(v1.1.0.9009) lose dependencies

2025-07-09 01:22:25 +02:00 · 2020-05-18 10:30:53 +02:00
parent 071bdc5a9e
commit bf0402a653
29 changed files with 405 additions and 374 deletions
--- a/docs/articles/AMR.html
+++ b/docs/articles/AMR.html
@ -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">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9009</span>
      </span>
    </div>

@ -186,7 +186,7 @@
      <h1 data-toc-skip>How to conduct AMR analysis</h1>
                        <h4 class="author">Matthijs S. Berends</h4>
            
-            <h4 class="date">15 April 2020</h4>
+            <h4 class="date">18 May 2020</h4>
      
      <small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/AMR.Rmd"><code>vignettes/AMR.Rmd</code></a></small>
      <div class="hidden name"><code>AMR.Rmd</code></div>
@ -195,15 +195,15 @@

    
    
-<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 April 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 18 May 2020.</p>
 <div id="introduction" class="section level1">
 <h1 class="hasAnchor">
 <a href="#introduction" class="anchor"></a>Introduction</h1>
 <p>Conducting antimicrobial resistance analysis unfortunately requires in-depth knowledge from different scientific fields, which makes it hard to do right. At least, it requires:</p>
 <ul>
-<li>Good questions (always start with these!)</li>
+<li>Good questions (always start with those!)</li>
 <li>A thorough understanding of (clinical) epidemiology, to understand the clinical and epidemiological relevance and possible bias of results</li>
-<li>A thorough understanding of (clinical) microbiology/infectious diseases, to understand which microorganisms are causal to which infections and the implications of pharmaceutical treatment</li>
+<li>A thorough understanding of (clinical) microbiology/infectious diseases, to understand which microorganisms are causal to which infections and the implications of pharmaceutical treatment, as well as understanding intrinsic and acquired microbial resistance</li>
 <li>Experience with data analysis with microbiological tests and their results, to understand the determination and limitations of MIC values and their interpretations to RSI values</li>
 <li>Availability of the biological taxonomy of microorganisms and probably normalisation factors for pharmaceuticals, such as defined daily doses (DDD)</li>
 <li>Available (inter-)national guidelines, and profound methods to apply them</li>
@ -226,21 +226,21 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2020-04-15</td>
+<td align="center">2020-05-18</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">2020-04-15</td>
+<td align="center">2020-05-18</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">2020-04-15</td>
+<td align="center">2020-05-18</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@ -258,7 +258,7 @@
 <span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">AMR</span>)

 <span class="co"># (if not yet installed, install with:)</span>
-<span class="co"># install.packages(c("tidyverse", "AMR"))</span></pre></body></html></div>
+<span class="co"># install.packages(c("dplyr", "ggplot2", "AMR"))</span></pre></body></html></div>
 </div>
 </div>
 <div id="creation-of-data" class="section level1">
@ -301,24 +301,24 @@
 <div id="put-everything-together" class="section level2">
 <h2 class="hasAnchor">
 <a href="#put-everything-together" class="anchor"></a>Put everything together</h2>
-<p>Using the <code><a href="https://rdrr.io/r/base/sample.html">sample()</a></code> function, we can randomly select items from all objects we defined earlier. To let our fake data reflect reality a bit, we will also approximately define the probabilities of bacteria and the antibiotic results with the <code>prob</code> parameter.</p>
+<p>Using the <code><a href="https://dplyr.tidyverse.org/reference/sample.html">sample()</a></code> function, we can randomly select items from all objects we defined earlier. To let our fake data reflect reality a bit, we will also approximately define the probabilities of bacteria and the antibiotic results with the <code>prob</code> parameter.</p>
 <div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="no">sample_size</span> <span class="kw">&lt;-</span> <span class="fl">20000</span>
-<span class="no">data</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="kw">date</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="no">dates</span>, <span class="kw">size</span> <span class="kw">=</span> <span class="no">sample_size</span>, <span class="kw">replace</span> <span class="kw">=</span> <span class="fl">TRUE</span>),
-                   <span class="kw">patient_id</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="no">patients</span>, <span class="kw">size</span> <span class="kw">=</span> <span class="no">sample_size</span>, <span class="kw">replace</span> <span class="kw">=</span> <span class="fl">TRUE</span>),
