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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">1.3.0.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
</span>
</div>
@ -75,6 +75,13 @@
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
@ -186,7 +193,7 @@
<h1 data-toc-skip>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">14 August 2020</h4>
<h4 class="date">21 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 +202,7 @@
<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 14 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 21 August 2020.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -226,21 +233,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2020-08-14</td>
<td align="center">2020-08-21</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">2020-08-14</td>
<td align="center">2020-08-21</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">2020-08-14</td>
<td align="center">2020-08-21</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -354,71 +361,71 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-03-16</td>
<td align="center">2011-03-20</td>
<td align="center">W2</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-12-03</td>
<td align="center">X9</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">Klebsiella pneumoniae</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">F</td>
</tr>
<tr class="even">
<td align="center">2013-10-27</td>
<td align="center">G3</td>
<td align="center">Hospital A</td>
<tr class="odd">
<td align="center">2012-11-11</td>
<td align="center">A5</td>
<td align="center">Hospital D</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">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2014-12-09</td>
<td align="center">F7</td>
<tr class="even">
<td align="center">2012-09-03</td>
<td align="center">Y3</td>
<td align="center">Hospital C</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">M</td>
</tr>
<tr class="even">
<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">R</td>
<td align="center">R</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">2012-11-19</td>
<td align="center">I3</td>
<td align="center">Hospital C</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">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-06-05</td>
<td align="center">Q7</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">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">M</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -452,16 +459,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</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>
<td align="right">10,358</td>
<td align="right">51.79%</td>
<td align="right">10,358</td>
<td align="right">51.79%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,724</td>
<td align="right">48.62%</td>
<td align="right">9,642</td>
<td align="right">48.21%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -511,7 +518,7 @@ 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 28.4% 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>
<p>So only 28.3% 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 +532,7 @@ 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 N8, 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 C8, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -541,10 +548,10 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-05-17</td>
<td align="center">N8</td>
<td align="center">2010-01-13</td>
<td align="center">C8</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>
@ -552,8 +559,8 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-07-03</td>
<td align="center">N8</td>
<td align="center">2010-02-19</td>
<td align="center">C8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -563,52 +570,52 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-07-31</td>
<td align="center">N8</td>
<td align="center">2010-03-12</td>
<td align="center">C8</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">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">4</td>
<td align="center">2010-09-13</td>
<td align="center">N8</td>
<td align="center">2010-03-25</td>
<td align="center">C8</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">S</td>
<td align="center">R</td>
<td align="center">FALSE</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">2010-04-28</td>
<td align="center">C8</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">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-10-16</td>
<td align="center">N8</td>
<td align="center">2010-07-22</td>
<td align="center">C8</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="odd">
<td align="center">7</td>
<td align="center">2010-10-17</td>
<td align="center">N8</td>
<td align="center">2010-12-05</td>
<td align="center">C8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -618,30 +625,30 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-10-24</td>
<td align="center">N8</td>
<td align="center">2011-01-18</td>
<td align="center">C8</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">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-12-27</td>
<td align="center">N8</td>
<td align="center">2011-05-24</td>
<td align="center">C8</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">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-02-25</td>
<td align="center">N8</td>
<td align="center">2011-06-24</td>
<td align="center">C8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -651,7 +658,7 @@ Longest: 1</p>
</tr>
</tbody>
</table>
<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>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>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>
@ -679,10 +686,10 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-05-17</td>
<td align="center">N8</td>
<td align="center">2010-01-13</td>
