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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>
<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>
<div class="hidden name"><code>italicise_taxonomy.Rd</code></div>
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@ -238,82 +161,77 @@
<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>
</div>
<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>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><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="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>
<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="op">)</span><span class="op">)</span></code></pre></div></div>
<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 <a href='https://rdrr.io/r/base/character.html'>character</a> (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>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>string</dt>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vector)</p></dd>
<dt>type</dt>
<dd><p>type of conversion of the taxonomic names, either "markdown" or "ansi", see <em>Details</em></p></dd>
</dl></div>
<div id="details">
<h2>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>*</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="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
</div>
<div id="stable-lifecycle">
<h2>Stable Lifecycle</h2>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</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><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
<div id="read-more-on-our-website-">
<h2>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>.</p>
<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>.</p>
</div>
<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>
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><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>
<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 class='co'># since ggplot2 supports no markdown (yet), use</span>
<span class='co'># italicise_taxonomy() and the `ggtext` package for titles:</span>
<span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://ggplot2.tidyverse.org'>"ggplot2"</a></span><span class='op'>)</span> <span class='op'>&amp;&amp;</span> <span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://wilkelab.org/ggtext/'>"ggtext"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/autoplot.html'>autoplot</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMC</span>,
title <span class='op'>=</span> <span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"Amoxi/clav in E. coli"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>+</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/theme.html'>theme</a></span><span class='op'>(</span>plot.title <span class='op'>=</span> <span class='fu'>ggtext</span><span class='fu'>::</span><span class='fu'><a href='https://wilkelab.org/ggtext/reference/element_markdown.html'>element_markdown</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
<span class="co"># since ggplot2 supports no markdown (yet), use</span>
<span class="co"># italicise_taxonomy() and the `ggtext` package for titles:</span>
<span class="co"># \donttest{</span>
<span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&amp;&amp;</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://wilkelab.org/ggtext/" class="external-link">"ggtext"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span>
<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMC</span>,
title <span class="op">=</span> <span class="fu">italicise_taxonomy</span><span class="op">(</span><span class="st">"Amoxi/clav in E. coli"</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span>
<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/theme.html" class="external-link">theme</a></span><span class="op">(</span>plot.title <span class="op">=</span> <span class="fu">ggtext</span><span class="fu">::</span><span class="fu"><a href="https://wilkelab.org/ggtext/reference/element_markdown.html" class="external-link">element_markdown</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
<span class="op">}</span>
<span class="co"># }</span>
</code></pre></div>
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