AMR/docs/reference/index.html

649 lines
27 KiB
HTML
Raw Blame History

This file contains ambiguous Unicode characters

This file contains Unicode characters that might be confused with other characters. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.

<!-- 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/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></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.svg" />
<!-- 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 data-spy="scroll" data-target="#toc">
<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="Latest development version">1.1.0.9005</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/PCA.html">
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</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/ab_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</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>
</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-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>
</tbody><tbody>
<tr>
<td>
<p><code><a href="as.ab.html">as.ab()</a></code> <code><a href="as.ab.html">is.ab()</a></code> </p>
</td>
<td><p>Transform to antibiotic ID</p></td>
</tr><tr>
<td>
<p><code><a href="as.disk.html">as.disk()</a></code> <code><a href="as.disk.html">is.disk()</a></code> </p>
</td>
<td><p>Class 'disk'</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> </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="eucast_rules.html">eucast_rules()</a></code> </p>
</td>
<td><p>Apply 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="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>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-enhancing-your-data" class="hasAnchor"><a href="#section-enhancing-your-data" class="anchor"></a>Enhancing your data</h2>
<p class="section-desc"><p>Functions to add new data to your existing data, such as 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>
</tbody><tbody>
<tr>
<td>
<p><code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_cid()</a></code> <code><a href="ab_property.html">ab_synonyms()</a></code> <code><a href="ab_property.html">ab_tradenames()</a></code> <code><a href="ab_property.html">ab_group()</a></code> <code><a href="ab_property.html">ab_atc_group1()</a></code> <code><a href="ab_property.html">ab_atc_group2()</a></code> <code><a href="ab_property.html">ab_loinc()</a></code> <code><a href="ab_property.html">ab_ddd()</a></code> <code><a href="ab_property.html">ab_info()</a></code> <code><a href="ab_property.html">ab_property()</a></code> </p>
</td>
<td><p>Property of an antibiotic</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="age.html">age()</a></code> </p>
</td>
<td><p>Age in years of individuals</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="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="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 microorganisms to a data set</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="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">mdr_tb()</a></code> <code><a href="mdro.html">mdr_cmi2012()</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="mo_property.html">mo_name()</a></code> <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_snomed()</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_synonyms()</a></code> <code><a href="mo_property.html">mo_info()</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="p_symbol.html">p_symbol()</a></code> </p>
</td>
<td><p>Symbol of a p-value</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, or make plots.</p></p>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="proportion.html">resistance()</a></code> <code><a href="proportion.html">susceptibility()</a></code> <code><a href="proportion.html">proportion_R()</a></code> <code><a href="proportion.html">proportion_IR()</a></code> <code><a href="proportion.html">proportion_I()</a></code> <code><a href="proportion.html">proportion_SI()</a></code> <code><a href="proportion.html">proportion_S()</a></code> <code><a href="proportion.html">proportion_df()</a></code> <code><a href="proportion.html">rsi_df()</a></code> </p>
</td>
<td><p>Calculate microbial resistance</p></td>
</tr><tr>
<td>
<p><code><a href="count.html">count_resistant()</a></code> <code><a href="count.html">count_susceptible()</a></code> <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 available isolates</p></td>
</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="bug_drug_combinations.html">bug_drug_combinations()</a></code> <code><a href="bug_drug_combinations.html">format(<i>&lt;bug_drug_combinations&gt;</i>)</a></code> </p>
</td>
<td><p>Determine bug-drug combinations</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>&lt;resistance_predict&gt;</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="pca.html">pca()</a></code> </p>
</td>
<td><p>Principal Component Analysis (for AMR)</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_5th_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 antimicrobial class</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="ggplot_pca.html">ggplot_pca()</a></code> </p>
</td>
<td><p>PCA biplot 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="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>Scientifically reliable references for microorganisms and antibiotics, and example data sets to use for practise.</p></p>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
</td>
<td><p>Data set with 69,447 microorganisms</p></td>
</tr><tr>
<td>
<p><code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code> </p>
</td>
<td><p>Data sets with 557 antimicrobials</p></td>
</tr><tr>
<td>
<p><code><a href="example_isolates.html">example_isolates</a></code> </p>
</td>
<td><p>Data set with 2,000 example isolates</p></td>
</tr><tr>
<td>
<p><code><a href="example_isolates_unclean.html">example_isolates_unclean</a></code> </p>
</td>
<td><p>Data set with unclean data</p></td>
</tr><tr>
<td>
<p><code><a href="rsi_translation.html">rsi_translation</a></code> </p>
</td>
<td><p>Data set for R/SI interpretation</p></td>
</tr><tr>
<td>
<p><code><a href="microorganisms.codes.html">microorganisms.codes</a></code> </p>
</td>
<td><p>Translation table for common 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><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>
</tbody><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 Tos</a> for more information about how to work with functions in this package.</p></p>
</th>
</tr>
</tbody><tbody>
<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><tr>
<td>
<p><code><a href="lifecycle.html">lifecycle</a></code> </p>
</td>
<td><p>Lifecycles of functions in the <code>AMR</code> package</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>
</tbody><tbody>
<tr>
<td>
<p><code><a href="translate.html">get_locale()</a></code> </p>
</td>
<td><p>Translate strings from AMR package</p></td>
</tr><tr>
<td>
<p><code><a href="like.html">like()</a></code> <code><a href="like.html">`%like%`</a></code> <code><a href="like.html">`%like_case%`</a></code> </p>
</td>
<td><p>Pattern Matching</p></td>
</tr><tr>
<td>
<p><code><a href="reexports.html">reexports</a></code> </p>
</td>
<td><p>Objects exported from other packages</p></td>
</tr><tr>
<td>
<p><code><a href="AMR-tidyverse.html">scale_type.mo()</a></code> <code><a href="AMR-tidyverse.html">scale_type.ab()</a></code> <code><a href="AMR-tidyverse.html">vec_ptype2.mo()</a></code> <code><a href="AMR-tidyverse.html">vec_cast.mo()</a></code> <code><a href="AMR-tidyverse.html">vec_ptype2.ab()</a></code> <code><a href="AMR-tidyverse.html">vec_cast.ab()</a></code> </p>
</td>
<td><p>Methods for tidyverse</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 will still work but show a warning with every use and will be removed in a future version.</p></p>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="AMR-deprecated.html">portion_R()</a></code> <code><a href="AMR-deprecated.html">portion_IR()</a></code> <code><a href="AMR-deprecated.html">portion_I()</a></code> <code><a href="AMR-deprecated.html">portion_SI()</a></code> <code><a href="AMR-deprecated.html">portion_S()</a></code> <code><a href="AMR-deprecated.html">portion_df()</a></code> </p>
</td>
<td><p>Deprecated functions</p></td>
</tr>
</tbody>
</table>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</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/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div>
</footer>
</div>
</body>
</html>