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(v1.3.0.9002) intrinsic_resistant data set

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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">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">10 August 2020</h4>
<h4 class="date">14 August 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 10 August 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 14 August 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">2020-08-10</td>
<td align="center">2020-08-14</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">2020-08-10</td>
<td align="center">2020-08-14</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">2020-08-10</td>
<td align="center">2020-08-14</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -354,70 +354,70 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-08-12</td>
<td align="center">M9</td>
<td align="center">Hospital D</td>
<td align="center">2010-03-16</td>
<td align="center">X9</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-03-13</td>
<td align="center">W1</td>
<td align="center">2013-10-27</td>
<td align="center">G3</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-12-02</td>
<td align="center">L5</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-09-11</td>
<td align="center">O7</td>
<td align="center">Hospital B</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="odd">
<td align="center">2014-06-03</td>
<td align="center">K4</td>
<td align="center">2014-12-09</td>
<td align="center">F7</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-07-19</td>
<td align="center">W4</td>
<td align="center">2014-06-08</td>
<td align="center">S9</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</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="odd">
<td align="center">2015-01-01</td>
<td align="center">N10</td>
<td align="center">Hospital A</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">2015-11-12</td>
<td align="center">H6</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
@ -452,16 +452,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,386</td>
<td align="right">51.93%</td>
<td align="right">10,386</td>
<td align="right">51.93%</td>
<td align="right">10,276</td>
<td align="right">51.38%</td>
<td align="right">10,276</td>
<td align="right">51.38%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,614</td>
<td align="right">48.07%</td>
<td align="right">9,724</td>
<td align="right">48.62%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -511,7 +511,7 @@ Longest: 1</p>
<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></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"><pre class="downlit">
<span class="kw">data_1st</span> <span class="op">&lt;-</span> <span class="kw">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw">first</span> <span class="op">==</span> <span class="fl">TRUE</span>)
@ -525,7 +525,7 @@ 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 A7, 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 N8, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -541,10 +541,10 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-02-03</td>
<td align="center">A7</td>
<td align="center">2010-05-17</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -552,10 +552,10 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-02-04</td>
<td align="center">A7</td>
<td align="center">2010-07-03</td>
<td align="center">N8</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>
@ -563,52 +563,52 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-04-05</td>
<td align="center">A7</td>
<td align="center">2010-07-31</td>
<td align="center">N8</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">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-06-15</td>
<td align="center">A7</td>
<td align="center">2010-09-13</td>
<td align="center">N8</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">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-08-28</td>
<td align="center">A7</td>
<td align="center">2010-09-15</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_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">R</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-09-03</td>
<td align="center">A7</td>
<td align="center">2010-10-16</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</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">2010-11-14</td>
<td align="center">A7</td>
<td align="center">2010-10-17</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -618,30 +618,30 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-02-14</td>
<td align="center">A7</td>
<td align="center">2010-10-24</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-03-06</td>
<td align="center">A7</td>
<td align="center">2010-12-27</td>
<td align="center">N8</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">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-03-09</td>
