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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">1.4.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9032</span>
</span>
</div>
@ -193,7 +193,7 @@
<h1 data-toc-skip>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">15 October 2020</h4>
<h4 class="date">08 December 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>
@ -202,7 +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 15 October 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 08 December 2020.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -233,21 +233,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2020-10-15</td>
<td align="center">2020-12-08</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">2020-10-15</td>
<td align="center">2020-12-08</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">2020-10-15</td>
<td align="center">2020-12-08</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -352,70 +352,70 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-04-04</td>
<td align="center">A3</td>
<td align="center">2015-10-08</td>
<td align="center">Y10</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-04-05</td>
<td align="center">O10</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2012-07-06</td>
<td align="center">H9</td>
<td align="center">Hospital A</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">2016-09-05</td>
<td align="center">U3</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</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">2011-10-13</td>
<td align="center">I4</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">M</td>
</tr>
<tr class="odd">
<td align="center">2015-11-20</td>
<td align="center">J6</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">M</td>
</tr>
<tr class="even">
<td align="center">2017-02-04</td>
<td align="center">X3</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</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="odd">
<td align="center">2010-10-17</td>
<td align="center">N9</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2017-05-23</td>
<td align="center">S5</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-06-04</td>
<td align="center">X3</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">2013-11-30</td>
<td align="center">J2</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</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">F</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
@ -449,16 +449,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,412</td>
<td align="right">52.06%</td>
<td align="right">10,412</td>
<td align="right">52.06%</td>
<td align="right">10,384</td>
<td align="right">51.92%</td>
<td align="right">10,384</td>
<td align="right">51.92%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,588</td>
<td align="right">47.94%</td>
<td align="right">9,616</td>
<td align="right">48.08%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -501,10 +501,10 @@ Longest: 1</p>
<div class="sourceCode" id="cb15"><pre class="downlit">
<span class="va">data</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>first <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span><span class="op">)</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></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>
<span class="co"># NOTE: Using column 'bacteria' as input for `col_mo`.</span>
<span class="co"># NOTE: Using column 'date' as input for `col_date`.</span>
<span class="co"># NOTE: Using column 'patient_id' as input for `col_patient_id`.</span></pre></div>
<p>So only 28.6% 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="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></pre></div>
@ -516,7 +516,7 @@ 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 Z7, 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 A3, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -532,21 +532,21 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-03-27</td>
<td align="center">Z7</td>
<td align="center">2010-01-04</td>
<td align="center">A3</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">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-06-10</td>
<td align="center">Z7</td>
<td align="center">2010-01-05</td>
<td align="center">A3</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>
@ -554,30 +554,30 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-06-25</td>
<td align="center">Z7</td>
<td align="center">2010-02-07</td>
<td align="center">A3</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>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-11-05</td>
<td align="center">Z7</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">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-06-17</td>
<td align="center">A3</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>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-11-22</td>
<td align="center">Z7</td>
<td align="center">2010-07-23</td>
<td align="center">A3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -587,8 +587,8 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-02-06</td>
<td align="center">Z7</td>
<td align="center">2010-11-16</td>
