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@ -39,7 +39,7 @@
</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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -134,7 +134,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -148,7 +148,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -164,10 +164,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">09 July 2020</h4>
<h4 class="date">24 July 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd"><code>vignettes/AMR.Rmd</code></a></small>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -195,7 +195,7 @@
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 09 July 2020.</p>
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 24 July 2020.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -226,21 +226,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2020-07-09</td>
<td align="center">2020-07-24</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2020-07-09</td>
<td align="center">2020-07-24</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2020-07-09</td>
<td align="center">2020-07-24</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -336,68 +336,68 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-01-30</td>
<td align="center">Y5</td>
<td align="center">2014-06-04</td>
<td align="center">V5</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2015-09-20</td>
<td align="center">M6</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-11-13</td>
<td align="center">Y1</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-07-21</td>
<td align="center">U10</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-03-14</td>
<td align="center">Q1</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2013-04-22</td>
<td align="center">O8</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-11-14</td>
<td align="center">J4</td>
<td align="center">Hospital A</td>
<td align="center">2017-05-14</td>
<td align="center">Q6</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-03-12</td>
<td align="center">O3</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2017-12-27</td>
<td align="center">P8</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-11-30</td>
<td align="center">B10</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
@ -432,18 +432,18 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,300</td>
<td align="right">51.5%</td>
<td align="right">10,300</td>
<td align="right">51.5%</td>
<td align="right">10,487</td>
<td align="right">52.44%</td>
<td align="right">10,487</td>
<td align="right">52.44%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,700</td>
<td align="right">48.5%</td>
<td align="right">9,513</td>
<td align="right">47.57%</td>
<td align="right">20,000</td>
<td align="right">100.0%</td>
<td align="right">100.00%</td>
</tr>
</tbody>
</table>
@ -481,7 +481,7 @@ Longest: 1</p>
<span class="co"># NOTE: Using column `bacteria` as input for `col_mo`.</span>
<span class="co"># NOTE: Using column `date` as input for `col_date`.</span>
<span class="co"># NOTE: Using column `patient_id` as input for `col_patient_id`.</span></pre></body></html></div>
<p>So only 28.5% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<p>So only 28.4% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb16"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">&lt;-</span> <span class="no">data</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="no">first</span> <span class="kw">==</span> <span class="fl">TRUE</span>)</pre></body></html></div>
<p>For future use, the above two syntaxes can be shortened with the <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> function:</p>
@ -491,7 +491,7 @@ Longest: 1</p>
<div id="first-weighted-isolates" class="section level2">
<h2 class="hasAnchor">
<a href="#first-weighted-isolates" class="anchor"></a>First <em>weighted</em> isolates</h2>
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient Y2, sorted on date:</p>
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient J1, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -507,19 +507,19 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-03-16</td>
<td align="center">Y2</td>
<td align="center">2010-04-08</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-08-04</td>
<td align="center">Y2</td>
<td align="center">2010-06-01</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -529,21 +529,21 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-10-06</td>
<td align="center">Y2</td>
<td align="center">2010-06-21</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-11-11</td>
<td align="center">Y2</td>
<td align="center">2010-07-08</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -551,30 +551,30 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-11-23</td>
<td align="center">Y2</td>
<td align="center">2011-01-29</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-04-01</td>
<td align="center">Y2</td>
<td align="center">2011-02-23</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">TRUE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-04-27</td>
<td align="center">Y2</td>
<td align="center">2011-02-23</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -584,19 +584,19 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-05-27</td>
<td align="center">Y2</td>
<td align="center">2011-02-28</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-07-05</td>
<td align="center">Y2</td>