-                   <span class="kw">hospital</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="no">hospitals</span>, <span class="kw">size</span> <span class="kw">=</span> <span class="no">sample_size</span>, <span class="kw">replace</span> <span class="kw">=</span> <span class="fl">TRUE</span>,
+<span class="no">data</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="kw">date</span> <span class="kw">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="no">dates</span>, <span class="kw">size</span> <span class="kw">=</span> <span class="no">sample_size</span>, <span class="kw">replace</span> <span class="kw">=</span> <span class="fl">TRUE</span>),
+                   <span class="kw">patient_id</span> <span class="kw">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="no">patients</span>, <span class="kw">size</span> <span class="kw">=</span> <span class="no">sample_size</span>, <span class="kw">replace</span> <span class="kw">=</span> <span class="fl">TRUE</span>),
+                   <span class="kw">hospital</span> <span class="kw">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="no">hospitals</span>, <span class="kw">size</span> <span class="kw">=</span> <span class="no">sample_size</span>, <span class="kw">replace</span> <span class="kw">=</span> <span class="fl">TRUE</span>,
                                     <span class="kw">prob</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.30</span>, <span class="fl">0.35</span>, <span class="fl">0.15</span>, <span class="fl">0.20</span>)),
-                   <span class="kw">bacteria</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="no">bacteria</span>, <span class="kw">size</span> <span class="kw">=</span> <span class="no">sample_size</span>, <span class="kw">replace</span> <span class="kw">=</span> <span class="fl">TRUE</span>,
+                   <span class="kw">bacteria</span> <span class="kw">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="no">bacteria</span>, <span class="kw">size</span> <span class="kw">=</span> <span class="no">sample_size</span>, <span class="kw">replace</span> <span class="kw">=</span> <span class="fl">TRUE</span>,
                                     <span class="kw">prob</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.50</span>, <span class="fl">0.25</span>, <span class="fl">0.15</span>, <span class="fl">0.10</span>)),
-                   <span class="kw">AMX</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="no">ab_interpretations</span>, <span class="kw">size</span> <span class="kw">=</span> <span class="no">sample_size</span>, <span class="kw">replace</span> <span class="kw">=</span> <span class="fl">TRUE</span>,
+                   <span class="kw">AMX</span> <span class="kw">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="no">ab_interpretations</span>, <span class="kw">size</span> <span class="kw">=</span> <span class="no">sample_size</span>, <span class="kw">replace</span> <span class="kw">=</span> <span class="fl">TRUE</span>,
                                 <span class="kw">prob</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.60</span>, <span class="fl">0.05</span>, <span class="fl">0.35</span>)),
-                   <span class="kw">AMC</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="no">ab_interpretations</span>, <span class="kw">size</span> <span class="kw">=</span> <span class="no">sample_size</span>, <span class="kw">replace</span> <span class="kw">=</span> <span class="fl">TRUE</span>,
+                   <span class="kw">AMC</span> <span class="kw">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="no">ab_interpretations</span>, <span class="kw">size</span> <span class="kw">=</span> <span class="no">sample_size</span>, <span class="kw">replace</span> <span class="kw">=</span> <span class="fl">TRUE</span>,
                                 <span class="kw">prob</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.75</span>, <span class="fl">0.10</span>, <span class="fl">0.15</span>)),
-                   <span class="kw">CIP</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="no">ab_interpretations</span>, <span class="kw">size</span> <span class="kw">=</span> <span class="no">sample_size</span>, <span class="kw">replace</span> <span class="kw">=</span> <span class="fl">TRUE</span>,
+                   <span class="kw">CIP</span> <span class="kw">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="no">ab_interpretations</span>, <span class="kw">size</span> <span class="kw">=</span> <span class="no">sample_size</span>, <span class="kw">replace</span> <span class="kw">=</span> <span class="fl">TRUE</span>,
                                 <span class="kw">prob</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.80</span>, <span class="fl">0.00</span>, <span class="fl">0.20</span>)),
-                   <span class="kw">GEN</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="no">ab_interpretations</span>, <span class="kw">size</span> <span class="kw">=</span> <span class="no">sample_size</span>, <span class="kw">replace</span> <span class="kw">=</span> <span class="fl">TRUE</span>,