<td align="center">A3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -598,45 +598,45 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-03-19</td>
<td align="center">Z7</td>
<td align="center">2010-12-05</td>
<td align="center">A3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</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">8</td>
<td align="center">2011-07-19</td>
<td align="center">Z7</td>
<td align="center">2011-01-17</td>
<td align="center">A3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-08-15</td>
<td align="center">Z7</td>
<td align="center">2011-01-26</td>
<td align="center">A3</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">R</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">2011-09-22</td>
<td align="center">Z7</td>
<td align="center">2011-02-12</td>
<td align="center">A3</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">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
@ -648,11 +648,12 @@ Longest: 1</p>
<span class="va">data</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>keyab <span class="op">=</span> <span class="fu"><a href="../reference/key_antibiotics.html">key_antibiotics</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>first_weighted <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span><span class="op">)</span>
<span class="co"># NOTE: Using column `bacteria` as input for `col_mo`.</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>
<span class="co"># NOTE: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.</span></pre></div>
<span class="co"># NOTE: Using column 'bacteria' as input for `col_mo`.</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>
<span class="co"># NOTE: Using column 'keyab' as input for `col_keyantibiotics`. Use</span>
<span class="co"># col_keyantibiotics = FALSE to prevent this.</span></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -669,22 +670,22 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-03-27</td>
<td align="center">Z7</td>
<td align="center">2010-01-04</td>
<td align="center">A3</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">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-06-10</td>
<td align="center">Z7</td>
<td align="center">2010-01-05</td>
<td align="center">A3</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>
@ -693,32 +694,20 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-06-25</td>
<td align="center">Z7</td>
<td align="center">2010-02-07</td>
<td align="center">A3</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">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-11-05</td>
<td align="center">Z7</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">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">2010-11-22</td>
<td align="center">Z7</td>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-06-17</td>
<td align="center">A3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -727,10 +716,22 @@ Longest: 1</p>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-07-23</td>
<td align="center">A3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-02-06</td>
<td align="center">Z7</td>
<td align="center">2010-11-16</td>
<td align="center">A3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -741,60 +742,60 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-03-19</td>
<td align="center">Z7</td>
<td align="center">2010-12-05</td>
<td align="center">A3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</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>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-07-19</td>
<td align="center">Z7</td>
<td align="center">2011-01-17</td>
<td align="center">A3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-08-15</td>
<td align="center">Z7</td>
<td align="center">2011-01-26</td>
<td align="center">A3</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">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="even">
<td align="center">10</td>
<td align="center">2011-09-22</td>
<td align="center">Z7</td>
<td align="center">2011-02-12</td>
<td align="center">A3</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">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Instead of 2, now 8 isolates are flagged. In total, 78.6% of all isolates are marked ‘first weighted’ - 50.2% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>Instead of 2, now 7 isolates are flagged. In total, 79.1% of all isolates are marked ‘first weighted’ - 50.6% 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="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span><span class="op">(</span><span class="op">)</span></pre></div>
<p>So we end up with 15,713 isolates for analysis.</p>
<p>So we end up with 15,822 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb20"><pre class="downlit">
<span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data_1st</span> <span class="op">%&gt;%</span>
@ -837,47 +838,15 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2011-04-04</td>
<td align="center">A3</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</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="even">
<td align="left">2</td>
<td align="center">2011-10-13</td>
