mirror of
https://github.com/msberends/AMR.git
synced 2024-12-27 07:26:11 +01:00
607 lines
26 KiB
HTML
607 lines
26 KiB
HTML
<!-- 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>Function reference • 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" />
|
||
<!-- 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" />
|
||
|
||
<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>
|
||
|
||
|
||
<!-- 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>
|
||
<meta property="og:title" content="Function reference" />
|
||
|
||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||
<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-index">
|
||
<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>
|
||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.0</span>
|
||
</span>
|
||
</div>
|
||
|
||
<div id="navbar" class="navbar-collapse collapse">
|
||
<ul class="nav navbar-nav">
|
||
<li>
|
||
<a href="../index.html">
|
||
<span class="fa fa-home"></span>
|
||
|
||
Home
|
||
</a>
|
||
</li>
|
||
<li class="dropdown">
|
||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||
<span class="fa fa-question-circle"></span>
|
||
|
||
How to
|
||
|
||
<span class="caret"></span>
|
||
</a>
|
||
<ul class="dropdown-menu" role="menu">
|
||
<li>
|
||
<a href="../articles/AMR.html">
|
||
<span class="fa fa-directions"></span>
|
||
|
||
Conduct AMR analysis
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../articles/resistance_predict.html">
|
||
<span class="fa fa-dice"></span>
|
||
|
||
Predict antimicrobial resistance
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../articles/WHONET.html">
|
||
<span class="fa fa-globe-americas"></span>
|
||
|
||
Work with WHONET data
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../articles/SPSS.html">
|
||
<span class="fa fa-file-upload"></span>
|
||
|
||
Import data from SPSS/SAS/Stata
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../articles/EUCAST.html">
|
||
<span class="fa fa-exchange-alt"></span>
|
||
|
||
Apply EUCAST rules
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../reference/mo_property.html">
|
||
<span class="fa fa-bug"></span>
|
||
|
||
Get properties of a microorganism
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../reference/atc_property.html">
|
||
<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>
|
||
<li>
|
||
<a href="../articles/benchmarks.html">
|
||
<span class="fa fa-shipping-fast"></span>
|
||
|
||
Other: benchmarks
|
||
</a>
|
||
</li>
|
||
</ul>
|
||
</li>
|
||
<li>
|
||
<a href="../reference/">
|
||
<span class="fa fa-book-open"></span>
|
||
|
||
Manual
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../authors.html">
|
||
<span class="fa fa-users"></span>
|
||
|
||
Authors
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../news/">
|
||
<span class="far fa far fa-newspaper"></span>
|
||
|
||
Changelog
|
||
</a>
|
||
</li>
|
||
</ul>
|
||
|
||
<ul class="nav navbar-nav navbar-right">
|
||
<li>
|
||
<a href="https://gitlab.com/msberends/AMR">
|
||
<span class="fab fa fab fa-gitlab"></span>
|
||
|
||
Source Code
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../LICENSE-text.html">
|
||
<span class="fa fa-book"></span>
|
||
|
||
Licence
|
||
</a>
|
||
</li>
|
||
</ul>
|
||
|
||
<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>
|
||
|
||
</div><!--/.nav-collapse -->
|
||
</div><!--/.container -->
|
||
</div><!--/.navbar -->
|
||
|
||
|
||
</header>
|
||
|
||
<div class="row">
|
||
<div class="contents col-md-9">
|
||
<div class="page-header">
|
||
<h1>Reference</h1>
|
||
</div>
|
||
|
||
<table class="ref-index">
|
||
|
||
<colgroup>
|
||
|
||
<col class="alias" />
|
||
<col class="title" />
|
||
</colgroup>
|
||
|
||
<tbody>
|
||
<tr>
|
||
<th colspan="2">
|
||
<h2 id="section-background-information" class="hasAnchor"><a href="#section-background-information" class="anchor"></a>Background information</h2>
|
||
<p class="section-desc"><p>Some pages about our package and its external sources. Be sure to read our <a href="./../articles/index.html">How To’s</a> for more information about how to work with functions in this package.</p></p>
|
||
</th>
|
||
</tr>
|
||
<tr>
|
||
|
||
<td>
|
||
<p><code><a href="AMR.html">AMR</a></code> </p>
|
||
</td>
|
||
<td><p>The <code>AMR</code> Package</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="catalogue_of_life.html">catalogue_of_life</a></code> </p>
|
||
</td>
|
||
<td><p>The Catalogue of Life</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code> </p>
|
||
</td>
|
||
<td><p>Version info of included Catalogue of Life</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="WHOCC.html">WHOCC</a></code> </p>
|
||
</td>