<td align="center">C8</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>
@ -691,59 +698,59 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-07-03</td>
<td align="center">N8</td>
<td align="center">2010-02-19</td>
<td align="center">C8</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>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-07-31</td>
<td align="center">N8</td>
<td align="center">2010-03-12</td>
<td align="center">C8</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">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">4</td>
<td align="center">2010-09-13</td>
<td align="center">N8</td>
<td align="center">2010-03-25</td>
<td align="center">C8</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">S</td>
<td align="center">R</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">2010-04-28</td>
<td align="center">C8</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">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">2010-10-16</td>
<td align="center">N8</td>
<td align="center">2010-07-22</td>
<td align="center">C8</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>
@ -751,61 +758,61 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-10-17</td>
<td align="center">N8</td>
<td align="center">2010-12-05</td>
<td align="center">C8</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>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-10-24</td>
<td align="center">N8</td>
<td align="center">2011-01-18</td>
<td align="center">C8</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">FALSE</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-12-27</td>
<td align="center">N8</td>
<td align="center">2011-05-24</td>
<td align="center">C8</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">I</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">10</td>
<td align="center">2011-02-25</td>
<td align="center">N8</td>
<td align="center">2011-06-24</td>
<td align="center">C8</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>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<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>Instead of 2, now 8 isolates are flagged. In total, 78.4% of all isolates are marked ‘first weighted’ - 50.1% 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 15,607 isolates for analysis.</p>
<p>So we end up with 15,686 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>
@ -851,76 +858,12 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="left">1</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">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="left">2</td>
<td align="center">2013-10-27</td>
<td align="center">G3</td>
<td align="center">Hospital A</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">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="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">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">2011-03-20</td>
<td align="center">W2</td>
<td align="center">Hospital A</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">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
@ -930,21 +873,85 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2014-08-04</td>
<td align="center">O9</td>
<td align="left">3</td>
<td align="center">2012-11-11</td>
<td align="center">A5</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">F</td>
<td align="center">S</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="odd">
<td align="left">4</td>
<td align="center">2012-09-03</td>
<td align="center">Y3</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">R</td>
<td align="center">R</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="left">5</td>
<td align="center">2012-11-19</td>
<td align="center">I3</td>
<td align="center">Hospital C</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">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="odd">
<td align="left">8</td>
<td align="center">2013-11-06</td>
<td align="center">B1</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">M</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">9</td>
<td align="center">2017-01-21</td>
<td align="center">U3</td>
<td align="center">Hospital D</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>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -968,8 +975,8 @@ Longest: 1</p>
</pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 15,607<br>
Available: 15,607 (100%, NA: 0 = 0%)<br>
Length: 15,686<br>
Available: 15,686 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -986,33 +993,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</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>
<td align="right">7,774</td>
<td align="right">49.56%</td>
<td align="right">7,774</td>
<td align="right">49.56%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</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>
<td align="right">3,952</td>
<td align="right">25.19%</td>
<td align="right">11,726</td>
<td align="right">74.75%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</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>
<td align="right">2,367</td>
<td align="right">15.09%</td>
<td align="right">14,093</td>
<td align="right">89.84%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,535</td>
<td align="right">9.84%</td>
<td align="right">15,607</td>
<td align="right">1,593</td>
<td align="right">10.16%</td>
<td align="right">15,686</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -1041,50 +1048,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">3854</td>
<td align="center">265</td>
<td align="center">3717</td>
<td align="center">7836</td>
<td align="center">3685</td>
<td align="center">257</td>
<td align="center">3832</td>
<td align="center">7774</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">6244</td>
