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<img src="../logo.svg" class="logo" alt=""><h1>Italicise Taxonomic Families, Genera, Species, Subspecies</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/italicise_taxonomy.R" class="external-link"><code>R/italicise_taxonomy.R</code></a></small>
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<div class="d-none name"><code>italicise_taxonomy.Rd</code></div>
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<div class="ref-description section level2">
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<p>According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italics. This function finds taxonomic names within strings and makes them italic.</p>
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</div>
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<div class="section level2">
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><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" class="external-link">c</a></span><span class="op">(</span><span class="st">"markdown"</span>, <span class="st">"ansi"</span>, <span class="st">"html"</span><span class="op">)</span><span class="op">)</span></span>
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<span></span>
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<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" class="external-link">c</a></span><span class="op">(</span><span class="st">"markdown"</span>, <span class="st">"ansi"</span>, <span class="st">"html"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
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</div>
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<div class="section level2">
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<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
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<dl><dt>string</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vector)</p></dd>
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<dt>type</dt>
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<dd><p>type of conversion of the taxonomic names, either "markdown", "html" or "ansi", see <em>Details</em></p></dd>
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</dl></div>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<p>This function finds the taxonomic names and makes them italic based on the <a href="microorganisms.html">microorganisms</a> data set.</p>
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<p>The taxonomic names can be italicised using markdown (the default) by adding <code>*</code> before and after the taxonomic names, or <code><i></code> and <code></i></code> when using html. When using 'ansi', ANSI colours will be added using <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>
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<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>
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</div>
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><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></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "An overview of *Staphylococcus aureus* isolates"</span>
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<span class="r-in"><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></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "An overview of *S. aureus* isolates"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/cat.html" class="external-link">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></span></span>
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<span class="r-out co"><span class="r-pr">#></span> An overview of <span style="font-style: italic;">S. aureus</span> isolates</span>
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</code></pre></div>
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<p></p><p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
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