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(v0.7.0.9010) mo_synonyms, plot/barplot fixes

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dr. M.S. (Matthijs) Berends
2019-06-16 21:42:40 +02:00
parent 980be2b22d
commit 9c39c35f86
72 changed files with 595 additions and 802 deletions
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@ -78,7 +78,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9010</span>
</span>
</div>
@ -232,16 +232,16 @@
</div>
<div id="amr-0709009" class="section level1">
<div id="amr-0709010" class="section level1">
<h1 class="page-header">
<a href="#amr-0709009" class="anchor"></a>AMR 0.7.0.9009<small> Unreleased </small>
<a href="#amr-0709010" class="anchor"></a>AMR 0.7.0.9010<small> Unreleased </small>
</h1>
<div id="new" class="section level4">
<h4 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h4>
<ul>
<li>
<p>Function <code><a href="../reference/portion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combinations of existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/portion.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p>
<p>Function <code><a href="../reference/portion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/portion.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb1-2" title="2"><span class="st"> </span><span class="kw">select</span>(AMX, CIP) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb1-3" title="3"><span class="st"> </span><span class="kw"><a href="../reference/portion.html">rsi_df</a></span>()</a>
@ -252,13 +252,30 @@
<a class="sourceLine" id="cb1-8" title="8"><span class="co"># 4 Ciprofloxacin R 0.1618169 228</span></a></code></pre></div>
</li>
<li>
<p>Support for all scientifically published pathotypes of <em>E. coli</em> to date. Supported are: AIEC (Adherent-Invasive <em>E. coli</em>), ATEC (Atypical Entero-pathogenic <em>E. coli</em>), DAEC (Diffusely Adhering <em>E. coli</em>), EAEC (Entero-Aggresive <em>E. coli</em>), EHEC (Entero-Haemorrhagic <em>E. coli</em>), EIEC (Entero-Invasive <em>E. coli</em>), EPEC (Entero-Pathogenic <em>E. coli</em>), ETEC (Entero-Toxigenic <em>E. coli</em>), NMEC (Neonatal Meningitis‐causing <em>E. coli</em>), STEC (Shiga-toxin producing <em>E. coli</em>) and UPEC (Uropathogenic <em>E. coli</em>). All these lead to the microbial ID of <em>E. coli</em>:</p>
<p>Support for all scientifically published pathotypes of <em>E. coli</em> to date. Supported are:</p>
<ul>
<li>AIEC (Adherent-Invasive <em>E. coli</em>)</li>
<li>ATEC (Atypical Entero-pathogenic <em>E. coli</em>)</li>
<li>DAEC (Diffusely Adhering <em>E. coli</em>)</li>
<li>EAEC (Entero-Aggresive <em>E. coli</em>)</li>
<li>EHEC (Entero-Haemorrhagic <em>E. coli</em>)</li>
<li>EIEC (Entero-Invasive <em>E. coli</em>)</li>
<li>EPEC (Entero-Pathogenic <em>E. coli</em>)</li>
<li>ETEC (Entero-Toxigenic <em>E. coli</em>)</li>
<li>NMEC (Neonatal Meningitis‐causing <em>E. coli</em>)</li>
<li>STEC (Shiga-toxin producing <em>E. coli</em>)</li>
<li>UPEC (Uropathogenic <em>E. coli</em>)</li>
</ul>
<p>All these lead to the microbial ID of <em>E. coli</em>:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)</a>
<a class="sourceLine" id="cb2-2" title="2"><span class="co"># B_ESCHR_COL</span></a>
<a class="sourceLine" id="cb2-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"UPEC"</span>)</a>
<a class="sourceLine" id="cb2-4" title="4"><span class="co"># "Escherichia coli"</span></a></code></pre></div>
<a class="sourceLine" id="cb2-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"UPEC"</span>)</a>
<a class="sourceLine" id="cb2-4" title="4"><span class="co"># "Escherichia coli"</span></a>
<a class="sourceLine" id="cb2-5" title="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"EHEC"</span>)</a>
<a class="sourceLine" id="cb2-6" title="6"><span class="co"># "Gram-negative"</span></a></code></pre></div>
</li>
<li><p>Function <code><a href="../reference/mo_property.html">mo_info()</a></code> as an analogy to <code><a href="../reference/ab_property.html">ab_info()</a></code>. The <code><a href="../reference/mo_property.html">mo_info()</a></code> prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism</p></li>
<li>Function <code><a href="../reference/mo_property.html">mo_info()</a></code> as an analogy to <code><a href="../reference/ab_property.html">ab_info()</a></code>. The <code><a href="../reference/mo_property.html">mo_info()</a></code> prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism</li>
<li><p>Function <code><a href="../reference/mo_property.html">mo_synonyms()</a></code> to get all previously accepted taxonomic names of a microorganism</p></li>
</ul>
</div>
<div id="changed" class="section level4">
@ -283,6 +300,7 @@
<li>Fixed bug where not all old taxonomic named would not be printed when using a vector as input for <code><a href="../reference/as.mo.html">as.mo()</a></code>
</li>
<li>Manually added <em>Trichomonas vaginalis</em> from the kingdom of Protozoa, which is missing from the Catalogue of Life</li>
<li>Small improvements to <code><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> and <code><a href="https://www.rdocumentation.org/packages/graphics/topics/barplot">barplot()</a></code> for MIC and RSI classes</li>
</ul>
</div>
<div id="other" class="section level4">
@ -1121,7 +1139,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0709009">0.7.0.9009</a></li>
<li><a href="#amr-0709010">0.7.0.9010</a></li>
<li><a href="#amr-070">0.7.0</a></li>
<li><a href="#amr-061">0.6.1</a></li>
<li><a href="#amr-060">0.6.0</a></li>