<td align="center">2011-03-13</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -606,14 +606,14 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-09-25</td>
<td align="center">Y2</td>
<td align="center">2011-05-14</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
@ -644,20 +644,20 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-03-16</td>
<td align="center">Y2</td>
<td align="center">2010-04-08</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-08-04</td>
<td align="center">Y2</td>
<td align="center">2010-06-01</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -668,56 +668,44 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-10-06</td>
<td align="center">Y2</td>
<td align="center">2010-06-21</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-11-11</td>
<td align="center">Y2</td>
<td align="center">2010-07-08</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-11-23</td>
<td align="center">Y2</td>
<td align="center">2011-01-29</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-04-01</td>
<td align="center">Y2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-04-27</td>
<td align="center">Y2</td>
<td align="center">2011-02-23</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -726,22 +714,34 @@ Longest: 1</p>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-02-23</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-05-27</td>
<td align="center">Y2</td>
<td align="center">2011-02-28</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-07-05</td>
<td align="center">Y2</td>
<td align="center">2011-03-13</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -752,23 +752,23 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-09-25</td>
<td align="center">Y2</td>
<td align="center">2011-05-14</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Instead of 2, now 10 isolates are flagged. In total, 78.3% of all isolates are marked ‘first weighted’ - 49.8% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>Instead of 2, now 7 isolates are flagged. In total, 78.6% of all isolates are marked ‘first weighted’ - 50.2% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>As with <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
<div class="sourceCode" id="cb19"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">&lt;-</span> <span class="no">data</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</pre></body></html></div>
<p>So we end up with 15,664 isolates for analysis.</p>
<p>So we end up with 15,719 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb20"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">&lt;-</span> <span class="no">data_1st</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(-<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">first</span>, <span class="no">keyab</span>))</pre></body></html></div>
@ -776,6 +776,7 @@ Longest: 1</p>
<div class="sourceCode" id="cb21"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="no">data_1st</span>)</pre></body></html></div>
<table class="table">
<colgroup>
<col width="2%">
<col width="8%">
<col width="8%">
<col width="8%">
@ -791,6 +792,7 @@ Longest: 1</p>
<col width="11%">
</colgroup>
<thead><tr class="header">
<th align="left"></th>
<th align="center">date</th>
<th align="center">patient_id</th>
<th align="center">hospital</th>
@ -807,24 +809,10 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-01-30</td>
<td align="center">Y5</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2010-11-13</td>
<td align="center">Y1</td>
<td align="center">Hospital D</td>
<td align="left">1</td>
<td align="center">2014-06-04</td>
<td align="center">V5</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
@ -836,66 +824,86 @@ Longest: 1</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">3</td>
<td align="center">2017-05-14</td>
<td align="center">Q6</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-07-21</td>
<td align="center">U10</td>
<td align="left">4</td>
<td align="center">2017-03-12</td>
<td align="center">O3</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">2017-12-27</td>
<td align="center">P8</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">2013-11-30</td>
<td align="center">B10</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2011-06-14</td>
<td align="center">A2</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-03-14</td>
<td align="center">Q1</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2013-04-22</td>
<td align="center">O8</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-11-14</td>
<td align="center">J4</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -915,8 +923,8 @@ Longest: 1</p>
<div class="sourceCode" id="cb23"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">genus</span>, <span class="no">species</span>)</pre></body></html></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 15,664<br>
Available: 15,664 (100%, NA: 0 = 0%)<br>
Length: 15,719<br>
Available: 15,719 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -933,33 +941,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,860</td>
<td align="right">50.18%</td>
<td align="right">7,860</td>
<td align="right">50.18%</td>
<td align="right">7,902</td>
<td align="right">50.27%</td>
<td align="right">7,902</td>
<td align="right">50.27%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,867</td>
<td align="right">24.69%</td>
<td align="right">11,727</td>