<td align="center">I4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">3</td>
<td align="center">2015-11-20</td>
<td align="center">J6</td>
<td align="center">2012-07-06</td>
<td align="center">H9</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
@ -886,45 +855,77 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">2017-02-04</td>
<td align="center">X3</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">2010-10-17</td>
<td align="center">N9</td>
<td align="center">Hospital D</td>
<td align="center">2016-09-05</td>
<td align="center">U3</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2011-06-10</td>
<td align="center">P2</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<tr class="odd">
<td align="left">5</td>
<td align="center">2017-05-23</td>
<td align="center">S5</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">I</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="even">
<td align="left">8</td>
<td align="center">2016-07-20</td>
<td align="center">D2</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</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="odd">
<td align="left">9</td>
<td align="center">2010-09-20</td>
<td align="center">H10</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</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="even">
<td align="left">10</td>
<td align="center">2012-03-30</td>
<td align="center">Y4</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</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>
<td align="center">Gram-positive</td>
@ -953,8 +954,8 @@ Longest: 1</p>
<span class="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 15,713<br>
Available: 15,713 (100%, NA: 0 = 0%)<br>
Length: 15,822<br>
Available: 15,822 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -971,33 +972,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,867</td>
<td align="right">50.07%</td>
<td align="right">7,867</td>
<td align="right">50.07%</td>
<td align="right">7,935</td>
<td align="right">50.15%</td>
<td align="right">7,935</td>
<td align="right">50.15%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,842</td>
<td align="right">24.45%</td>
<td align="right">11,709</td>
<td align="right">74.52%</td>
<td align="right">3,933</td>
<td align="right">24.86%</td>
<td align="right">11,868</td>
<td align="right">75.01%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,346</td>
<td align="right">14.93%</td>
<td align="right">14,055</td>
<td align="right">89.45%</td>
<td align="right">2,376</td>
<td align="right">15.02%</td>
<td align="right">14,244</td>
<td align="right">90.03%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,658</td>
<td align="right">10.55%</td>
<td align="right">15,713</td>
<td align="right">1,578</td>
<td align="right">9.97%</td>
<td align="right">15,822</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -1011,7 +1012,7 @@ Longest: 24</p>
<span class="va">data_1st</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="op">)</span> <span class="co"># show first 6 rows</span></pre></div>
<pre><code># NOTE: Using column `bacteria` as input for `col_mo`.</code></pre>
<pre><code># NOTE: Using column 'bacteria' as input for `col_mo`.</code></pre>
<table class="table">
<thead><tr class="header">
<th align="center">mo</th>
@ -1025,50 +1026,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">3806</td>
<td align="center">262</td>
<td align="center">3799</td>
<td align="center">7867</td>
<td align="center">3811</td>
<td align="center">259</td>
<td align="center">3865</td>
<td align="center">7935</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">6223</td>
<td align="center">321</td>
<td align="center">1323</td>
<td align="center">7867</td>
<td align="center">6278</td>
<td align="center">298</td>
<td align="center">1359</td>
<td align="center">7935</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">6006</td>
<td align="center">6070</td>
<td align="center">0</td>
<td align="center">1861</td>
<td align="center">7867</td>
<td align="center">1865</td>
<td align="center">7935</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">7072</td>
<td align="center">7138</td>
<td align="center">0</td>
<td align="center">795</td>
<td align="center">7867</td>
<td align="center">797</td>
<td align="center">7935</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">1658</td>
<td align="center">1658</td>
<td align="center">1578</td>
<td align="center">1578</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">1298</td>
<td align="center">56</td>
<td align="center">304</td>
<td align="center">1658</td>
<td align="center">1248</td>
<td align="center">57</td>
<td align="center">273</td>
<td align="center">1578</td>
</tr>
</tbody>
</table>
@ -1077,8 +1078,8 @@ Longest: 24</p>
<span class="va">data_1st</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">fluoroquinolones</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span><span class="op">(</span><span class="op">)</span></pre></div>
<pre><code># Selecting fluoroquinolones: `CIP` (ciprofloxacin)
# NOTE: Using column `bacteria` as input for `col_mo`.</code></pre>
<pre><code># Selecting fluoroquinolones: 'CIP' (ciprofloxacin)