|
||
<td><p>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</p></td>
|
||
</tr>
|
||
</tbody><tbody>
|
||
<tr>
|
||
<th colspan="2">
|
||
<h2 id="section-cleaning-your-data" class="hasAnchor"><a href="#section-cleaning-your-data" class="anchor"></a>Cleaning your data</h2>
|
||
<p class="section-desc"><p>Functions for cleaning and optimising your data, to be able to add variables later on (like taxonomic properties) or to fix and extend antibiotic interpretations by applying <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST rules</a>.</p></p>
|
||
</th>
|
||
</tr>
|
||
<tr>
|
||
|
||
<td>
|
||
<p><code><a href="as.atc.html">as.atc()</a></code> <code><a href="as.atc.html">is.atc()</a></code> </p>
|
||
</td>
|
||
<td><p>Transform to ATC code</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="as.mic.html">as.mic()</a></code> <code><a href="as.mic.html">is.mic()</a></code> </p>
|
||
</td>
|
||
<td><p>Class 'mic'</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> <code><a href="as.mo.html">clean_mo_history()</a></code> </p>
|
||
</td>
|
||
<td><p>Transform to microorganism ID</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="as.rsi.html">as.rsi()</a></code> <code><a href="as.rsi.html">is.rsi()</a></code> <code><a href="as.rsi.html">is.rsi.eligible()</a></code> </p>
|
||
</td>
|
||
<td><p>Class 'rsi'</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="mo_source.html">set_mo_source()</a></code> <code><a href="mo_source.html">get_mo_source()</a></code> </p>
|
||
</td>
|
||
<td><p>Use predefined reference data set</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="eucast_rules.html">eucast_rules()</a></code> <code><a href="eucast_rules.html">EUCAST_rules()</a></code> <code><a href="eucast_rules.html">interpretive_reading()</a></code> </p>
|
||
</td>
|
||
<td><p>EUCAST rules</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="guess_ab_col.html">guess_ab_col()</a></code> </p>
|
||
</td>
|
||
<td><p>Guess antibiotic column</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="read.4D.html">read.4D()</a></code> </p>
|
||
</td>
|
||
<td><p>Read data from 4D database</p></td>
|
||
</tr>
|
||
</tbody><tbody>
|
||
<tr>
|
||
<th colspan="2">
|
||
<h2 id="section-adding-variables-to-your-data" class="hasAnchor"><a href="#section-adding-variables-to-your-data" class="anchor"></a>Adding variables to your data</h2>
|
||
<p class="section-desc"><p>Functions to add new data to existing data, like the determination of first isolates, multi-drug resistant microorganisms (MDRO), getting properties of microorganisms or antibiotics and determining the age of patients or divide ages into age groups.</p></p>
|
||
</th>
|
||
</tr>
|
||
<tr>
|
||
|
||
<td>
|
||
<p><code><a href="first_isolate.html">first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_weighted_isolate()</a></code> </p>
|
||
</td>
|
||
<td><p>Determine first (weighted) isolates</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="mdro.html">mdro()</a></code> <code><a href="mdro.html">brmo()</a></code> <code><a href="mdro.html">mrgn()</a></code> <code><a href="mdro.html">eucast_exceptional_phenotypes()</a></code> </p>
|
||
</td>
|
||
<td><p>Determine multidrug-resistant organisms (MDRO)</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="key_antibiotics.html">key_antibiotics()</a></code> <code><a href="key_antibiotics.html">key_antibiotics_equal()</a></code> </p>
|
||
</td>
|
||
<td><p>Key antibiotics for first <em>weighted</em> isolates</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
|
||
</td>
|
||
<td><p>Property of a microorganism</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="atc_property.html">atc_property()</a></code> <code><a href="atc_property.html">atc_official()</a></code> <code><a href="atc_property.html">atc_name()</a></code> <code><a href="atc_property.html">atc_trivial_nl()</a></code> <code><a href="atc_property.html">atc_certe()</a></code> <code><a href="atc_property.html">atc_umcg()</a></code> <code><a href="atc_property.html">atc_tradenames()</a></code> </p>
|
||
</td>
|
||
<td><p>Property of an antibiotic</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="atc_online.html">atc_online_property()</a></code> <code><a href="atc_online.html">atc_online_groups()</a></code> <code><a href="atc_online.html">atc_online_ddd()</a></code> </p>
|
||
</td>
|
||
<td><p>Get ATC properties from WHOCC website</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="abname.html">abname()</a></code> </p>
|
||
</td>
|
||
<td><p>Name of an antibiotic</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="age.html">age()</a></code> </p>
|
||
</td>
|
||
