<metaproperty="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."/>
<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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<preclass="usage"><spanclass='fu'>italicise_taxonomy</span><spanclass='op'>(</span><spanclass='va'>string</span>, type <spanclass='op'>=</span><spanclass='fu'><ahref='https://rdrr.io/r/base/c.html'>c</a></span><spanclass='op'>(</span><spanclass='st'>"markdown"</span>, <spanclass='st'>"ansi"</span><spanclass='op'>)</span><spanclass='op'>)</span>
<spanclass='fu'>italicize_taxonomy</span><spanclass='op'>(</span><spanclass='va'>string</span>, type <spanclass='op'>=</span><spanclass='fu'><ahref='https://rdrr.io/r/base/c.html'>c</a></span><spanclass='op'>(</span><spanclass='st'>"markdown"</span>, <spanclass='st'>"ansi"</span><spanclass='op'>)</span><spanclass='op'>)</span></pre>
<p>This function finds the taxonomic names and makes them italic based on the <ahref='microorganisms.html'>microorganisms</a> data set.</p>
<p>The taxonomic names can be italicised using markdown (the default) by adding <code><ahref='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>
The <ahref='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 <ahref='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <ahref='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<h2class="hasAnchor"id="read-more-on-our-website-"><aclass="anchor"href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
<p>On our website <ahref='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <ahref='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <ahref='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <ahref='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 <ahref='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<preclass="examples"><spanclass='fu'>italicise_taxonomy</span><spanclass='op'>(</span><spanclass='st'>"An overview of Staphylococcus aureus isolates"</span><spanclass='op'>)</span>
<spanclass='fu'>italicise_taxonomy</span><spanclass='op'>(</span><spanclass='st'>"An overview of S. aureus isolates"</span><spanclass='op'>)</span>
<spanclass='fu'><ahref='https://rdrr.io/r/base/cat.html'>cat</a></span><spanclass='op'>(</span><spanclass='fu'>italicise_taxonomy</span><spanclass='op'>(</span><spanclass='st'>"An overview of S. aureus isolates"</span>, type <spanclass='op'>=</span><spanclass='st'>"ansi"</span><spanclass='op'>)</span><spanclass='op'>)</span>
title <spanclass='op'>=</span><spanclass='fu'>italicise_taxonomy</span><spanclass='op'>(</span><spanclass='st'>"Amoxi/clav in E. coli"</span><spanclass='op'>)</span><spanclass='op'>)</span><spanclass='op'>+</span>
<p>Developed by <ahref='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <ahref='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <ahref='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <ahref='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <ahref='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <ahref='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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