# NOTE: Using column 'bacteria' as input for `col_mo`.</code></pre>
<table class="table">
<thead><tr class="header">
<th align="center">mo</th>
@ -1092,34 +1093,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">6006</td>
<td align="center">6070</td>
<td align="center">0</td>
<td align="center">1861</td>
<td align="center">7867</td>
<td align="center">1865</td>
<td align="center">7935</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">CIP</td>
<td align="center">1257</td>
<td align="center">1219</td>
<td align="center">0</td>
<td align="center">401</td>
<td align="center">1658</td>
<td align="center">359</td>
<td align="center">1578</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">CIP</td>
<td align="center">2963</td>
<td align="center">3015</td>
<td align="center">0</td>
<td align="center">879</td>
<td align="center">3842</td>
<td align="center">918</td>
<td align="center">3933</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">CIP</td>
<td align="center">1785</td>
<td align="center">1798</td>
<td align="center">0</td>
<td align="center">561</td>
<td align="center">2346</td>
<td align="center">578</td>
<td align="center">2376</td>
</tr>
</tbody>
</table>
@ -1132,7 +1133,7 @@ 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="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>
<span class="co"># [1] 0.5382168</span></pre></div>
<span class="co"># [1] 0.535457</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">
<span class="va">data_1st</span> <span class="op">%&gt;%</span>
@ -1147,19 +1148,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5459117</td>
<td align="center">0.5309604</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5280457</td>
<td align="center">0.5345539</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5268007</td>
<td align="center">0.5403226</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5537583</td>
<td align="center">0.5401970</td>
</tr>
</tbody>
</table>
@ -1179,23 +1180,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5459117</td>
<td align="center">4574</td>
<td align="center">0.5309604</td>
<td align="center">4748</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5280457</td>
<td align="center">5598</td>
<td align="center">0.5345539</td>
<td align="center">5571</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5268007</td>
<td align="center">2388</td>
<td align="center">0.5403226</td>
<td align="center">2356</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5537583</td>
<td align="center">3153</td>
<td align="center">0.5401970</td>
<td align="center">3147</td>
</tr>
</tbody>
</table>
@ -1217,27 +1218,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.8318292</td>
<td align="center">0.8989450</td>
<td align="center">0.9853820</td>
<td align="center">0.8287335</td>
<td align="center">0.8995589</td>
<td align="center">0.9863894</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8166466</td>
<td align="center">0.8908323</td>
<td align="center">0.9782871</td>
<td align="center">0.8269962</td>
<td align="center">0.8941698</td>
<td align="center">0.9828897</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8232691</td>
<td align="center">0.9190526</td>
<td align="center">0.9880271</td>
<td align="center">0.8245614</td>
<td align="center">0.9211798</td>
<td align="center">0.9839817</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5264280</td>
<td align="center">0.5366162</td>
<td align="center">0.0000000</td>
<td align="center">0.5264280</td>
<td align="center">0.5366162</td>
</tr>
</tbody>
</table>

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@ -318,18 +318,18 @@ 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="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
<span class="co"># 1 S I R S R R</span>
<span class="co"># 2 R S S R I S</span>
<span class="co"># 3 I R I S R S</span>
<span class="co"># 4 I S S R S R</span>
<span class="co"># 5 R R S S R R</span>
<span class="co"># 6 S R I S S I</span>
<span class="co"># 1 S S R R R R</span>
<span class="co"># 2 R S S R S S</span>
<span class="co"># 3 S R R R S S</span>
<span class="co"># 4 S S S S S S</span>
<span class="co"># 5 R S R S R S</span>
<span class="co"># 6 S S R S S S</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 R</span>
<span class="co"># 2 S</span>
<span class="co"># 3 S</span>
<span class="co"># 4 R</span>
<span class="co"># 5 R</span>
<span class="co"># 2 R</span>
<span class="co"># 3 R</span>
<span class="co"># 4 S</span>
<span class="co"># 5 S</span>
<span class="co"># 6 S</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">
@ -361,40 +361,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3313</td>
<td align="right">66.26%</td>
<td align="right">3313</td>
<td align="right">66.26%</td>
<td align="right">3327</td>
<td align="right">66.54%</td>
<td align="right">3327</td>
<td align="right">66.54%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">631</td>
<td align="right">12.62%</td>
<td align="right">3944</td>
<td align="right">78.88%</td>
<td align="right">632</td>
<td align="right">12.64%</td>
<td align="right">3959</td>
<td align="right">79.18%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">575</td>
