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<meta property="og:description" content="According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italic. This function finds taxonomic names within strings and makes them italic." />
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<h1>Italicise Taxonomic Families, Genera, Species, Subspecies</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/italicise_taxonomy.R'><code>R/italicise_taxonomy.R</code></a></small>
<div class="hidden name"><code>italicise_taxonomy.Rd</code></div>
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<p>According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italic. This function finds taxonomic names within strings and makes them italic.</p>
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<pre class="usage"><span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='va'>string</span>, type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"markdown"</span>, <span class='st'>"ansi"</span><span class='op'>)</span><span class='op'>)</span>
<span class='fu'>italicize_taxonomy</span><span class='op'>(</span><span class='va'>string</span>, type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"markdown"</span>, <span class='st'>"ansi"</span><span class='op'>)</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>string</th>
<td><p>a character (vector)</p></td>
</tr>
<tr>
<th>type</th>
<td><p>type of conversion of the taxonomic names, either "markdown" or "ansi", see <em>Details</em></p></td>
</tr>
</table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>This function finds the taxonomic names and makes them italic based on the <a href='microorganisms.html'>microorganisms</a> data set.</p>
<p>The taxonomic names can be italicised using markdown (the default) by adding <code><a href='https://rdrr.io/r/base/Arithmetic.html'>*</a></code> before and after the taxonomic names, or using ANSI colours by adding <code>\033[3m</code> before and <code>\033[23m</code> after the taxonomic names. If multiple ANSI colours are not available, no conversion will occur.</p>
<p>This function also supports abbreviation of the genus if it is followed by a species, such as "E. coli" and "K. pneumoniae ozaenae".</p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing Lifecycle</h2>
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"An overview of Staphylococcus aureus isolates"</span><span class='op'>)</span>
<span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"An overview of S. aureus isolates"</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/cat.html'>cat</a></span><span class='op'>(</span><span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"An overview of S. aureus isolates"</span>, type <span class='op'>=</span> <span class='st'>"ansi"</span><span class='op'>)</span><span class='op'>)</span>
</pre>
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