<td><p>Age in years of individuals</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="age_groups.html">age_groups()</a></code> </p>
|
||
</td>
|
||
<td><p>Split ages into age groups</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="p.symbol.html">p.symbol()</a></code> </p>
|
||
</td>
|
||
<td><p>Symbol of a p value</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="join.html">inner_join_microorganisms()</a></code> <code><a href="join.html">left_join_microorganisms()</a></code> <code><a href="join.html">right_join_microorganisms()</a></code> <code><a href="join.html">full_join_microorganisms()</a></code> <code><a href="join.html">semi_join_microorganisms()</a></code> <code><a href="join.html">anti_join_microorganisms()</a></code> </p>
|
||
</td>
|
||
<td><p>Join a table with <code>microorganisms</code></p></td>
|
||
</tr>
|
||
</tbody><tbody>
|
||
<tr>
|
||
<th colspan="2">
|
||
<h2 id="section-analysing-your-data" class="hasAnchor"><a href="#section-analysing-your-data" class="anchor"></a>Analysing your data</h2>
|
||
<p class="section-desc"><p>Functions for conducting AMR analysis, like counting isolates, calculating resistance or susceptibility, creating frequency tables or make plots.</p></p>
|
||
</th>
|
||
</tr>
|
||
<tr>
|
||
|
||
<td>
|
||
<p><code><a href="availability.html">availability()</a></code> </p>
|
||
</td>
|
||
<td><p>Check availability of columns</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="count.html">count_R()</a></code> <code><a href="count.html">count_IR()</a></code> <code><a href="count.html">count_I()</a></code> <code><a href="count.html">count_SI()</a></code> <code><a href="count.html">count_S()</a></code> <code><a href="count.html">count_all()</a></code> <code><a href="count.html">n_rsi()</a></code> <code><a href="count.html">count_df()</a></code> </p>
|
||
</td>
|
||
<td><p>Count isolates</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="portion.html">portion_R()</a></code> <code><a href="portion.html">portion_IR()</a></code> <code><a href="portion.html">portion_I()</a></code> <code><a href="portion.html">portion_SI()</a></code> <code><a href="portion.html">portion_S()</a></code> <code><a href="portion.html">portion_df()</a></code> </p>
|
||
</td>
|
||
<td><p>Calculate resistance of isolates</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="filter_ab_class.html">filter_ab_class()</a></code> <code><a href="filter_ab_class.html">filter_aminoglycosides()</a></code> <code><a href="filter_ab_class.html">filter_carbapenems()</a></code> <code><a href="filter_ab_class.html">filter_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_1st_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_2nd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_3rd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_4th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_fluoroquinolones()</a></code> <code><a href="filter_ab_class.html">filter_glycopeptides()</a></code> <code><a href="filter_ab_class.html">filter_macrolides()</a></code> <code><a href="filter_ab_class.html">filter_tetracyclines()</a></code> </p>
|
||
</td>
|
||
<td><p>Filter isolates on result in antibiotic class</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="freq.html">frequency_tbl()</a></code> <code><a href="freq.html">freq()</a></code> <code><a href="freq.html">top_freq()</a></code> <code><a href="freq.html">header()</a></code> <code><a href="freq.html">print(<i><frequency_tbl></i>)</a></code> </p>
|
||
</td>
|
||
<td><p>Frequency table</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="g.test.html">g.test()</a></code> </p>
|
||
</td>
|
||
<td><p><em>G</em>-test for Count Data</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="ggplot_rsi.html">ggplot_rsi()</a></code> <code><a href="ggplot_rsi.html">geom_rsi()</a></code> <code><a href="ggplot_rsi.html">facet_rsi()</a></code> <code><a href="ggplot_rsi.html">scale_y_percent()</a></code> <code><a href="ggplot_rsi.html">scale_rsi_colours()</a></code> <code><a href="ggplot_rsi.html">theme_rsi()</a></code> <code><a href="ggplot_rsi.html">labels_rsi_count()</a></code> </p>
|
||
</td>
|
||
<td><p>AMR plots with <code>ggplot2</code></p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="kurtosis.html">kurtosis()</a></code> </p>
|
||
</td>
|
||
<td><p>Kurtosis of the sample</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="resistance_predict.html">resistance_predict()</a></code> <code><a href="resistance_predict.html">rsi_predict()</a></code> <code><a href="resistance_predict.html">plot(<i><resistance_predict></i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_predict()</a></code> </p>
|
||
</td>
|
||
<td><p>Predict antimicrobial resistance</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="rsi.html">rsi()</a></code> </p>