<td align="right">11.50%</td>
<td align="right">4519</td>
<td align="right">90.38%</td>
<td align="right">536</td>
<td align="right">10.72%</td>
<td align="right">4495</td>
<td align="right">89.90%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">275</td>
<td align="right">5.50%</td>
<td align="right">4794</td>
<td align="right">95.88%</td>
<td align="right">277</td>
<td align="right">5.54%</td>
<td align="right">4772</td>
<td align="right">95.44%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">206</td>
<td align="right">4.12%</td>
<td align="right">228</td>
<td align="right">4.56%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

9
docs/articles/PCA.html
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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9032</span>
</span>
</div>
@ -187,8 +187,7 @@
</header><script src="PCA_files/accessible-code-block-0.0.1/empty-anchor.js"></script><link href="PCA_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
<script src="PCA_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
</header><script src="PCA_files/header-attrs-2.4/header-attrs.js"></script><script src="PCA_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>How to conduct principal component analysis (PCA) for AMR</h1>
@ -292,8 +291,8 @@
<p>The new <code><a href="../reference/pca.html">pca()</a></code> function will automatically filter on rows that contain numeric values in all selected variables, so we now only need to do:</p>
<div class="sourceCode" id="cb3"><pre class="downlit">
<span class="va">pca_result</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/pca.html">pca</a></span><span class="op">(</span><span class="va">resistance_data</span><span class="op">)</span>
<span class="co"># NOTE: Columns selected for PCA: AMC CXM CTX CAZ GEN TOB TMP SXT.</span>
<span class="co"># Total observations available: 7.</span></pre></div>
<span class="co"># NOTE: Columns selected for PCA: AMC CXM CTX CAZ GEN TOB TMP SXT. Total</span>
<span class="co"># observations available: 7.</span></pre></div>
<p>The result can be reviewed with the good old <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> function:</p>
<div class="sourceCode" id="cb4"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span>

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@ -0,0 +1,12 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

37
docs/articles/SPSS.html
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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9032</span>
</span>
</div>
@ -187,14 +187,13 @@
</header><script src="SPSS_files/accessible-code-block-0.0.1/empty-anchor.js"></script><link href="SPSS_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
<script src="SPSS_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
</header><script src="SPSS_files/header-attrs-2.4/header-attrs.js"></script><script src="SPSS_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">26 October 2020</h4>
<h4 class="date">08 December 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>
@ -294,7 +293,7 @@
<p>If additional packages are needed, RStudio will ask you if they should be installed on beforehand.</p>
<p>In the the window that opens, you can define all options (parameters) that should be used for import and you’re ready to go:</p>
<p><img src="https://github.com/msberends/AMR/raw/master/docs/import2.png"></p>
<p>If you want named variables to be imported as factors so it resembles SPSS more, use <code>as_factor()</code>.</p>
<p>If you want named variables to be imported as factors so it resembles SPSS more, use <code><a href="https://haven.tidyverse.org/reference/as_factor.html">as_factor()</a></code>.</p>
<p>The difference is this:</p>
<div class="sourceCode" id="cb2"><pre class="downlit">
<span class="va">SPSS_data</span>
@ -337,7 +336,7 @@
<span class="co"># download and install the latest version:</span>
<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"haven"</span><span class="op">)</span>
<span class="co"># load the package you just installed:</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va">haven</span><span class="op">)</span> </pre></div>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="http://haven.tidyverse.org">haven</a></span><span class="op">)</span> </pre></div>
<p>You can now import files as follows:</p>
<div id="spss" class="section level4">
<h4 class="hasAnchor">
@ -345,21 +344,21 @@
<p>To read files from SPSS into R:</p>
<div class="sourceCode" id="cb4"><pre class="downlit">
<span class="co"># read any SPSS file based on file extension (best way):</span>
<span class="fu">read_spss</span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_spss</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
<span class="co"># read .sav or .zsav file:</span>
<span class="fu">read_sav</span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_sav</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
<span class="co"># read .por file:</span>
<span class="fu">read_por</span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span></pre></div>
<p>Do not forget about <code>as_factor()</code>, as mentioned above.</p>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_por</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span></pre></div>