<td align="right">74.87%</td>
<td align="right">3,926</td>
<td align="right">24.98%</td>
<td align="right">11,828</td>
<td align="right">75.25%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,386</td>
<td align="right">15.23%</td>
<td align="right">14,113</td>
<td align="right">90.10%</td>
<td align="right">2,350</td>
<td align="right">14.95%</td>
<td align="right">14,178</td>
<td align="right">90.20%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,551</td>
<td align="right">9.90%</td>
<td align="right">15,664</td>
<td align="right">1,541</td>
<td align="right">9.80%</td>
<td align="right">15,719</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -986,50 +994,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">3765</td>
<td align="center">268</td>
<td align="center">3827</td>
<td align="center">7860</td>
<td align="center">3775</td>
<td align="center">258</td>
<td align="center">3869</td>
<td align="center">7902</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">6198</td>
<td align="center">6238</td>
<td align="center">319</td>
<td align="center">1343</td>
<td align="center">7860</td>
<td align="center">1345</td>
<td align="center">7902</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">5971</td>
<td align="center">6031</td>
<td align="center">0</td>
<td align="center">1889</td>
<td align="center">7860</td>
<td align="center">1871</td>
<td align="center">7902</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">7088</td>
<td align="center">7105</td>
<td align="center">0</td>
<td align="center">772</td>
<td align="center">7860</td>
<td align="center">797</td>
<td align="center">7902</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1551</td>
<td align="center">1551</td>
<td align="center">1541</td>
<td align="center">1541</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">1209</td>
<td align="center">72</td>
<td align="center">270</td>
<td align="center">1551</td>
<td align="center">1230</td>
<td align="center">43</td>
<td align="center">268</td>
<td align="center">1541</td>
</tr>
</tbody>
</table>
@ -1052,34 +1060,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">5971</td>
<td align="center">6031</td>
<td align="center">0</td>
<td align="center">1889</td>
<td align="center">7860</td>
<td align="center">1871</td>
<td align="center">7902</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">CIP</td>
<td align="center">1192</td>
<td align="center">1174</td>
<td align="center">0</td>
<td align="center">359</td>
<td align="center">1551</td>
<td align="center">367</td>
<td align="center">1541</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">CIP</td>
<td align="center">2946</td>
<td align="center">2993</td>
<td align="center">0</td>
<td align="center">921</td>
<td align="center">3867</td>
<td align="center">933</td>
<td align="center">3926</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">CIP</td>
<td align="center">1813</td>
<td align="center">1807</td>
<td align="center">0</td>
<td align="center">573</td>
<td align="center">2386</td>
<td align="center">543</td>
<td align="center">2350</td>
</tr>
</tbody>
</table>
@ -1091,7 +1099,7 @@ Longest: 24</p>
<p>The functions <code><a href="../reference/proportion.html">resistance()</a></code> and <code><a href="../reference/proportion.html">susceptibility()</a></code> can be used to calculate antimicrobial resistance or susceptibility. For more specific analyses, the functions <code><a href="../reference/proportion.html">proportion_S()</a></code>, <code><a href="../reference/proportion.html">proportion_SI()</a></code>, <code><a href="../reference/proportion.html">proportion_I()</a></code>, <code><a href="../reference/proportion.html">proportion_IR()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code> can be used to determine the proportion of a specific antimicrobial outcome.</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb28"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="no">AMX</span>)
<span class="co"># [1] 0.5335802</span></pre></body></html></div>
<span class="co"># [1] 0.5350213</span></pre></body></html></div>
<p>Or can be used in conjuction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb29"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="no">hospital</span>) <span class="kw">%&gt;%</span>
@ -1105,19 +1113,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5286835</td>
<td align="center">0.5308117</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5301545</td>
<td align="center">0.5304522</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5366460</td>
<td align="center">0.5364381</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5447207</td>
<td align="center">0.5479751</td>
</tr>
</tbody>
</table>
@ -1136,23 +1144,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5286835</td>
<td align="center">4846</td>
<td align="center">0.5308117</td>
<td align="center">4706</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5301545</td>
<td align="center">5306</td>
<td align="center">0.5304522</td>
<td align="center">5484</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5366460</td>
<td align="center">2415</td>
<td align="center">0.5364381</td>
<td align="center">2319</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5447207</td>
<td align="center">3097</td>
<td align="center">0.5479751</td>
<td align="center">3210</td>
</tr>
</tbody>
</table>
