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dr. M.S. (Matthijs) Berends
2019-11-30 12:01:50 +01:00
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docs/reference/mo_property.html
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<script src="../extra.js"></script>
<meta property="og:title" content="Property of a microorganism — mo_property" />
<meta property="og:description" content="Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with as.mo(), which makes it possible for input of these functions to use microbial abbreviations, codes and names. See Examples." />
<meta property="og:description" content="Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with as.mo(), which makes it possible to use microbial abbreviations, codes and names as input. Please see Examples." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
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</div>
<div class="ref-description">
<p>Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with <code><a href='as.mo.html'>as.mo()</a></code>, which makes it possible for input of these functions to use microbial abbreviations, codes and names. See Examples.</p>
<p>Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with <code><a href='as.mo.html'>as.mo()</a></code>, which makes it possible to use microbial abbreviations, codes and names as input. Please see <em>Examples</em>.</p>
</div>
<pre class="usage"><span class='fu'>mo_name</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
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<ul>
<li><p>An <code><a href='https://rdrr.io/r/base/integer.html'>integer</a></code> in case of <code>mo_year()</code></p></li>
<li><p>A <code><a href='https://rdrr.io/r/base/list.html'>list</a></code> in case of <code>mo_taxonomy()</code></p></li>
<li><p>A <code><a href='https://rdrr.io/r/base/list.html'>list</a></code> in case of <code>mo_taxonomy()</code> and <code>mo_info()</code></p></li>
<li><p>A named <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> in case of <code>mo_url()</code></p></li>
<li><p>A <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> in all other cases</p></li>
</ul>
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<li><p><code>mo_ref("Chlamydophila psittaci")</code> will return <code>"Everett et al., 1999"</code> (without a warning)</p></li>
</ul>
<p>The Gram stain - <code>mo_gramstain()</code> - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram positive - all other bacteria are considered Gram negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>.</p>
<p>The Gram stain - <code>mo_gramstain()</code> - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>.</p>
<p>All output will be <a href='translate.html'>translate</a>d where possible.</p>
<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>