<td align="center">A7</td>
<td align="center">2011-02-25</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -651,14 +651,13 @@ Longest: 1</p>
</tr>
</tbody>
</table>
<p>Only 2 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>Only 1 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>If a column exists with a name like ‘key(…)ab’ the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> function will automatically use it and determine the first weighted isolates. Mind the NOTEs in below output:</p>
<div class="sourceCode" id="cb18"><pre class="downlit">
<span class="kw">data</span> <span class="op">&lt;-</span> <span class="kw">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(keyab = <span class="fu"><a href="../reference/key_antibiotics.html">key_antibiotics</a></span>(<span class="kw">.</span>)) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(first_weighted = <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="kw">.</span>))
<span class="co"># NOTE: Using column `bacteria` as input for `col_mo`.</span>
<span class="co"># NOTE: more than one result was found for item 1: amoxicillin/clavulanic acid, azidocillin</span>
<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>
@ -680,10 +679,10 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-02-03</td>
<td align="center">A7</td>
<td align="center">2010-05-17</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -692,10 +691,10 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-02-04</td>
<td align="center">A7</td>
<td align="center">2010-07-03</td>
<td align="center">N8</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>
@ -704,56 +703,56 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-04-05</td>
<td align="center">A7</td>
<td align="center">2010-07-31</td>
<td align="center">N8</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">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-06-15</td>
<td align="center">A7</td>
<td align="center">2010-09-13</td>
<td align="center">N8</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="odd">
<td align="center">5</td>
<td align="center">2010-08-28</td>
<td align="center">A7</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">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-09-15</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_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">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-09-03</td>
<td align="center">A7</td>
<td align="center">2010-10-16</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-11-14</td>
<td align="center">A7</td>
<td align="center">2010-10-17</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -764,49 +763,49 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-02-14</td>
<td align="center">A7</td>
<td align="center">2010-10-24</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-03-06</td>
<td align="center">A7</td>
<td align="center">2010-12-27</td>
<td align="center">N8</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">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-03-09</td>
<td align="center">A7</td>
<td align="center">2011-02-25</td>
<td align="center">N8</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">TRUE</td>
<td align="center">FALSE</td>
</tr>
</tbody>
</table>
<p>Instead of 2, now 9 isolates are flagged. In total, 79.0% of all isolates are marked ‘first weighted’ - 50.5% 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 1, now 9 isolates are flagged. In total, 78.0% of all isolates are marked ‘first weighted’ - 49.7% 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"><pre class="downlit">
<span class="kw">data_1st</span> <span class="op">&lt;-</span> <span class="kw">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()
</pre></div>
<p>So we end up with 15,794 isolates for analysis.</p>
<p>So we end up with 15,607 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb20"><pre class="downlit">
<span class="kw">data_1st</span> <span class="op">&lt;-</span> <span class="kw">data_1st</span> <span class="op">%&gt;%</span>
@ -852,15 +851,15 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2014-08-12</td>
<td align="center">M9</td>
<td align="center">Hospital D</td>
<td align="center">2010-03-16</td>
<td align="center">X9</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
@ -868,27 +867,11 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2013-03-13</td>
<td align="center">W1</td>
<td align="center">2013-10-27</td>
<td align="center">G3</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</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-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">2015-12-02</td>
<td align="center">L5</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
@ -898,11 +881,43 @@ Longest: 1</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">2014-12-09</td>
<td align="center">F7</td>
