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(v1.8.1.9011) update prevalence of some genera

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dr. M.S. (Matthijs) Berends
2022-06-03 12:43:25 +02:00
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commit 1b84564d36
35 changed files with 278 additions and 429 deletions
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docs/articles/datasets.html
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@ -44,7 +44,7 @@
</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">1.8.1.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9011</span>
</span>
</div>
@ -190,7 +190,7 @@
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">16 May 2022</h4>
<h4 data-toc-skip class="date">03 June 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="hidden name"><code>datasets.Rmd</code></div>
@ -883,7 +883,7 @@ Dipivoxil, …</td>
<div class="section level2">
<h2 id="interpretation-from-mic-values-disk-diameters-to-rsi">Interpretation from MIC values / disk diameters to R/SI<a class="anchor" aria-label="anchor" href="#interpretation-from-mic-values-disk-diameters-to-rsi"></a>
</h2>
<p>A data set with 20,318 rows and 11 columns, containing the following
<p>A data set with 20,369 rows and 11 columns, containing the following
column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>,
<em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>,
<em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
@ -915,8 +915,8 @@ file</a> (3.8 MB)</li>
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
</h3>
<p>This data set contains interpretation rules for MIC values and disk
diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
(2011-2021).</p>
diffusion diameters. Included guidelines are CLSI (2011-2022) and EUCAST
(2011-2022).</p>
</div>
<div class="section level3">
<h3 id="example-content-4">Example content<a class="anchor" aria-label="anchor" href="#example-content-4"></a>
@ -954,7 +954,7 @@ diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">EUCAST 2021</td>
<td align="center">EUCAST 2022</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_ASPRG_MGTS</td>
@ -965,11 +965,11 @@ diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
<td align="center">Aspergillus</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">4</td>
<td align="center">1</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2021</td>
<td align="center">EUCAST 2022</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_ASPRG_NIGR</td>
@ -980,11 +980,11 @@ diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
<td align="center">Aspergillus</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">4</td>
<td align="center">1</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2021</td>
<td align="center">EUCAST 2022</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_CANDD</td>
@ -995,11 +995,11 @@ diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
<td align="center">Candida</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">2</td>
<td align="center">1</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2021</td>
<td align="center">EUCAST 2022</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_CANDD_ALBC</td>
@ -1010,11 +1010,26 @@ diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
<td align="center">Candida</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">2</td>
<td align="center">1</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2021</td>
<td align="center">EUCAST 2022</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_CANDD_DBLN</td>
<td align="center">Candida dubliniensis</td>
<td align="center">2</td>
<td align="center">AMB</td>
<td align="center">Amphotericin B</td>
<td align="center">Candida</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2022</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_CANDD_KRUS</td>
@ -1025,22 +1040,7 @@ diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
<td align="center">Candida</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">2</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2021</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_CANDD_PRPS</td>
<td align="center">Candida parapsilosis</td>
<td align="center">2</td>
<td align="center">AMB</td>
<td align="center">Amphotericin B</td>
<td align="center">Candida</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">2</td>
<td align="center">FALSE</td>
</tr>
</tbody>