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(v0.6.1.9053) prerelease fixes

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dr. M.S. (Matthijs) Berends
2019-06-02 19:23:19 +02:00
parent 8de0495008
commit bd73988f15
38 changed files with 337 additions and 327 deletions
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docs/reference/microorganisms.html
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>
@ -252,24 +252,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 67,903 observations and 16 variables:</p><dl class='dl-horizontal'>
<dt><code>mo</code></dt><dd><p>ID of microorganism as used by this package</p></dd>
<dt><code>col_id</code></dt><dd><p>Catalogue of Life ID</p></dd>
<dt><code>fullname</code></dt><dd><p>Full name, like <code>"Echerichia coli"</code></p></dd>
<dt><code>kingdom</code></dt><dd><p>Taxonomic kingdom of the microorganism</p></dd>
<dt><code>phylum</code></dt><dd><p>Taxonomic phylum of the microorganism</p></dd>
<dt><code>class</code></dt><dd><p>Taxonomic class of the microorganism</p></dd>
<dt><code>order</code></dt><dd><p>Taxonomic order of the microorganism</p></dd>
<dt><code>family</code></dt><dd><p>Taxonomic family of the microorganism</p></dd>
<dt><code>genus</code></dt><dd><p>Taxonomic genus of the microorganism</p></dd>
<dt><code>species</code></dt><dd><p>Taxonomic species of the microorganism</p></dd>
<dt><code>subspecies</code></dt><dd><p>Taxonomic subspecies of the microorganism</p></dd>
<dt><code>rank</code></dt><dd><p>Taxonomic rank of the microorganism, like <code>"species"</code> or <code>"genus"</code></p></dd>
<dt><code>ref</code></dt><dd><p>Author(s) and year of concerning scientific publication</p></dd>
<dt><code>species_id</code></dt><dd><p>ID of the species as used by the Catalogue of Life</p></dd>
<dt><code>source</code></dt><dd><p>Either <code>"CoL"</code>, <code>"DSMZ"</code> (see source) or "manually added"</p></dd>
<dt><code>prevalence</code></dt><dd><p>Prevalence of the microorganism, see <code><a href='as.mo.html'>?as.mo</a></code></p></dd>
</dl>
<p>An object of class <code>data.frame</code> with 67903 rows and 16 columns.</p>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>