@ -1173,27 +1181,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.8291349</td>
<td align="center">0.9017812</td>
<td align="center">0.9870229</td>
<td align="center">0.8297899</td>
<td align="center">0.8991395</td>
<td align="center">0.9851936</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8259188</td>
<td align="center">0.8994197</td>
<td align="center">0.9890393</td>
<td align="center">0.8260870</td>
<td align="center">0.8994160</td>
<td align="center">0.9883193</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8233773</td>
<td align="center">0.9229377</td>
<td align="center">0.9847427</td>
<td align="center">0.8352012</td>
<td align="center">0.9238411</td>
<td align="center">0.9852267</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5481978</td>
<td align="center">0.5425532</td>
<td align="center">0.0000000</td>
<td align="center">0.5481978</td>
<td align="center">0.5425532</td>
</tr>
</tbody>
</table>

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@ -39,7 +39,7 @@
</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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -134,7 +134,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -148,7 +148,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -164,10 +164,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">09 July 2020</h4>
<h4 class="date">24 July 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/EUCAST.Rmd"><code>vignettes/EUCAST.Rmd</code></a></small>
<div class="hidden name"><code>EUCAST.Rmd</code></div>

60
docs/articles/MDR.html
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@ -39,7 +39,7 @@
</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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -134,7 +134,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -148,7 +148,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -164,10 +164,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">09 July 2020</h4>
<h4 class="date">24 July 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/MDR.Rmd"><code>vignettes/MDR.Rmd</code></a></small>
<div class="hidden name"><code>MDR.Rmd</code></div>
@ -306,19 +306,19 @@ Unique: 2</p>
<p>The data set now looks like this:</p>
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="no">my_TB_data</span>)
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
<span class="co"># 1 S R R S S I</span>
<span class="co"># 2 S R S S S S</span>
<span class="co"># 3 S S S S S S</span>
<span class="co"># 4 S R S S S R</span>
<span class="co"># 5 R S S S R R</span>
<span class="co"># 6 S R I R R S</span>
<span class="co"># 1 R S S R R R</span>
<span class="co"># 2 R R R R I S</span>
<span class="co"># 3 S S S S R S</span>
<span class="co"># 4 S S R S S S</span>
<span class="co"># 5 R S R R I S</span>
<span class="co"># 6 R S R I S S</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 S</span>
<span class="co"># 2 R</span>
<span class="co"># 1 R</span>
<span class="co"># 2 S</span>
<span class="co"># 3 R</span>
<span class="co"># 4 S</span>
<span class="co"># 5 R</span>
<span class="co"># 6 S</span></pre></body></html></div>
<span class="co"># 6 R</span></pre></body></html></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="fu"><a href="../reference/mdro.html">mdro</a></span>(<span class="no">my_TB_data</span>, <span class="kw">guideline</span> <span class="kw">=</span> <span class="st">"TB"</span>)</pre></body></html></div>
<p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
@ -347,32 +347,32 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3300</td>
<td align="right">66.00%</td>
<td align="right">3300</td>
<td align="right">66.00%</td>
<td align="right">3196</td>
<td align="right">63.92%</td>
<td align="right">3196</td>
<td align="right">63.92%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">636</td>
<td align="right">12.72%</td>
<td align="right">3936</td>
<td align="right">78.72%</td>
<td align="right">694</td>
<td align="right">13.88%</td>
<td align="right">3890</td>
<td align="right">77.80%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">561</td>
<td align="right">11.22%</td>
<td align="right">4497</td>
<td align="right">89.94%</td>
<td align="right">606</td>
<td align="right">12.12%</td>
<td align="right">4496</td>
<td align="right">89.92%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">310</td>
<td align="right">6.20%</td>
<td align="right">311</td>
<td align="right">6.22%</td>
<td align="right">4807</td>
<td align="right">96.14%</td>
</tr>

14
docs/articles/PCA.html
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@ -39,7 +39,7 @@
</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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -134,7 +134,7 @@
</ul>
</li>
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<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -148,7 +148,7 @@
</a>
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<a href="../news/">
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<span class="far fa far fa-newspaper"></span>
Changelog
@ -164,10 +164,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to conduct principal component analysis (PCA) for AMR</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">09 July 2020</h4>
<h4 class="date">24 July 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/PCA.Rmd"><code>vignettes/PCA.Rmd</code></a></small>
<div class="hidden name"><code>PCA.Rmd</code></div>