<p>Do not forget about <code><a href="https://haven.tidyverse.org/reference/as_factor.html">as_factor()</a></code>, as mentioned above.</p>
<p>To export your R objects to the SPSS file format:</p>
<div class="sourceCode" id="cb5"><pre class="downlit">
<span class="co"># save as .sav file:</span>
<span class="fu">write_sav</span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
<span class="co"># save as compressed .zsav file:</span>
<span class="fu">write_sav</span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span>, compress <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></pre></div>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span>, compress <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></pre></div>
</div>
<div id="sas" class="section level4">
<h4 class="hasAnchor">
@ -367,18 +366,18 @@
<p>To read files from SAS into R:</p>
<div class="sourceCode" id="cb6"><pre class="downlit">
<span class="co"># read .sas7bdat + .sas7bcat files:</span>
<span class="fu">read_sas</span><span class="op">(</span>data_file <span class="op">=</span> <span class="st">"path/to/file"</span>, catalog_file <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html">read_sas</a></span><span class="op">(</span>data_file <span class="op">=</span> <span class="st">"path/to/file"</span>, catalog_file <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span>
<span class="co"># read SAS transport files (version 5 and version 8):</span>
<span class="fu">read_xpt</span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span></pre></div>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html">read_xpt</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span></pre></div>
<p>To export your R objects to the SAS file format:</p>
<div class="sourceCode" id="cb7"><pre class="downlit">
<span class="co"># save as regular SAS file:</span>
<span class="fu">write_sas</span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html">write_sas</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
<span class="co"># the SAS transport format is an open format </span>
<span class="co"># (required for submission of the data to the FDA)</span>
<span class="fu">write_xpt</span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span>, version <span class="op">=</span> <span class="fl">8</span><span class="op">)</span></pre></div>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html">write_xpt</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span>, version <span class="op">=</span> <span class="fl">8</span><span class="op">)</span></pre></div>
</div>
<div id="stata" class="section level4">
<h4 class="hasAnchor">
@ -386,15 +385,15 @@
<p>To read files from Stata into R:</p>
<div class="sourceCode" id="cb8"><pre class="downlit">
<span class="co"># read .dta file:</span>
<span class="fu">read_stata</span><span class="op">(</span>file <span class="op">=</span> <span class="st">"/path/to/file"</span><span class="op">)</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_stata</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"/path/to/file"</span><span class="op">)</span>
<span class="co"># works exactly the same:</span>
<span class="fu">read_dta</span><span class="op">(</span>file <span class="op">=</span> <span class="st">"/path/to/file"</span><span class="op">)</span></pre></div>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_dta</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"/path/to/file"</span><span class="op">)</span></pre></div>
<p>To export your R objects to the Stata file format:</p>
<div class="sourceCode" id="cb9"><pre class="downlit">
<span class="co"># save as .dta file, Stata version 14:</span>
<span class="co"># (supports Stata v8 until v15 at the time of writing)</span>
<span class="fu">write_dta</span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"/path/to/file"</span>, version <span class="op">=</span> <span class="fl">14</span><span class="op">)</span></pre></div>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">write_dta</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"/path/to/file"</span>, version <span class="op">=</span> <span class="fl">14</span><span class="op">)</span></pre></div>
</div>
</div>
</div>

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// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

5
docs/articles/WHONET.html
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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9032</span>
</span>
</div>
@ -187,8 +187,7 @@
</header><script src="WHONET_files/accessible-code-block-0.0.1/empty-anchor.js"></script><link href="WHONET_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
<script src="WHONET_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
</header><script src="WHONET_files/header-attrs-2.4/header-attrs.js"></script><script src="WHONET_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>How to work with WHONET data</h1>

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@ -0,0 +1,12 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