+                   <span class="kw">GEN</span> <span class="kw">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="no">ab_interpretations</span>, <span class="kw">size</span> <span class="kw">=</span> <span class="no">sample_size</span>, <span class="kw">replace</span> <span class="kw">=</span> <span class="fl">TRUE</span>,
                                 <span class="kw">prob</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.92</span>, <span class="fl">0.00</span>, <span class="fl">0.08</span>)))</pre></body></html></div>
-<p>Using the <code><a href="https://dplyr.tidyverse.org/reference/mutate-joins.html">left_join()</a></code> function from the <code>dplyr</code> package, we can ‘map’ the gender to the patient ID using the <code>patients_table</code> object we created earlier:</p>
-<div class="sourceCode" id="cb8"><html><body><pre class="r"><span class="no">data</span> <span class="kw">&lt;-</span> <span class="no">data</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate-joins.html">left_join</a></span>(<span class="no">patients_table</span>)</pre></body></html></div>
+<p>Using the <code><a href="https://dplyr.tidyverse.org/reference/join.html">left_join()</a></code> function from the <code>dplyr</code> package, we can ‘map’ the gender to the patient ID using the <code>patients_table</code> object we created earlier:</p>
+<div class="sourceCode" id="cb8"><html><body><pre class="r"><span class="no">data</span> <span class="kw">&lt;-</span> <span class="no">data</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/join.html">left_join</a></span>(<span class="no">patients_table</span>)</pre></body></html></div>
 <p>The resulting data set contains 20,000 blood culture isolates. With the <code><a href="https://rdrr.io/r/utils/head.html">head()</a></code> function we can preview the first 6 rows of this data set:</p>
 <div class="sourceCode" id="cb9"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="no">data</span>)</pre></body></html></div>
 <table class="table">
@ -335,64 +335,64 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2015-12-27</td>
-<td align="center">Y9</td>
-<td align="center">Hospital A</td>
-<td align="center">Escherichia coli</td>
-<td align="center">R</td>
+<td align="center">2013-06-23</td>
+<td align="center">V9</td>
+<td align="center">Hospital C</td>
+<td align="center">Staphylococcus aureus</td>
+<td align="center">S</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
 <tr class="even">
-<td align="center">2014-01-17</td>
-<td align="center">X10</td>
-<td align="center">Hospital C</td>
-<td align="center">Staphylococcus aureus</td>
+<td align="center">2016-12-25</td>
+<td align="center">S10</td>
+<td align="center">Hospital D</td>
+<td align="center">Escherichia coli</td>
 <td align="center">R</td>
 <td align="center">S</td>
-<td align="center">R</td>
 <td align="center">S</td>
+<td align="center">R</td>
 <td align="center">F</td>
 </tr>
 <tr class="odd">
-<td align="center">2015-10-31</td>
-<td align="center">I3</td>
+<td align="center">2011-01-27</td>
+<td align="center">Z10</td>
 <td align="center">Hospital B</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">M</td>
-</tr>
-<tr class="even">
-<td align="center">2014-10-30</td>
-<td align="center">D9</td>
-<td align="center">Hospital A</td>
-<td align="center">Escherichia coli</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">M</td>
-</tr>
-<tr class="odd">
-<td align="center">2011-02-15</td>
-<td align="center">P6</td>
-<td align="center">Hospital D</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">S</td>
 <td align="center">F</td>
 </tr>
 <tr class="even">
-<td align="center">2011-10-07</td>
-<td align="center">G2</td>
-<td align="center">Hospital C</td>
+<td align="center">2010-09-14</td>
+<td align="center">N1</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">R</td>
+<td align="center">R</td>
+<td align="center">M</td>
+</tr>
+<tr class="odd">
+<td align="center">2017-10-31</td>
+<td align="center">W1</td>
+<td align="center">Hospital D</td>
+<td align="center">Klebsiella pneumoniae</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">F</td>
+</tr>
+<tr class="even">
+<td align="center">2014-03-29</td>
+<td align="center">L4</td>
+<td align="center">Hospital B</td>
 <td align="center">Staphylococcus aureus</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -412,11 +412,12 @@
 <p>For example, for the <code>gender</code> variable:</p>
 <div class="sourceCode" id="cb10"><html><body><pre class="r"><span class="no">data</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">gender</span>) <span class="co"># this would be the same: freq(data$gender)</span></pre></body></html></div>
 <p><strong>Frequency table</strong></p>
-<p>Class: factor (numeric)<br>
+<p>Class: character<br>
 Length: 20,000<br>
-Levels: 2: F, M<br>
 Available: 20,000 (100%, NA: 0 = 0%)<br>
 Unique: 2</p>
+<p>Shortest: 1<br>
+Longest: 1</p>
 <table class="table">
 <thead><tr class="header">
 <th align="left"></th>
@ -430,16 +431,16 @@ Unique: 2</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">M</td>