14
docs/articles/SPSS.html
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@ -39,7 +39,7 @@
</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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -134,7 +134,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -148,7 +148,7 @@
</a>
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<a href="../news/">
<a href="../news/index.html">
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Changelog
@ -164,10 +164,10 @@
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<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">09 July 2020</h4>
<h4 class="date">24 July 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="hidden name"><code>SPSS.Rmd</code></div>

14
docs/articles/WHONET.html
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@ -39,7 +39,7 @@
</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">1.2.0.9033</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -134,7 +134,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -148,7 +148,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -164,10 +164,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to work with WHONET data</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">12 July 2020</h4>
<h4 class="date">24 July 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/WHONET.Rmd"><code>vignettes/WHONET.Rmd</code></a></small>
<div class="hidden name"><code>WHONET.Rmd</code></div>

100
docs/articles/benchmarks.html
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@ -39,7 +39,7 @@
</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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -134,7 +134,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -148,7 +148,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -164,10 +164,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -186,7 +186,7 @@
<h1 data-toc-skip>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">09 July 2020</h4>
<h4 class="date">24 July 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd"><code>vignettes/benchmarks.Rmd</code></a></small>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -221,21 +221,21 @@
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">S.aureus</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">2</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 9.9 14 22 15 36 48 10</span>
<span class="co"># as.mo("stau") 160.0 160 180 170 210 210 10</span>
<span class="co"># as.mo("STAU") 160.0 160 180 170 200 210 10</span>
<span class="co"># as.mo("staaur") 9.5 13 14 14 16 17 10</span>
<span class="co"># as.mo("STAAUR") 9.7 11 13 13 15 19 10</span>
<span class="co"># as.mo("S. aureus") 12.0 13 17 15 18 35 10</span>
<span class="co"># as.mo("S aureus") 11.0 16 26 19 42 43 10</span>
<span class="co"># as.mo("Staphylococcus aureus") 8.7 11 19 13 14 55 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 890.0 910 930 920 950 1000 10</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 420.0 430 450 440 470 510 10</span>
<span class="co"># as.mo("MRSA") 9.8 10 13 12 14 19 10</span>
<span class="co"># as.mo("VISA") 12.0 14 33 18 43 120 10</span>
<span class="co"># as.mo("VRSA") 12.0 15 24 17 37 48 10</span>
<span class="co"># as.mo(22242419) 140.0 150 150 150 150 180 10</span></pre></body></html></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 11 13 16 14 15 38 10</span>
<span class="co"># as.mo("stau") 170 170 180 180 190 200 10</span>
<span class="co"># as.mo("STAU") 160 170 190 190 200 210 10</span>
<span class="co"># as.mo("staaur") 12 13 15 14 15 20 10</span>
<span class="co"># as.mo("STAAUR") 13 14 17 15 15 38 10</span>
<span class="co"># as.mo("S. aureus") 13 14 23 17 36 42 10</span>
<span class="co"># as.mo("S aureus") 14 15 31 25 43 82 10</span>
<span class="co"># as.mo("Staphylococcus aureus") 11 11 17 12 14 42 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 920 940 960 950 970 1100 10</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 420 440 460 460 460 500 10</span>
<span class="co"># as.mo("MRSA") 13 14 20 14 16 43 10</span>
<span class="co"># as.mo("VISA") 15 15 28 27 40 42 10</span>
<span class="co"># as.mo("VRSA") 13 15 18 15 17 45 10</span>
<span class="co"># as.mo(22242419) 130 140 150 150 170 180 10</span></pre></body></html></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="562.5"></p>
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second.</p>
<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside of this is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Methanosarcina semesiae</em> (<code>B_MTHNSR_SEMS</code>), a bug probably never found before in humans:</p>
@ -247,12 +247,12 @@
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">M.semesiae</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">4</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("metsem") 169.600 189.900 199.30 199.70 211.00 223.90</span>
<span class="co"># as.mo("METSEM") 170.000 186.900 197.40 191.80 210.70 232.30</span>
<span class="co"># as.mo("M. semesiae") 11.330 11.620 12.37 12.21 13.20 13.78</span>
<span class="co"># as.mo("M. semesiae") 11.410 12.090 15.74 12.48 13.55 43.19</span>
<span class="co"># as.mo("Methanosarcina semesiae") 8.592 8.906 12.89 9.31 11.54 41.08</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("metsem") 180.20 190.40 199.00 199.10 204.40 218.80</span>
<span class="co"># as.mo("METSEM") 190.00 191.50 203.30 193.70 221.00 236.30</span>
