
< strong > SXT< / strong > : trimethoprim/sulfamethoxazole (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01EE01' > J01EE01< / a > ),
< strong > VAN< / strong > : vancomycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XA01' > J01XA01< / a > ).< / p >
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 >
2019-10-07 14:32:06 +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 >
2018-12-23 21:26:21 +01:00
< h2 class = "hasAnchor" id = "examples" > < a class = "anchor" href = "#examples" > < / a > Examples< / h2 >
2019-10-07 14:32:06 +02:00
< pre class = "examples" > < span class = 'no' > a< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/data.frame.html' > data.frame< / a > < / span > (< span class = 'kw' > mo< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/c.html' > c< / a > < / span > (< span class = 'st' > "Staphylococcus aureus"< / span > ,
2018-12-23 21:26:21 +01:00
< span class = 'st' > "Enterococcus faecalis"< / span > ,
< span class = 'st' > "Escherichia coli"< / span > ,
< span class = 'st' > "Klebsiella pneumoniae"< / span > ,
< span class = 'st' > "Pseudomonas aeruginosa"< / span > ),
2019-05-10 16:44:59 +02:00
< span class = 'kw' > VAN< / span > < span class = 'kw' > =< / span > < span class = 'st' > "-"< / span > , < span class = 'co' > # Vancomycin< / span >
< span class = 'kw' > AMX< / span > < span class = 'kw' > =< / span > < span class = 'st' > "-"< / span > , < span class = 'co' > # Amoxicillin< / span >
< span class = 'kw' > COL< / span > < span class = 'kw' > =< / span > < span class = 'st' > "-"< / span > , < span class = 'co' > # Colistin< / span >
< span class = 'kw' > CAZ< / span > < span class = 'kw' > =< / span > < span class = 'st' > "-"< / span > , < span class = 'co' > # Ceftazidime< / span >
< span class = 'kw' > CXM< / span > < span class = 'kw' > =< / span > < span class = 'st' > "-"< / span > , < span class = 'co' > # Cefuroxime< / span >
< span class = 'kw' > PEN< / span > < span class = 'kw' > =< / span > < span class = 'st' > "S"< / span > , < span class = 'co' > # Penicillin G< / span >
< span class = 'kw' > FOX< / span > < span class = 'kw' > =< / span > < span class = 'st' > "S"< / span > , < span class = 'co' > # Cefoxitin< / span >
2018-12-23 21:26:21 +01:00
< span class = 'kw' > stringsAsFactors< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > )
2019-01-02 23:24:07 +01:00
< span class = 'no' > a< / span >
2019-05-10 16:44:59 +02:00
< span class = 'co' > # mo VAN AMX COL CAZ CXM PEN FOX< / span >
2018-12-23 21:26:21 +01:00
< span class = 'co' > # 1 Staphylococcus aureus - - - - - S S< / span >
< span class = 'co' > # 2 Enterococcus faecalis - - - - - S S< / span >
< span class = 'co' > # 3 Escherichia coli - - - - - S S< / span >
< span class = 'co' > # 4 Klebsiella pneumoniae - - - - - S S< / span >
< span class = 'co' > # 5 Pseudomonas aeruginosa - - - - - S S< / span >
2019-02-08 16:06:54 +01:00
< span class = 'co' > # apply EUCAST rules: 18 results are forced as R or S< / span >
< span class = 'no' > b< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > eucast_rules< / span > (< span class = 'no' > a< / span > )
2019-01-02 23:24:07 +01:00
< span class = 'no' > b< / span >
2019-05-10 16:44:59 +02:00
< span class = 'co' > # mo VAN AMX COL CAZ CXM PEN FOX< / span >
2019-01-02 23:24:07 +01:00
< span class = 'co' > # 1 Staphylococcus aureus - S R R S S S< / span >
< span class = 'co' > # 2 Enterococcus faecalis - - R R R S R< / span >
< span class = 'co' > # 3 Escherichia coli R - - - - R S< / span >
< span class = 'co' > # 4 Klebsiella pneumoniae R R - - - R S< / span >
< span class = 'co' > # 5 Pseudomonas aeruginosa R R - - R R R< / span >
2019-02-08 16:06:54 +01:00
2019-10-07 14:32:06 +02:00
< span class = 'co' > # \donttest{< / span >
2019-07-30 13:12:40 +02:00
< span class = 'co' > # do not apply EUCAST rules, but rather get a data.frame< / span >
2019-02-08 16:06:54 +01:00
< span class = 'co' > # with 18 rows, containing all details about the transformations:< / span >
< span class = 'no' > c< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > eucast_rules< / span > (< span class = 'no' > a< / span > , < span class = 'kw' > verbose< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > )
2019-01-02 23:24:07 +01:00
< 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 = "#source" > Source< / a > < / li >
< li > < a href = "#value" > Value< / a > < / li >
2019-04-05 18:47:39 +02:00
< li > < a href = "#details" > Details< / a > < / li >
2018-12-23 21:26:21 +01:00
< li > < a href = "#antibiotics" > 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 = "#examples" > Examples< / a > < / li >
< / ul >
< / div >
< / div >
2019-10-07 14:32:06 +02:00
2018-12-23 21:26:21 +01:00
< footer >
< div class = "copyright" >
2019-08-27 22:41:09 +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 >
2018-12-23 21:26:21 +01:00
< / div >
< div class = "pkgdown" >
2019-10-07 14:32:06 +02:00
< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.4.1.< / p >
2018-12-23 21:26:21 +01:00
< / div >
2019-10-07 14:32:06 +02:00
2018-12-23 21:26:21 +01:00
< / 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
2019-10-07 14:32:06 +02:00
2018-12-23 21:26:21 +01:00
< / body >
< / html >
2019-10-07 14:32:06 +02:00