-<td align="right">10,277</td>
-<td align="right">51.39%</td>
-<td align="right">10,277</td>
-<td align="right">51.39%</td>
+<td align="right">10,293</td>
+<td align="right">51.47%</td>
+<td align="right">10,293</td>
+<td align="right">51.47%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">F</td>
-<td align="right">9,723</td>
-<td align="right">48.62%</td>
+<td align="right">9,707</td>
+<td align="right">48.54%</td>
 <td align="right">20,000</td>
 <td align="right">100.00%</td>
 </tr>
@ -476,10 +477,10 @@ Unique: 2</p>
 <p>This <code>AMR</code> package includes this methodology with the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> function. It adopts the episode of a year (can be changed by user) and it starts counting days after every selected isolate. This new variable can easily be added to our data:</p>
 <div class="sourceCode" id="cb15"><html><body><pre class="r"><span class="no">data</span> <span class="kw">&lt;-</span> <span class="no">data</span> <span class="kw">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="kw">first</span> <span class="kw">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="no">.</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></body></html></div>
-<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>
+<span class="co"># [34mNOTE: Using column `[1mbacteria[22m` as input for `col_mo`.[39m</span>
+<span class="co"># [34mNOTE: Using column `[1mdate[22m` as input for `col_date`.[39m</span>
+<span class="co"># [34mNOTE: Using column `[1mpatient_id[22m` as input for `col_patient_id`.[39m</span></pre></body></html></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"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">&lt;-</span> <span class="no">data</span> <span class="kw">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="no">first</span> <span class="kw">==</span> <span class="fl">TRUE</span>)</pre></body></html></div>
 <p>For future use, the above two syntaxes can be shortened with the <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> function:</p>
@ -489,7 +490,7 @@ Unique: 2</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 R8, 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 N1, sorted on date:</p>
 <table class="table">
 <thead><tr class="header">
 <th align="center">isolate</th>
@ -505,10 +506,10 @@ Unique: 2</p>
 <tbody>
 <tr class="odd">
 <td align="center">1</td>
-<td align="center">2010-03-01</td>
-<td align="center">R8</td>
+<td align="center">2010-03-16</td>
+<td align="center">N1</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>
@ -516,8 +517,8 @@ Unique: 2</p>
 </tr>
 <tr class="even">
 <td align="center">2</td>
-<td align="center">2010-04-16</td>
-<td align="center">R8</td>
+<td align="center">2010-04-19</td>
+<td align="center">N1</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -527,8 +528,8 @@ Unique: 2</p>
 </tr>
 <tr class="odd">
 <td align="center">3</td>
-<td align="center">2010-04-18</td>
-<td align="center">R8</td>
+<td align="center">2010-06-26</td>
+<td align="center">N1</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -538,10 +539,10 @@ Unique: 2</p>
 </tr>
 <tr class="even">
 <td align="center">4</td>
-<td align="center">2010-05-08</td>
-<td align="center">R8</td>
+<td align="center">2010-07-17</td>
+<td align="center">N1</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>
@ -549,30 +550,30 @@ Unique: 2</p>
 </tr>
 <tr class="odd">
 <td align="center">5</td>
-<td align="center">2010-06-06</td>
-<td align="center">R8</td>
+<td align="center">2010-09-14</td>
+<td align="center">N1</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">R</td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="even">
 <td align="center">6</td>
-<td align="center">2010-06-14</td>
-<td align="center">R8</td>
+<td align="center">2010-09-23</td>
+<td align="center">N1</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">2010-07-28</td>
-<td align="center">R8</td>
+<td align="center">2010-12-14</td>
+<td align="center">N1</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -582,19 +583,19 @@ Unique: 2</p>
 </tr>
 <tr class="even">
 <td align="center">8</td>
-<td align="center">2010-07-31</td>
-<td align="center">R8</td>
+<td align="center">2011-07-30</td>
+<td align="center">N1</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>
 </tr>
 <tr class="odd">
 <td align="center">9</td>
-<td align="center">2010-08-25</td>
-<td align="center">R8</td>
+<td align="center">2011-08-21</td>
+<td align="center">N1</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -604,27 +605,27 @@ Unique: 2</p>
 </tr>
 <tr class="even">
 <td align="center">10</td>
-<td align="center">2010-09-30</td>
-<td align="center">R8</td>
+<td align="center">2011-09-09</td>
+<td align="center">N1</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">S</td>
 <td align="center">FALSE</td>
