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(v1.0.1.9005) as.mo() improvements

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dr. M.S. (Matthijs) Berends
2020-04-13 21:09:56 +02:00
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<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" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
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</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-index">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
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</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9005</span>
</span>
</div>
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<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>
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<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>
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<p class="section-desc"><p>Functions for conducting AMR analysis, like counting isolates, calculating resistance or susceptibility, or make plots.</p></p>
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<p class="section-desc"><p>Scientifically reliable references for microorganisms and antibiotics, and example data sets to use for practise.</p></p>
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<tr>
<td>
<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
</td>
<td><p>Data set with ~70,000 microorganisms</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 ~550 antimicrobials</p></td>
<td><p>Data sets with 554 antimicrobials</p></td>
</tr><tr>
<td>
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<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>
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<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>
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<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>
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</tbody><tbody>
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<td>
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</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-cleaning-your-data">Cleaning your data</a></li>
<li><a href="#section-enhancing-your-data">Enhancing 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-background-information">Background information</a></li>
<li><a href="#section-other-functions">Other functions</a></li>
<li><a href="#section-deprecated-functions">Deprecated functions</a></li>
</ul>
<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>
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