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2024-11-21 09:17:08 +00:00
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<link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/Lato-0.4.9/font.css" rel="stylesheet">
<link href="deps/Fira_Code-0.4.9/font.css" rel="stylesheet">
<link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
<link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
<link href="deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet">
<link href="deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet">
<script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet">
<script src="extra.js"></script><meta property="og:title" content="Antimicrobial Resistance Data Analysis">
<meta name="description" content="Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in &lt;doi:10.18637/jss.v104.i03&gt;.">
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<span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"bacteria"</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span></code></pre></div>
<p>This base R code will work in any version of R since April 2013 (R-3.0). Moreover, this code works identically with the <code>data.table</code> package, only by starting with:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">example_isolates</span> <span class="op">&lt;-</span> <span class="fu">data.table</span><span class="fu">::</span><span class="fu"><a href="https://rdatatable.gitlab.io/data.table/reference/as.data.table.html" class="external-link">as.data.table</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></code></pre></div>
<code class="sourceCode R"><span><span class="va">example_isolates</span> <span class="op">&lt;-</span> <span class="fu">data.table</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/data.table/man/as.data.table.html" class="external-link">as.data.table</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level4">
<h4 id="generating-antibiograms">Generating antibiograms<a class="anchor" aria-label="anchor" href="#generating-antibiograms"></a>
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<p>Manually, using:</p>
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span></span>
<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></span></code></pre></div>
<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu">install_github</span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></span></code></pre></div>
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<p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our R-universe address</a> to your list of repositories (‘repos’):</p>