<td align="center">287</td>
<td align="center">1305</td>
<td align="center">7836</td>
<td align="center">6104</td>
<td align="center">275</td>
<td align="center">1395</td>
<td align="center">7774</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">5880</td>
<td align="center">5979</td>
<td align="center">0</td>
<td align="center">1956</td>
<td align="center">7836</td>
<td align="center">1795</td>
<td align="center">7774</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">7050</td>
<td align="center">6986</td>
<td align="center">0</td>
<td align="center">786</td>
<td align="center">7836</td>
<td align="center">788</td>
<td align="center">7774</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">1535</td>
<td align="center">1535</td>
<td align="center">1593</td>
<td align="center">1593</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">1199</td>
<td align="center">50</td>
<td align="center">286</td>
<td align="center">1535</td>
<td align="center">1269</td>
<td align="center">57</td>
<td align="center">267</td>
<td align="center">1593</td>
</tr>
</tbody>
</table>
@ -1109,34 +1116,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">5880</td>
<td align="center">5979</td>
<td align="center">0</td>
<td align="center">1956</td>
<td align="center">7836</td>
<td align="center">1795</td>
<td align="center">7774</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">CIP</td>
<td align="center">1166</td>
<td align="center">1213</td>
<td align="center">0</td>
<td align="center">369</td>
<td align="center">1535</td>
<td align="center">380</td>
<td align="center">1593</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">CIP</td>
<td align="center">2942</td>
<td align="center">3003</td>
<td align="center">0</td>
<td align="center">957</td>
<td align="center">3899</td>
<td align="center">949</td>
<td align="center">3952</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">CIP</td>
<td align="center">1799</td>
<td align="center">1820</td>
<td align="center">0</td>
<td align="center">538</td>
<td align="center">2337</td>
<td align="center">547</td>
<td align="center">2367</td>
</tr>
</tbody>
</table>
@ -1149,7 +1156,7 @@ 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] 0.5233549</span>
<span class="co"># [1] 0.5350631</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">
@ -1166,19 +1173,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5238399</td>
<td align="center">0.5338783</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5201802</td>
<td align="center">0.5368875</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5259455</td>
<td align="center">0.5367068</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5264182</td>
<td align="center">0.5322422</td>
</tr>
</tbody>
</table>
@ -1199,23 +1206,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5238399</td>
<td align="center">4698</td>
<td align="center">0.5338783</td>
<td align="center">4649</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5201802</td>
<td align="center">5550</td>
<td align="center">0.5368875</td>
<td align="center">5571</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5259455</td>
<td align="center">2274</td>
<td align="center">0.5367068</td>
<td align="center">2411</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5264182</td>
<td align="center">3085</td>
<td align="center">0.5322422</td>
<td align="center">3055</td>
</tr>
</tbody>
</table>
@ -1238,27 +1245,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.8334609</td>
<td align="center">0.8996937</td>
<td align="center">0.9857070</td>
<td align="center">0.8205557</td>
<td align="center">0.8986365</td>
<td align="center">0.9855930</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8136808</td>
<td align="center">0.8983713</td>
<td align="center">0.9798046</td>
<td align="center">0.8323917</td>
<td align="center">0.8901444</td>
<td align="center">0.9855618</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8304694</td>
<td align="center">0.9253655</td>
<td align="center">0.9894845</td>
<td align="center">0.8276822</td>
<td align="center">0.9210526</td>
<td align="center">0.9868421</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5537013</td>
<td align="center">0.5504858</td>
<td align="center">0.0000000</td>
<td align="center">0.5537013</td>
<td align="center">0.5504858</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">1.3.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
</span>
</div>

52
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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">1.3.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
</span>
</div>
@ -320,17 +320,17 @@ 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 S S S S S R</span>
<span class="co"># 2 S R S R S S</span>
<span class="co"># 3 R S S S I R</span>
<span class="co"># 4 R S R S R R</span>
<span class="co"># 5 R S S R S R</span>
<span class="co"># 6 S R I S R S</span>
<span class="co"># 1 I S S S S R</span>
<span class="co"># 2 S S S R R I</span>
<span class="co"># 3 R S S R S I</span>
<span class="co"># 4 R S S R S S</span>
<span class="co"># 5 S R I R I R</span>
<span class="co"># 6 R R S R R R</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 S</span>
<span class="co"># 2 R</span>
<span class="co"># 3 R</span>
<span class="co"># 4 S</span>
<span class="co"># 4 I</span>
<span class="co"># 5 R</span>
<span class="co"># 6 R</span>
</pre></div>
@ -368,40 +368,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3203</td>
<td align="right">64.06%</td>
<td align="right">3203</td>
<td align="right">64.06%</td>
<td align="right">3233</td>
<td align="right">64.66%</td>
<td align="right">3233</td>
<td align="right">64.66%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">682</td>
<td align="right">13.64%</td>
