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Built site for AMR@2.1.1.9253: 4e7fca3

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2025-04-26 13:56:15 +00:00
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reference/top_n_microorganisms.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9252</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9253</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -55,7 +55,7 @@
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">top_n_microorganisms</span><span class="op">(</span><span class="va">x</span>, <span class="va">n</span>, property <span class="op">=</span> <span class="st">"fullname"</span>, n_for_each <span class="op">=</span> <span class="cn">NULL</span>,</span>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">top_n_microorganisms</span><span class="op">(</span><span class="va">x</span>, <span class="va">n</span>, property <span class="op">=</span> <span class="st">"species"</span>, n_for_each <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> col_mo <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
</div>
@ -72,7 +72,7 @@
<dt id="arg-property">property<a class="anchor" aria-label="anchor" href="#arg-property"></a></dt>
<dd><p>A character string indicating the microorganism property to use for filtering. Must be one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "mycobank", "mycobank_parent", "mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed". If <code>NULL</code>, the raw values from <code>col_mo</code> will be used without transformation.</p></dd>
<dd><p>A character string indicating the microorganism property to use for filtering. Must be one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "mycobank", "mycobank_parent", "mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed". If <code>NULL</code>, the raw values from <code>col_mo</code> will be used without transformation. When using <code>"species"</code> (default) or <code>"subpecies"</code>, the genus will be added to make sure each (sub)species still belongs to the right genus.</p></dd>
<dt id="arg-n-for-each">n_for_each<a class="anchor" aria-label="anchor" href="#arg-n-for-each"></a></dt>