<td align="center">Hospital C</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">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="left">4</td>
<td align="center">2017-09-11</td>
<td align="center">O7</td>
<td align="center">2014-06-08</td>
<td align="center">S9</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</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">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="center">2015-01-01</td>
<td align="center">N10</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
@ -914,36 +929,20 @@ Longest: 1</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="center">2014-06-03</td>
<td align="center">K4</td>
<td align="center">Hospital C</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>
<tr class="even">
<td align="left">7</td>
<td align="center">2011-02-14</td>
<td align="center">B9</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">2014-08-04</td>
<td align="center">O9</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -969,8 +968,8 @@ Longest: 1</p>
</pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 15,794<br>
Available: 15,794 (100%, NA: 0 = 0%)<br>
Length: 15,607<br>
Available: 15,607 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -987,33 +986,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,828</td>
<td align="right">49.56%</td>
<td align="right">7,828</td>
<td align="right">49.56%</td>
<td align="right">7,836</td>
<td align="right">50.21%</td>
<td align="right">7,836</td>
<td align="right">50.21%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,925</td>
<td align="right">24.85%</td>
<td align="right">11,753</td>
<td align="right">74.41%</td>
<td align="right">3,899</td>
<td align="right">24.98%</td>
<td align="right">11,735</td>
<td align="right">75.19%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,399</td>
<td align="right">15.19%</td>
<td align="right">14,152</td>
<td align="right">89.60%</td>
<td align="right">2,337</td>
<td align="right">14.97%</td>
<td align="right">14,072</td>
<td align="right">90.16%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,642</td>
<td align="right">10.40%</td>
<td align="right">15,794</td>
<td align="right">1,535</td>
<td align="right">9.84%</td>
<td align="right">15,607</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -1042,50 +1041,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">3722</td>
<td align="center">247</td>
<td align="center">3859</td>
<td align="center">7828</td>
<td align="center">3854</td>
<td align="center">265</td>
<td align="center">3717</td>
<td align="center">7836</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">6127</td>
<td align="center">293</td>
<td align="center">1408</td>
<td align="center">7828</td>
<td align="center">6244</td>
<td align="center">287</td>
<td align="center">1305</td>
<td align="center">7836</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">5959</td>
<td align="center">5880</td>
<td align="center">0</td>
<td align="center">1869</td>
<td align="center">7828</td>
<td align="center">1956</td>
<td align="center">7836</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">7073</td>
<td align="center">7050</td>
<td align="center">0</td>
<td align="center">755</td>
<td align="center">7828</td>
<td align="center">786</td>
<td align="center">7836</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">1642</td>
<td align="center">1642</td>
<td align="center">1535</td>
<td align="center">1535</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">1304</td>
<td align="center">58</td>
<td align="center">280</td>
<td align="center">1642</td>
<td align="center">1199</td>
<td align="center">50</td>
<td align="center">286</td>
<td align="center">1535</td>
</tr>
</tbody>
</table>
@ -1110,34 +1109,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">5959</td>
<td align="center">5880</td>
<td align="center">0</td>
<td align="center">1869</td>
<td align="center">7828</td>
<td align="center">1956</td>
<td align="center">7836</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">CIP</td>
<td align="center">1237</td>
<td align="center">1166</td>
<td align="center">0</td>
<td align="center">405</td>
<td align="center">1642</td>
<td align="center">369</td>
<td align="center">1535</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">CIP</td>
<td align="center">3006</td>
<td align="center">2942</td>
<td align="center">0</td>
<td align="center">919</td>
<td align="center">3925</td>
<td align="center">957</td>
<td align="center">3899</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">CIP</td>
<td align="center">1801</td>
<td align="center">1799</td>
<td align="center">0</td>
<td align="center">598</td>
<td align="center">2399</td>
<td align="center">538</td>
<td align="center">2337</td>
</tr>
</tbody>
</table>
@ -1150,7 +1149,7 @@ Longest: 24</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"><pre class="downlit">
<span class="kw">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="kw">AMX</span>)