<td align="right">3885</td>
<td align="right">77.70%</td>
<td align="right">698</td>
<td align="right">13.96%</td>
<td align="right">3931</td>
<td align="right">78.62%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">627</td>
<td align="right">12.54%</td>
<td align="right">4512</td>
<td align="right">90.24%</td>
<td align="right">556</td>
<td align="right">11.12%</td>
<td align="right">4487</td>
<td align="right">89.74%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">268</td>
<td align="right">5.36%</td>
<td align="right">4780</td>
<td align="right">95.60%</td>
<td align="right">300</td>
<td align="right">6.00%</td>
<td align="right">4787</td>
<td align="right">95.74%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">220</td>
<td align="right">4.40%</td>
<td align="right">213</td>
<td align="right">4.26%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

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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">1.3.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</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">1.3.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
</span>
</div>
@ -193,7 +193,7 @@
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">17 August 2020</h4>
<h4 class="date">21 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">1.3.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
</span>
</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">1.3.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
</span>
</div>
@ -229,21 +229,21 @@
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") 8.8 10.0 24 12 38 57 10</span>
<span class="co"># as.mo("stau") 170.0 170.0 180 170 190 210 10</span>
<span class="co"># as.mo("STAU") 160.0 170.0 180 170 200 220 10</span>
<span class="co"># as.mo("staaur") 9.6 10.0 13 11 12 36 10</span>
<span class="co"># as.mo("STAAUR") 10.0 10.0 25 12 34 80 10</span>
<span class="co"># as.mo("S. aureus") 14.0 15.0 21 15 18 47 10</span>
<span class="co"># as.mo("S aureus") 12.0 15.0 21 16 18 45 10</span>
<span class="co"># as.mo("Staphylococcus aureus") 8.9 9.4 15 11 12 37 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 900.0 920.0 940 940 960 1000 10</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 410.0 420.0 450 450 470 520 10</span>
<span class="co"># as.mo("MRSA") 8.8 10.0 16 11 12 38 10</span>
<span class="co"># as.mo("VISA") 13.0 16.0 27 19 41 47 10</span>
<span class="co"># as.mo("VRSA") 13.0 16.0 22 18 19 42 10</span>
<span class="co"># as.mo(22242419) 140.0 140.0 150 140 160 170 10</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 8.7 9.3 13 9.8 12 40 10</span>
<span class="co"># as.mo("stau") 160.0 180.0 200 200.0 210 220 10</span>
<span class="co"># as.mo("STAU") 160.0 180.0 190 190.0 200 210 10</span>
<span class="co"># as.mo("staaur") 9.8 12.0 15 12.0 12 42 10</span>
<span class="co"># as.mo("STAAUR") 8.4 8.7 13 10.0 12 37 10</span>
<span class="co"># as.mo("S. aureus") 13.0 16.0 38 18.0 45 150 10</span>
<span class="co"># as.mo("S aureus") 12.0 17.0 21 17.0 18 48 10</span>
<span class="co"># as.mo("Staphylococcus aureus") 7.1 8.7 12 9.7 11 38 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 880.0 920.0 930 930.0 960 980 10</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 400.0 430.0 450 440.0 460 500 10</span>
<span class="co"># as.mo("MRSA") 8.6 12.0 20 12.0 37 42 10</span>
<span class="co"># as.mo("VISA") 15.0 17.0 20 18.0 19 40 10</span>
<span class="co"># as.mo("VRSA") 13.0 14.0 19 17.0 19 46 10</span>
<span class="co"># as.mo(22242419) 140.0 140.0 160 150.0 170 210 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>
@ -278,9 +278,9 @@
<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) 1810 1850 1980 1940 2130 2230 10</span>
<span class="co"># mo_name(x) 1750 1790 1830 1810 1850 1950 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 1.81 seconds. You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -293,12 +293,12 @@
times = <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">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 5.080 5.220 5.81 5.66 6.46 7.16 10</span>
<span class="co"># B 10.000 10.200 14.40 10.60 11.30 49.00 10</span>
<span class="co"># C 0.862 0.875 1.04 1.05 1.14 1.40 10</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 6.08 6.23 10.40 6.56 7.03 44.90 10</span>
<span class="co"># B 11.70 12.00 12.70 12.70 13.60 13.90 10</span>
<span class="co"># C 1.05 1.11 1.19 1.13 1.25 1.55 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 0.001 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="cb5"><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>),
@ -311,15 +311,15 @@
times = <span class="fl">10</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">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 0.869 0.889 0.951 0.904 1.010 1.19 10</span>
<span class="co"># B 0.837 0.873 0.977 0.937 1.010 1.36 10</span>
<span class="co"># C 0.869 0.874 1.020 0.921 1.130 1.40 10</span>
<span class="co"># D 0.829 0.858 0.898 0.862 0.873 1.21 10</span>
<span class="co"># E 0.862 0.870 0.983 0.918 1.050 1.36 10</span>
<span class="co"># F 0.841 0.850 0.915 0.867 0.907 1.24 10</span>
<span class="co"># G 0.842 0.851 0.940 0.898 1.000 1.16 10</span>
<span class="co"># H 0.854 0.864 1.030 0.920 1.170 1.60 10</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 0.886 1.010 1.040 1.020 1.06 1.25 10</span>
<span class="co"># B 1.010 1.030 1.150 1.040 1.27 1.64 10</span>
<span class="co"># C 0.885 1.030 1.110 1.060 1.26 1.29 10</span>
<span class="co"># D 0.812 0.822 1.000 1.000 1.05 1.43 10</span>
<span class="co"># E 0.827 0.989 1.070 1.030 1.23 1.35 10</span>
<span class="co"># F 0.887 0.994 1.070 1.040 1.08 1.35 10</span>
<span class="co"># G 0.812 0.839 0.969 0.916 1.04 1.32 10</span>