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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">1.4.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9032</span>
</span>
</div>
@ -227,20 +227,20 @@
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("sau") 11.0 12 16.0 14.0 15.0 40.0</span>
<span class="co"># as.mo("stau") 110.0 120 140.0 140.0 150.0 160.0</span>
<span class="co"># as.mo("STAU") 110.0 120 140.0 140.0 140.0 150.0</span>
<span class="co"># as.mo("staaur") 12.0 13 20.0 15.0 16.0 45.0</span>
<span class="co"># as.mo("STAAUR") 15.0 15 26.0 16.0 41.0 58.0</span>
<span class="co"># as.mo("S. aureus") 31.0 35 50.0 59.0 62.0 65.0</span>
<span class="co"># as.mo("S aureus") 27.0 33 59.0 59.0 62.0 160.0</span>
<span class="co"># as.mo("Staphylococcus aureus") 1.9 2 2.4 2.4 2.7 2.9</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 910.0 960 980.0 970.0 1000.0 1100.0</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 400.0 410 430.0 420.0 440.0 560.0</span>
<span class="co"># as.mo("MRSA") 12.0 13 19.0 15.0 15.0 42.0</span>
<span class="co"># as.mo("VISA") 20.0 22 31.0 24.0 47.0 54.0</span>
<span class="co"># as.mo("VRSA") 22.0 23 35.0 24.0 52.0 56.0</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("sau") 13.0 13.0 17.0 15.0 16.0 43.0</span>
<span class="co"># as.mo("stau") 120.0 120.0 140.0 150.0 150.0 160.0</span>
<span class="co"># as.mo("STAU") 120.0 150.0 150.0 150.0 160.0 160.0</span>
<span class="co"># as.mo("staaur") 13.0 13.0 17.0 14.0 16.0 44.0</span>
<span class="co"># as.mo("STAAUR") 13.0 14.0 19.0 16.0 16.0 48.0</span>
<span class="co"># as.mo("S. aureus") 34.0 58.0 61.0 63.0 68.0 86.0</span>
<span class="co"># as.mo("S aureus") 33.0 34.0 46.0 36.0 63.0 63.0</span>
<span class="co"># as.mo("Staphylococcus aureus") 2.3 2.5 2.5 2.5 2.6 2.7</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 980.0 980.0 1000.0 1000.0 1000.0 1100.0</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 430.0 430.0 440.0 440.0 440.0 460.0</span>
<span class="co"># as.mo("MRSA") 13.0 14.0 18.0 16.0 17.0 43.0</span>
<span class="co"># as.mo("VISA") 21.0 22.0 23.0 22.0 24.0 25.0</span>
<span class="co"># as.mo("VRSA") 22.0 23.0 35.0 27.0 52.0 55.0</span>
<span class="co"># neval</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
@ -284,8 +284,8 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</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) 165 176 223 202 274 318 10</span></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.202 seconds. You only lose time on your unique input values.</p>
<span class="co"># mo_name(x) 145 190 221 213 248 313 10</span></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.213 seconds. You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -299,10 +299,10 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 7.83 8.05 9.56 9.43 10.90 12.90 10</span>
<span class="co"># B 23.50 24.40 30.20 25.50 26.80 74.50 10</span>
<span class="co"># C 2.00 2.19 2.42 2.41 2.56 3.06 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 0.0024 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<span class="co"># A 8.36 8.59 8.99 9.07 9.29 9.62 10</span>
<span class="co"># B 26.80 27.50 28.10 28.00 29.10 29.80 10</span>
<span class="co"># C 2.06 2.15 6.68 2.50 2.69 45.20 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 0.0025 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="va">run_it</span> <span class="op">&lt;-</span> <span class="fu">microbenchmark</span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"Staphylococcus"</span><span class="op">)</span>,
@ -316,14 +316,14 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 1.69 1.75 1.90 1.86 2.00 2.25 10</span>
<span class="co"># B 1.69 1.72 1.86 1.79 1.87 2.43 10</span>
<span class="co"># C 1.67 1.75 1.89 1.81 1.93 2.67 10</span>
<span class="co"># D 1.64 1.73 1.87 1.87 1.94 2.23 10</span>
<span class="co"># E 1.65 1.75 1.90 1.83 1.92 2.35 10</span>
<span class="co"># F 1.70 1.75 1.87 1.85 1.93 2.20 10</span>
<span class="co"># G 1.73 1.83 1.93 1.93 2.01 2.25 10</span>
<span class="co"># H 1.65 1.73 1.85 1.77 2.06 2.11 10</span></pre></div>
<span class="co"># A 1.68 1.91 2.13 2.08 2.43 2.62 10</span>
<span class="co"># B 1.89 1.99 2.16 2.05 2.30 2.69 10</span>
<span class="co"># C 1.87 1.91 2.09 2.00 2.28 2.46 10</span>
<span class="co"># D 1.65 1.71 1.92 1.87 1.98 2.58 10</span>
<span class="co"># E 1.64 1.74 1.90 1.87 1.98 2.34 10</span>
<span class="co"># F 1.86 1.92 2.05 2.05 2.16 2.27 10</span>
<span class="co"># G 1.73 1.80 1.99 1.97 2.14 2.29 10</span>
<span class="co"># H 1.85 1.93 2.08 1.98 2.15 2.93 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>
<div id="results-in-other-languages" class="section level3">
@ -351,13 +351,13 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 16.23 16.62 21.00 17.00 18.51 59.06 100</span>
<span class="co"># de 19.27 19.96 22.73 20.36 21.08 69.70 100</span>
<span class="co"># nl 31.40 32.54 38.76 33.16 35.34 82.43 100</span>
<span class="co"># es 19.36 19.75 23.61 20.26 20.88 67.39 100</span>
<span class="co"># it 19.24 19.64 21.23 20.00 20.72 62.92 100</span>
<span class="co"># fr 19.19 19.82 25.12 20.16 21.49 70.00 100</span>