<span class="co"># [1] 0.5372293</span>
<span class="co"># [1] 0.5233549</span>
</pre></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"><pre class="downlit">
@ -1167,19 +1166,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5349377</td>
<td align="center">0.5238399</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5382268</td>
<td align="center">0.5201802</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5455691</td>
<td align="center">0.5259455</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5325387</td>
<td align="center">0.5264182</td>
</tr>
</tbody>
</table>
@ -1200,23 +1199,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5349377</td>
<td align="center">4737</td>
<td align="center">0.5238399</td>
<td align="center">4698</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5382268</td>
<td align="center">5572</td>
<td align="center">0.5201802</td>
<td align="center">5550</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5455691</td>
<td align="center">2381</td>
<td align="center">0.5259455</td>
<td align="center">2274</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5325387</td>
<td align="center">3104</td>
<td align="center">0.5264182</td>
<td align="center">3085</td>
</tr>
</tbody>
</table>
@ -1239,27 +1238,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.8201329</td>
<td align="center">0.9035514</td>
<td align="center">0.9853091</td>
<td align="center">0.8334609</td>
<td align="center">0.8996937</td>
<td align="center">0.9857070</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8294762</td>
<td align="center">0.9025579</td>
<td align="center">0.9829476</td>
<td align="center">0.8136808</td>
<td align="center">0.8983713</td>
<td align="center">0.9798046</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8219108</td>
<td align="center">0.9141401</td>
<td align="center">0.9844586</td>
<td align="center">0.8304694</td>
<td align="center">0.9253655</td>
<td align="center">0.9894845</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5414756</td>
<td align="center">0.5537013</td>
<td align="center">0.0000000</td>
<td align="center">0.5414756</td>
<td align="center">0.5537013</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">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">10 August 2020</h4>
<h4 class="date">14 August 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
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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">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -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">10 August 2020</h4>
<h4 class="date">14 August 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>
@ -315,19 +315,19 @@ Unique: 2</p>
<div class="sourceCode" id="cb5"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="kw">my_TB_data</span>)
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
<span class="co"># 1 R R R R I I</span>
<span class="co"># 2 S S S R S R</span>
<span class="co"># 3 S I S S S S</span>
<span class="co"># 4 S I S R R R</span>
<span class="co"># 5 S S R S S R</span>
<span class="co"># 6 S R S R R R</span>
<span class="co"># 1 R R R R R S</span>
<span class="co"># 2 S R S I I S</span>
<span class="co"># 3 R R R S S S</span>
<span class="co"># 4 S I S R I S</span>
<span class="co"># 5 S R R R S R</span>
<span class="co"># 6 S S R S S R</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 S</span>
<span class="co"># 2 R</span>
<span class="co"># 3 S</span>
<span class="co"># 4 S</span>
<span class="co"># 2 I</span>
<span class="co"># 3 R</span>
<span class="co"># 4 R</span>
<span class="co"># 5 S</span>
<span class="co"># 6 R</span>
<span class="co"># 6 I</span>
</pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb6"><pre class="downlit">
@ -363,40 +363,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3229</td>
<td align="right">64.58%</td>
<td align="right">3229</td>
<td align="right">64.58%</td>
<td align="right">3241</td>
<td align="right">64.82%</td>
<td align="right">3241</td>
<td align="right">64.82%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">674</td>
<td align="right">13.48%</td>
<td align="right">3903</td>
<td align="right">78.06%</td>
<td align="right">642</td>
<td align="right">12.84%</td>
<td align="right">3883</td>
<td align="right">77.66%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">616</td>
<td align="right">12.32%</td>
<td align="right">4519</td>
<td align="right">90.38%</td>
<td align="right">595</td>
<td align="right">11.90%</td>
<td align="right">4478</td>
<td align="right">89.56%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">285</td>
<td align="right">5.70%</td>
<td align="right">4804</td>
<td align="right">96.08%</td>
<td align="right">311</td>
<td align="right">6.22%</td>
<td align="right">4789</td>
<td align="right">95.78%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">196</td>
<td align="right">3.92%</td>