<span class="co"># H 0.815 1.020 1.090 1.050 1.30 1.37 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>
@ -347,14 +347,14 @@
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 10.72 11.54 15.34 12.76 13.82 44.53 100</span>
<span class="co"># de 11.47 12.77 17.24 13.60 14.78 55.48 100</span>
<span class="co"># nl 14.58 15.91 19.06 16.96 18.46 46.24 100</span>
<span class="co"># es 11.24 11.96 16.86 13.17 14.70 50.05 100</span>
<span class="co"># it 11.35 12.42 17.79 13.52 16.28 50.31 100</span>
<span class="co"># fr 11.41 12.29 17.08 13.43 15.44 53.91 100</span>
<span class="co"># pt 11.34 12.06 16.23 13.25 14.80 51.96 100</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 12.88 13.52 16.72 14.63 16.00 55.03 100</span>
<span class="co"># de 13.79 14.51 18.36 15.11 16.67 136.90 100</span>
<span class="co"># nl 17.72 18.59 22.30 20.15 21.87 54.69 100</span>
<span class="co"># es 13.78 14.38 19.16 15.35 16.86 49.96 100</span>
<span class="co"># it 13.83 14.40 18.57 15.24 16.32 58.12 100</span>
<span class="co"># fr 13.72 14.47 19.67 15.21 17.46 52.22 100</span>
<span class="co"># pt 13.73 14.43 17.76 15.10 16.85 51.69 100</span>
</pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</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">1.3.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
</span>
</div>
@ -200,15 +200,14 @@
<p>This package contains a lot of reference data sets that are all reliable, up-to-date and free to download. You can even use them outside of R, for example to teach your laboratory information system (LIS) about intrinsic resistance!</p>
<p>We included them in our <code>AMR</code> package, but also automatically ‘mirror’ them to our public repository in different software formats. On this page, we explain how to download them and how the structure of the data sets look like. The tab separated files <strong>allow for machine reading taxonomic data and EUCAST and CLSI interpretation guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. We also offer all data sets in formats for R, SPSS, SAS, Stata and Excel.</p>
<p><em>Note: Years and dates of updates mentioned on this page, are from on <code>AMR</code> package version 1.3.0.9005, online released on 17 August 2020. <strong>If you are reading this page from within R, please <a href="https://msberends.github.io/AMR/articles/datasets.html">visit our website</a> for the latest update.</strong></em></p>
<p>All reference data (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are reliable, up-to-date and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply tab separated files that are machine-readable and suitable for input in any software program, such as laboratory information systems.</p>
<p>On this page, we explain how to download them and how the structure of the data sets look like. If you are reading this page from within R, please <a href="https://msberends.github.io/AMR/articles/datasets.html">visit our website</a>, which is automatically updated with every code change.</p>
<div id="microorganisms-currently-accepted-names" class="section level2">
<h2 class="hasAnchor">
<a href="#microorganisms-currently-accepted-names" class="anchor"></a>Microorganisms (currently accepted names)</h2>
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 28 July 2020 20:52:40 CEST.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds">R file (.rds)</a>, 2.7 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.xlsx">Excel workbook (.xlsx)</a>, 6.1 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sav">SPSS file (.sav)</a>, 28.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sav">Stata file (.dta)</a>, 28.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.dta">SAS file (.sas)</a>, 25.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.txt">Tab separated file (.txt)</a>, 13.3 MB.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds">R file (.rds)</a>, 2.7 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.xlsx">Excel workbook (.xlsx)</a>, 6.1 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sav">SPSS file (.sav)</a>, 28.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.dta">Stata file (.dta)</a>, 25.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sas">SAS file (.sas)</a>, 26.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.txt">tab separated file (.txt)</a>, 13.3 MB.</p>
<div id="source" class="section level3">
<h3 class="hasAnchor">
<a href="#source" class="anchor"></a>Source</h3>
@ -413,7 +412,7 @@
<a href="#microorganisms-previously-accepted-names" class="anchor"></a>Microorganisms (previously accepted names)</h2>
<p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 28 May 2020 11:17:56 CEST.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.rds">R file (.rds)</a>, 0.3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.xlsx">Excel workbook (.xlsx)</a>, 0.4 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sav">SPSS file (.sav)</a>, 1.9 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sav">Stata file (.dta)</a>, 1.9 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.dta">SAS file (.sas)</a>, 1.8 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.txt">Tab separated file (.txt)</a>, 0.8 MB.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.rds">R file (.rds)</a>, 0.3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.xlsx">Excel workbook (.xlsx)</a>, 0.4 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sav">SPSS file (.sav)</a>, 1.9 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.dta">Stata file (.dta)</a>, 1.8 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sas">SAS file (.sas)</a>, 1.9 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.txt">tab separated file (.txt)</a>, 0.8 MB.</p>