<span class="co"># pt 19.18 19.64 22.44 20.23 21.47 60.56 100</span></pre></div>
<span class="co"># en 16.16 17.85 22.42 18.54 19.61 68.28 100</span>
<span class="co"># de 19.55 21.38 24.37 21.96 22.95 61.55 100</span>
<span class="co"># nl 31.64 35.08 40.58 36.34 37.88 79.00 100</span>
<span class="co"># es 18.03 21.46 25.61 22.09 23.30 64.97 100</span>
<span class="co"># it 17.82 21.01 23.29 21.80 22.82 58.47 100</span>
<span class="co"># fr 18.19 21.29 25.63 21.93 23.20 60.48 100</span>
<span class="co"># pt 17.76 21.07 24.81 21.83 23.39 65.00 100</span></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</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">1.4.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9032</span>
</span>
</div>
@ -807,7 +807,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<div id="source-4" class="section level3">
<h3 class="hasAnchor">
<a href="#source-4" class="anchor"></a>Source</h3>
<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on ‘EUCAST Expert Rules / EUCAST Intrinsic Resistance and Unusual Phenotypes’, v3.2 from 2020.</p>
<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on ‘’EUCAST Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’’, v3.2 from 2020.</p>
</div>
<div id="example-content-4" class="section level3">
<h3 class="hasAnchor">

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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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9033</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">1.4.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9032</span>
</span>
</div>
@ -187,8 +187,7 @@
</header><script src="resistance_predict_files/accessible-code-block-0.0.1/empty-anchor.js"></script><link href="resistance_predict_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
<script src="resistance_predict_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
</header><script src="resistance_predict_files/header-attrs-2.4/header-attrs.js"></script><script src="resistance_predict_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>How to predict antimicrobial resistance</h1>
@ -233,7 +232,7 @@
<span id="cb2-12"><a href="#cb2-12"></a> <span class="dt">model =</span> <span class="st">"binomial"</span>)</span></code></pre></div>
<p>The function will look for a date column itself if <code>col_date</code> is not set.</p>
<p>When running any of these commands, a summary of the regression model will be printed unless using <code><a href="../reference/resistance_predict.html">resistance_predict(..., info = FALSE)</a></code>.</p>
<pre><code># NOTE: Using column `date` as input for `col_date`.</code></pre>
<pre><code># NOTE: Using column 'date' as input for `col_date`.</code></pre>
<p>This text is only a printed summary - the actual result (output) of the function is a <code>data.frame</code> containing for each year: the number of observations, the actual observed resistance, the estimated resistance and the standard error below and above the estimation:</p>
<div class="sourceCode" id="cb4"><pre class="downlit">
<span class="va">predict_TZP</span>
@ -290,7 +289,7 @@
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"binomial"</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span>
<span class="co"># NOTE: Using column `date` as input for `col_date`.</span></pre></div>
<span class="co"># NOTE: Using column 'date' as input for `col_date`.</span></pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-6-1.png" width="720"></p>
<p>Vancomycin resistance could be 100% in ten years, but might also stay around 0%.</p>
<p>You can define the model with the <code>model</code> parameter. The model chosen above is a generalised linear regression model using a binomial distribution, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance.</p>
@ -336,7 +335,7 @@
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"linear"</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span>
<span class="co"># NOTE: Using column `date` as input for `col_date`.</span></pre></div>
<span class="co"># NOTE: Using column 'date' as input for `col_date`.</span></pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
<p>This seems more likely, doesn’t it?</p>
<p>The model itself is also available from the object, as an <code>attribute</code>:</p>

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// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

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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">1.4.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9032</span>
</span>
</div>
@ -187,8 +187,7 @@
</header><script src="welcome_to_AMR_files/accessible-code-block-0.0.1/empty-anchor.js"></script><link href="welcome_to_AMR_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
<script src="welcome_to_AMR_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
</header><script src="welcome_to_AMR_files/header-attrs-2.4/header-attrs.js"></script><script src="welcome_to_AMR_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>Welcome to the AMR package</h1>

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// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});