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(v1.8.1.9014) add Toxoplasma

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dr. M.S. (Matthijs) Berends
2022-08-12 23:27:15 +02:00
parent 7f981e7778
commit ab97268f4c
20 changed files with 808 additions and 728 deletions
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docs/reference/rsi_translation.html
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@ -17,7 +17,7 @@
</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="Released version">1.8.1.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
</span>
</div>
@ -162,7 +162,7 @@
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">rsi_translation</span></code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">rsi_translation</span></span></code></pre></div>
</div>
<div id="format">
@ -182,8 +182,21 @@
<div id="details">
<h2>Details</h2>
<p>Overview of the data set:</p>
<p></p><div class="sourceCode r"><pre><code><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">rsi_translation</span><span class="op">)</span></code></pre><p></p></div>
<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
<p></p><div class="sourceCode r"><pre><code><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">rsi_translation</span><span class="op">)</span></span>
<span><span class="co">#&gt; guideline method site mo rank_index ab ref_tbl disk_dose</span></span>
<span><span class="co">#&gt; 1 EUCAST 2022 MIC &lt;NA&gt; F_ASPRG_MGTS 2 AMB Aspergillus &lt;NA&gt;</span></span>
<span><span class="co">#&gt; 2 EUCAST 2022 MIC &lt;NA&gt; F_ASPRG_NIGR 2 AMB Aspergillus &lt;NA&gt;</span></span>
<span><span class="co">#&gt; 3 EUCAST 2022 MIC &lt;NA&gt; F_CANDD 3 AMB Candida &lt;NA&gt;</span></span>
<span><span class="co">#&gt; 4 EUCAST 2022 MIC &lt;NA&gt; F_CANDD_ALBC 2 AMB Candida &lt;NA&gt;</span></span>
<span><span class="co">#&gt; 5 EUCAST 2022 MIC &lt;NA&gt; F_CANDD_DBLN 2 AMB Candida &lt;NA&gt;</span></span>
<span><span class="co">#&gt; 6 EUCAST 2022 MIC &lt;NA&gt; F_CANDD_KRUS 2 AMB Candida &lt;NA&gt;</span></span>
<span><span class="co">#&gt; breakpoint_S breakpoint_R uti</span></span>
<span><span class="co">#&gt; 1 1 1 FALSE</span></span>
<span><span class="co">#&gt; 2 1 1 FALSE</span></span>
<span><span class="co">#&gt; 3 1 1 FALSE</span></span>
<span><span class="co">#&gt; 4 1 1 FALSE</span></span>
<span><span class="co">#&gt; 5 1 1 FALSE</span></span>
<span><span class="co">#&gt; 6 1 1 FALSE</span></span></code></pre><p></p></div>
<p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href="https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt</a>. This file <strong>allows for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the <code>mo</code> and <code>ab</code> columns have been transformed to contain the full official names instead of codes.</p>
</div>
<div id="reference-data-publicly-available">
@ -215,7 +228,7 @@
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
</div>
</footer></div>