|
||
</td>
|
||
<td><p>Calculate resistance of isolates</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="skewness.html">skewness()</a></code> </p>
|
||
</td>
|
||
<td><p>Skewness of the sample</p></td>
|
||
</tr>
|
||
</tbody><tbody>
|
||
<tr>
|
||
<th colspan="2">
|
||
<h2 id="section-included-data-sets" class="hasAnchor"><a href="#section-included-data-sets" class="anchor"></a>Included data sets</h2>
|
||
<p class="section-desc"><p>References for microorganisms and antibiotics, and even a genuine data set with isolates from septic patients.</p></p>
|
||
</th>
|
||
</tr>
|
||
<tr>
|
||
|
||
<td>
|
||
<p><code><a href="antibiotics.html">antibiotics</a></code> </p>
|
||
</td>
|
||
<td><p>Data set with ~500 antibiotics</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
|
||
</td>
|
||
<td><p>Data set with ~65,000 microorganisms</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="septic_patients.html">septic_patients</a></code> </p>
|
||
</td>
|
||
<td><p>Data set with 2,000 blood culture isolates from septic patients</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="WHONET.html">WHONET</a></code> </p>
|
||
</td>
|
||
<td><p>Data set with 500 isolates - WHONET example</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="microorganisms.codes.html">microorganisms.codes</a></code> </p>
|
||
</td>
|
||
<td><p>Translation table for microorganism codes</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="microorganisms.old.html">microorganisms.old</a></code> </p>
|
||
</td>
|
||
<td><p>Data set with previously accepted taxonomic names</p></td>
|
||
</tr>
|
||
</tbody><tbody>
|
||
<tr>
|
||
<th colspan="2">
|
||
<h2 id="section-other-functions" class="hasAnchor"><a href="#section-other-functions" class="anchor"></a>Other functions</h2>
|
||
<p class="section-desc"><p>These functions are mostly for internal use, but some of them may also be suitable for your analysis. Especially the ‘like’ function can be useful: <code>if (x %like% y) {...}</code>.</p></p>
|
||
</th>
|
||
</tr>
|
||
<tr>
|
||
|
||
<td>
|
||
<p><code><a href="get_locale.html">get_locale()</a></code> </p>
|
||
</td>
|
||
<td><p>Get language for AMR</p></td>
|
||
</tr><tr>
|
||
|
||
<td>
|
||
<p><code><a href="like.html">like()</a></code> <code><a href="like.html">`%like%`</a></code> </p>
|
||
</td>
|
||
<td><p>Pattern Matching</p></td>
|
||
</tr>
|
||
</tbody><tbody>
|
||
<tr>
|
||
<th colspan="2">
|
||
<h2 id="section-deprecated-functions" class="hasAnchor"><a href="#section-deprecated-functions" class="anchor"></a>Deprecated functions</h2>
|
||
<p class="section-desc"><p>These functions are deprecated, meaning that they still work but show a warning with every use and will be removed in a future version.</p></p>
|
||
</th>
|
||
</tr>
|
||
<tr>
|
||
|
||
<td>
|
||
<p><code><a href="AMR-deprecated.html">ratio()</a></code> <code><a href="AMR-deprecated.html">guess_mo()</a></code> <code><a href="AMR-deprecated.html">guess_atc()</a></code> <code><a href="AMR-deprecated.html">ab_property()</a></code> <code><a href="AMR-deprecated.html">ab_atc()</a></code> <code><a href="AMR-deprecated.html">ab_official()</a></code> <code><a href="AMR-deprecated.html">ab_name()</a></code> <code><a href="AMR-deprecated.html">ab_trivial_nl()</a></code> <code><a href="AMR-deprecated.html">ab_certe()</a></code> <code><a href="AMR-deprecated.html">ab_umcg()</a></code> <code><a href="AMR-deprecated.html">ab_tradenames()</a></code> <code><a href="AMR-deprecated.html">atc_ddd()</a></code> <code><a href="AMR-deprecated.html">atc_groups()</a></code> </p>
|
||
</td>
|
||
<td><p>Deprecated functions</p></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</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="#section-background-information">Background information</a></li>
|
||
<li><a href="#section-cleaning-your-data">Cleaning your data</a></li>
|
||
<li><a href="#section-adding-variables-to-your-data">Adding variables to your data</a></li>
|
||
<li><a href="#section-analysing-your-data">Analysing your data</a></li>
|
||
<li><a href="#section-included-data-sets">Included data sets</a></li>
|
||
<li><a href="#section-other-functions">Other functions</a></li>
|
||
<li><a href="#section-deprecated-functions">Deprecated functions</a></li>
|
||
</ul>
|
||
</div>
|
||
</div>
|
||
|
||
<footer>
|
||
<div class="copyright">
|
||
<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>
|
||
</div>
|
||
|
||
<div class="pkgdown">
|
||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
|
||
</div>
|
||
</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>
|
||
|
||
|
||
</body>
|
||
</html>
|
||
|