<div id="source-1" class="section level3">
<h3 class="hasAnchor">
<a href="#source-1" class="anchor"></a>Source</h3>
@ -466,7 +465,7 @@
<a href="#antibiotic-agents" class="anchor"></a>Antibiotic agents</h2>
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 31 July 2020 12:12:13 CEST.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds">R file (.rds)</a>, 37 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.xlsx">Excel workbook (.xlsx)</a>, 65 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sav">SPSS file (.sav)</a>, 1.3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sav">Stata file (.dta)</a>, 1.3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.dta">SAS file (.sas)</a>, 0.3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.txt">Tab separated file (.txt)</a>, 0.1 MB.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds">R file (.rds)</a>, 37 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.xlsx">Excel workbook (.xlsx)</a>, 65 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sav">SPSS file (.sav)</a>, 1.3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.dta">Stata file (.dta)</a>, 0.3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sas">SAS file (.sas)</a>, 1.8 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.txt">tab separated file (.txt)</a>, 0.1 MB.</p>
<div id="source-2" class="section level3">
<h3 class="hasAnchor">
<a href="#source-2" class="anchor"></a>Source</h3>
@ -622,7 +621,7 @@
<a href="#antiviral-agents" class="anchor"></a>Antiviral agents</h2>
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 23 November 2019 19:03:43 CET.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.rds">R file (.rds)</a>, 5 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.xlsx">Excel workbook (.xlsx)</a>, 14 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sav">SPSS file (.sav)</a>, 68 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sav">Stata file (.dta)</a>, 68 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.dta">SAS file (.sas)</a>, 67 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.txt">Tab separated file (.txt)</a>, 16 kB.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.rds">R file (.rds)</a>, 5 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.xlsx">Excel workbook (.xlsx)</a>, 14 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sav">SPSS file (.sav)</a>, 68 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.dta">Stata file (.dta)</a>, 67 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sas">SAS file (.sas)</a>, 80 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.txt">tab separated file (.txt)</a>, 16 kB.</p>
<div id="source-3" class="section level3">
<h3 class="hasAnchor">
<a href="#source-3" class="anchor"></a>Source</h3>
@ -737,7 +736,7 @@
<a href="#intrinsic-bacterial-resistance" class="anchor"></a>Intrinsic bacterial resistance</h2>
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 14 August 2020 14:18:20 CEST.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.rds">R file (.rds)</a>, 97 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.xlsx">Excel workbook (.xlsx)</a>, 0.5 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sav">SPSS file (.sav)</a>, 4.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sav">Stata file (.dta)</a>, 4.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.dta">SAS file (.sas)</a>, 3.7 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.txt">Tab separated file (.txt)</a>, 1.8 MB.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.rds">R file (.rds)</a>, 97 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.xlsx">Excel workbook (.xlsx)</a>, 0.5 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sav">SPSS file (.sav)</a>, 4.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.dta">Stata file (.dta)</a>, 3.7 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sas">SAS file (.sas)</a>, 3.8 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.txt">tab separated file (.txt)</a>, 1.8 MB.</p>
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<a href="#interpretation-from-mic-values-disk-diameters-to-rsi" class="anchor"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 July 2020 13:12:34 CEST.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds">R file (.rds)</a>, 55 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.xlsx">Excel workbook (.xlsx)</a>, 0.6 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sav">SPSS file (.sav)</a>, 3.4 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sav">Stata file (.dta)</a>, 3.4 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.dta">SAS file (.sas)</a>, 3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.txt">Tab separated file (.txt)</a>, 1.5 MB.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds">R file (.rds)</a>, 55 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.xlsx">Excel workbook (.xlsx)</a>, 0.6 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sav">SPSS file (.sav)</a>, 3.4 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.dta">Stata file (.dta)</a>, 3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sas">SAS file (.sas)</a>, 3.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.txt">tab separated file (.txt)</a>, 1.5 MB.</p>
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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">1.3.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
</span>
</div>

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<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">1.3.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
</span>
</div>

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<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">1.3.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
</span>
</div>