<td align="right">211</td>
<td align="right">4.22%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

4
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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">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -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">10 August 2020</h4>
<h4 class="date">14 August 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>

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</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">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -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">10 August 2020</h4>
<h4 class="date">14 August 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>

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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">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -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">10 August 2020</h4>
<h4 class="date">14 August 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>

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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">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">10 August 2020</h4>
<h4 class="date">14 August 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>
@ -224,21 +224,21 @@
times = <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">S.aureus</span>, unit = <span class="st">"ms"</span>, signif = <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") 11.0 14 21 15 16 51 10</span>
<span class="co"># as.mo("stau") 170.0 170 190 190 210 240 10</span>
<span class="co"># as.mo("STAU") 160.0 170 180 180 200 210 10</span>
<span class="co"># as.mo("staaur") 11.0 13 19 14 18 48 10</span>
<span class="co"># as.mo("STAAUR") 11.0 13 22 17 37 40 10</span>
<span class="co"># as.mo("S. aureus") 15.0 15 24 17 26 56 10</span>
<span class="co"># as.mo("S aureus") 12.0 13 21 16 23 49 10</span>
<span class="co"># as.mo("Staphylococcus aureus") 9.8 13 21 14 15 65 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 960.0 960 1100 980 1100 1400 10</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 440.0 450 480 470 480 570 10</span>
<span class="co"># as.mo("MRSA") 12.0 14 22 15 17 86 10</span>
<span class="co"># as.mo("VISA") 15.0 18 25 19 40 42 10</span>
<span class="co"># as.mo("VRSA") 14.0 15 30 22 44 69 10</span>
<span class="co"># as.mo(22242419) 130.0 150 160 170 180 190 10</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 9.1 11.0 21 11 13 77 10</span>
<span class="co"># as.mo("stau") 180.0 180.0 190 180 190 210 10</span>
<span class="co"># as.mo("STAU") 170.0 170.0 190 180 210 210 10</span>
<span class="co"># as.mo("staaur") 8.7 12.0 18 12 14 47 10</span>
<span class="co"># as.mo("STAAUR") 9.9 10.0 12 12 12 13 10</span>
<span class="co"># as.mo("S. aureus") 13.0 15.0 29 28 43 47 10</span>
<span class="co"># as.mo("S aureus") 12.0 16.0 25 17 40 52 10</span>
<span class="co"># as.mo("Staphylococcus aureus") 9.1 9.7 14 11 11 44 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 920.0 960.0 990 980 1000 1100 10</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 430.0 440.0 460 460 460 510 10</span>
<span class="co"># as.mo("MRSA") 9.1 11.0 16 12 12 37 10</span>
<span class="co"># as.mo("VISA") 15.0 17.0 23 18 20 47 10</span>
<span class="co"># as.mo("VRSA") 15.0 17.0 27 19 44 50 10</span>
<span class="co"># as.mo(22242419) 140.0 140.0 150 150 160 170 10</span>
</pre></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>
@ -252,12 +252,12 @@
times = <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">M.semesiae</span>, unit = <span class="st">"ms"</span>, signif = <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") 186.900 192.90 204.70 199.10 207.70 251.20</span>
<span class="co"># as.mo("METSEM") 175.500 199.70 215.20 218.20 232.00 240.40</span>
<span class="co"># as.mo("M. semesiae") 11.500 13.29 16.47 13.85 16.84 36.90</span>
<span class="co"># as.mo("M. semesiae") 11.690 11.94 16.81 14.40 15.75 42.76</span>
<span class="co"># as.mo("Methanosarcina semesiae") 9.688 10.28 14.55 11.99 13.72 39.41</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("metsem") 193.600 200.200 209.30 202.800 218.00 238.20</span>
<span class="co"># as.mo("METSEM") 186.500 193.500 208.40 202.600 228.90 244.80</span>
<span class="co"># as.mo("M. semesiae") 12.280 13.090 18.86 14.430 15.48 59.40</span>
<span class="co"># as.mo("M. semesiae") 14.060 14.520 20.98 16.420 17.56 46.18</span>
<span class="co"># as.mo("Methanosarcina semesiae") 8.065 9.203 12.65 9.715 10.65 39.96</span>
<span class="co"># neval</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
@ -299,9 +299,9 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <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) 1840 1870 1950 1940 1980 2140 10</span>
<span class="co"># mo_name(x) 1920 1940 2010 1990 2060 2120 10</span>
</pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.94 seconds. You only lose time on your unique input values.</p>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.99 seconds. You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -315,11 +315,11 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <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 8.17 8.49 9.32 9.32 9.90 10.90 10</span>
<span class="co"># B 10.90 11.80 16.30 13.20 14.70 45.60 10</span>
<span class="co"># C 1.06 1.22 1.32 1.28 1.44 1.57 10</span>
<span class="co"># A 5.90 6.16 6.93 7.24 7.43 7.89 10</span>
<span class="co"># B 11.40 12.00 16.20 13.20 14.20 45.20 10</span>
<span class="co"># C 1.05 1.07 1.18 1.13 1.28 1.40 10</span>
</pre></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>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0011 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"><pre class="downlit">
<span class="kw">run_it</span> <span class="op">&lt;-</span> <span class="fu">microbenchmark</span>(A = <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),
B = <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),
@ -333,14 +333,14 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <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 1.020 1.030 1.11 1.060 1.22 1.33 10</span>
<span class="co"># B 0.982 1.010 1.10 1.040 1.21 1.38 10</span>
<span class="co"># C 0.992 1.020 1.13 1.040 1.24 1.58 10</span>
<span class="co"># D 0.987 1.000 1.07 1.030 1.08 1.29 10</span>
<span class="co"># E 0.978 0.982 1.02 0.999 1.03 1.15 10</span>
<span class="co"># F 0.975 0.992 1.05 1.000 1.03 1.26 10</span>
<span class="co"># G 0.976 0.983 1.02 0.994 1.03 1.22 10</span>
<span class="co"># H 0.977 1.010 1.11 1.090 1.21 1.28 10</span>
<span class="co"># A 0.976 0.993 1.13 1.07 1.29 1.34 10</span>
<span class="co"># B 1.000 1.060 1.13 1.07 1.15 1.40 10</span>
<span class="co"># C 0.927 1.030 1.08 1.06 1.11 1.35 10</span>
<span class="co"># D 0.896 0.983 1.11 1.08 1.27 1.41 10</span>
<span class="co"># E 0.866 1.020 1.10 1.07 1.23 1.37 10</span>
<span class="co"># F 0.967 0.993 1.16 1.05 1.32 1.61 10</span>
<span class="co"># G 0.855 1.020 1.07 1.07 1.17 1.31 10</span>
<span class="co"># H 0.966 1.010 1.12 1.06 1.19 1.36 10</span>
</pre></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>
@ -368,14 +368,14 @@
times = <span class="fl">100</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <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 12.40 14.34 17.88 14.89 15.48 55.22 100</span>
<span class="co"># de 13.17 14.30 17.90 15.84 16.66 56.60 100</span>
<span class="co"># nl 17.14 19.86 24.99 20.78 21.70 64.66 100</span>
<span class="co"># es 13.43 15.29 17.65 15.93 16.59 54.38 100</span>
<span class="co"># it 13.33 14.83 18.35 15.68 16.36 57.61 100</span>
<span class="co"># fr 13.40 15.43 18.66 16.01 16.59 54.35 100</span>
<span class="co"># pt 13.47 15.33 18.93 16.15 16.84 57.28 100</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 13.09 14.02 18.36 14.59 16.22 61.92 100</span>
<span class="co"># de 14.00 14.83 18.06 15.48 16.85 56.01 100</span>
<span class="co"># nl 17.71 18.99 24.79 20.09 22.22 58.50 100</span>
<span class="co"># es 13.99 15.02 20.94 15.88 16.70 141.90 100</span>
<span class="co"># it 13.68 14.97 19.02 15.52 16.72 50.26 100</span>
<span class="co"># fr 13.96 15.05 20.63 15.72 17.14 52.71 100</span>
<span class="co"># pt 14.13 14.86 19.81 15.69 17.46 53.89 100</span>
</pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>

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</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">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

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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">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to predict antimicrobial resistance</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">10 August 2020</h4>
<h4 class="date">14 August 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>

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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">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>Welcome to the AMR package</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">10 August 2020</h4>
<h4 class="date">14 August 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/welcome_to_AMR.Rmd"><code>vignettes/welcome_to_AMR.Rmd</code></a></small>
<div class="hidden name"><code>welcome_to_AMR.Rmd</code></div>
@ -195,7 +195,7 @@
<p><strong>READ ALL VIGNETTES <a href="https://msberends.github.io/AMR/articles/">ON OUR WEBSITE</a></strong></p>
<p><strong>READ ALL VIGNETTES <a href="https://msberends.github.io/AMR/articles/">ON OUR WEBSITE</a>.</strong></p>
<div id="welcome-to-the-amr-package" class="section level1">
<h1 class="hasAnchor">
<a href="#welcome-to-the-amr-package" class="anchor"></a>Welcome to the AMR package</h1>