<span class="co"># as.mo("M. semesiae") 11.60 12.58 15.84 13.42 14.40 37.45</span>
<span class="co"># as.mo("M. semesiae") 12.14 12.59 19.44 14.19 14.78 43.90</span>
<span class="co"># as.mo("Methanosarcina semesiae") 10.65 10.78 16.81 12.13 14.08 37.01</span>
<span class="co"># neval</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
@ -292,8 +292,8 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># mo_name(x) 1610 1650 1680 1670 1710 1780 10</span></pre></body></html></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.67 seconds. You only lose time on your unique input values.</p>
<span class="co"># mo_name(x) 1840 1850 1910 1900 1950 2020 10</span></pre></body></html></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.9 seconds. You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -306,10 +306,10 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 8.15 8.69 9.63 9.05 10.40 12.40 10</span>
<span class="co"># B 11.30 12.70 17.50 13.40 14.80 54.30 10</span>
<span class="co"># C 1.04 1.17 1.28 1.28 1.38 1.59 10</span></pre></body></html></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0013 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<span class="co"># A 8.08 8.52 8.94 8.57 9.49 10.50 10</span>
<span class="co"># B 10.40 10.70 14.60 11.00 11.70 45.70 10</span>
<span class="co"># C 1.04 1.10 1.19 1.15 1.29 1.46 10</span></pre></body></html></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0012 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="no">run_it</span> <span class="kw">&lt;-</span> <span class="fu">microbenchmark</span>(<span class="kw">A</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),
<span class="kw">B</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),
<span class="kw">C</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),
@ -321,15 +321,15 @@
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 0.852 0.977 1.040 0.990 1.040 1.29 10</span>
<span class="co"># B 0.802 0.933 1.070 0.994 1.160 1.65 10</span>
<span class="co"># C 0.804 0.983 1.060 1.000 1.210 1.32 10</span>
<span class="co"># D 0.783 0.855 0.996 0.989 1.030 1.36 10</span>
<span class="co"># E 0.820 0.962 1.020 0.982 1.070 1.27 10</span>
<span class="co"># F 0.770 0.785 0.937 0.953 0.996 1.30 10</span>
<span class="co"># G 0.963 0.981 1.140 1.160 1.250 1.38 10</span>
<span class="co"># H 0.778 0.842 0.985 0.977 0.995 1.30 10</span></pre></body></html></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 0.862 1.030 1.070 1.060 1.08 1.33 10</span>
<span class="co"># B 0.837 1.020 1.010 1.030 1.05 1.13 10</span>
<span class="co"># C 0.836 0.936 0.993 1.020 1.03 1.17 10</span>
<span class="co"># D 0.838 0.947 1.030 1.050 1.10 1.31 10</span>
<span class="co"># E 0.807 0.906 0.994 1.010 1.03 1.28 10</span>
<span class="co"># F 0.804 0.920 1.060 1.040 1.11 1.54 10</span>
<span class="co"># G 0.805 0.906 1.000 1.030 1.07 1.25 10</span>
<span class="co"># H 0.792 0.805 0.949 0.941 1.04 1.29 10</span></pre></body></html></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
</div>
<div id="results-in-other-languages" class="section level3">
@ -356,13 +356,13 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">4</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 12.84 13.10 18.11 14.63 15.54 58.10 100</span>
<span class="co"># de 13.58 14.02 18.05 14.61 16.58 69.21 100</span>
<span class="co"># nl 17.07 17.89 22.36 18.97 20.85 68.70 100</span>
<span class="co"># es 13.63 14.20 20.75 15.82 16.79 73.94 100</span>
<span class="co"># it 13.64 13.95 16.95 15.40 16.57 50.96 100</span>
<span class="co"># fr 13.74 14.12 19.84 15.81 16.62 61.13 100</span>
<span class="co"># pt 13.58 14.02 19.00 14.90 16.49 53.41 100</span></pre></body></html></div>
<span class="co"># en 12.09 12.45 16.18 12.63 13.57 48.69 100</span>
<span class="co"># de 13.01 13.51 16.67 13.82 15.26 48.22 100</span>
<span class="co"># nl 16.88 17.25 19.13 17.54 18.36 51.99 100</span>
<span class="co"># es 13.13 13.42 18.26 13.69 14.59 53.66 100</span>
<span class="co"># it 13.01 13.35 17.33 13.71 15.16 50.65 100</span>
<span class="co"># fr 13.13 13.40 16.31 13.64 13.88 49.44 100</span>
<span class="co"># pt 13.17 13.38 15.10 13.54 13.94 49.61 100</span></pre></body></html></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>

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docs/articles/index.html
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@ -81,7 +81,7 @@
</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">1.2.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -176,7 +176,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -190,7 +190,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -206,10 +206,10 @@
</a>
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<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
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</li>
</ul>

14
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@ -39,7 +39,7 @@
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<h1 data-toc-skip>How to predict antimicrobial resistance</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">09 July 2020</h4>
<h4 class="date">24 July 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/resistance_predict.Rmd"><code>vignettes/resistance_predict.Rmd</code></a></small>
<div class="hidden name"><code>resistance_predict.Rmd</code></div>