 </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"><html><body><pre class="r"><span class="no">data</span> <span class="kw">&lt;-</span> <span class="no">data</span> <span class="kw">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="kw">keyab</span> <span class="kw">=</span> <span class="fu"><a href="../reference/key_antibiotics.html">key_antibiotics</a></span>(<span class="no">.</span>)) <span class="kw">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="kw">first_weighted</span> <span class="kw">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="no">.</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></body></html></div>
+<span class="co"># [34mNOTE: Using column `[1mbacteria[22m` as input for `col_mo`.[39m</span>
+<span class="co"># [34mNOTE: Using column `[1mbacteria[22m` as input for `col_mo`.[39m</span>
+<span class="co"># [34mNOTE: Using column `[1mdate[22m` as input for `col_date`.[39m</span>
+<span class="co"># [34mNOTE: Using column `[1mpatient_id[22m` as input for `col_patient_id`.[39m</span>
+<span class="co"># [34mNOTE: Using column `[1mkeyab[22m` as input for `col_keyantibiotics`. Use [1mcol_keyantibiotics = FALSE[22m to prevent this.[39m</span></pre></body></html></div>
 <table class="table">
 <thead><tr class="header">
 <th align="center">isolate</th>
@ -641,10 +642,10 @@ Unique: 2</p>
 <tbody>
 <tr class="odd">
 <td align="center">1</td>
-<td align="center">2010-03-01</td>
-<td align="center">R8</td>
+<td align="center">2010-03-16</td>
+<td align="center">N1</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>
@ -653,20 +654,20 @@ Unique: 2</p>
 </tr>
 <tr class="even">
 <td align="center">2</td>
-<td align="center">2010-04-16</td>
-<td align="center">R8</td>
+<td align="center">2010-04-19</td>
+<td align="center">N1</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">2010-04-18</td>
-<td align="center">R8</td>
+<td align="center">2010-06-26</td>
+<td align="center">N1</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -677,35 +678,35 @@ Unique: 2</p>
 </tr>
 <tr class="even">
 <td align="center">4</td>
-<td align="center">2010-05-08</td>
-<td align="center">R8</td>
+<td align="center">2010-07-17</td>
+<td align="center">N1</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
-<td align="center">TRUE</td>
+<td align="center">FALSE</td>
 </tr>
 <tr class="odd">
 <td align="center">5</td>
-<td align="center">2010-06-06</td>
-<td align="center">R8</td>
+<td align="center">2010-09-14</td>
+<td align="center">N1</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">R</td>
 <td align="center">FALSE</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">6</td>
-<td align="center">2010-06-14</td>
-<td align="center">R8</td>
+<td align="center">2010-09-23</td>
+<td align="center">N1</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>
@ -713,32 +714,32 @@ Unique: 2</p>
 </tr>
 <tr class="odd">
 <td align="center">7</td>
-<td align="center">2010-07-28</td>
-<td align="center">R8</td>
+<td align="center">2010-12-14</td>
+<td align="center">N1</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">2010-07-31</td>
-<td align="center">R8</td>
+<td align="center">2011-07-30</td>
+<td align="center">N1</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>
+<td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">9</td>
-<td align="center">2010-08-25</td>
-<td align="center">R8</td>
+<td align="center">2011-08-21</td>
+<td align="center">N1</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -749,23 +750,23 @@ Unique: 2</p>
 </tr>
 <tr class="even">
 <td align="center">10</td>
-<td align="center">2010-09-30</td>
-<td align="center">R8</td>
+<td align="center">2011-09-09</td>
+<td align="center">N1</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">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 7 isolates are flagged. In total, 75.2% of all isolates are marked ‘first weighted’ - 46.9% 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 4 isolates are flagged. In total, 75.4% of all isolates are marked ‘first weighted’ - 46.8% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
 <p>As with <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
 <div class="sourceCode" id="cb19"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">&lt;-</span> <span class="no">data</span> <span class="kw">%&gt;%</span>
  <span class="fu"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</pre></body></html></div>
-<p>So we end up with 15,034 isolates for analysis.</p>
+<p>So we end up with 15,085 isolates for analysis.</p>
 <p>We can remove unneeded columns:</p>
 <div class="sourceCode" id="cb20"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">&lt;-</span> <span class="no">data_1st</span> <span class="kw">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(-<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">first</span>, <span class="no">keyab</span>))</pre></body></html></div>
@ -773,6 +774,7 @@ Unique: 2</p>
 <div class="sourceCode" id="cb21"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="no">data_1st</span>)</pre></body></html></div>
 <table class="table">
 <thead><tr class="header">
+<th></th>
 <th align="center">date</th>
 <th align="center">patient_id</th>
 <th align="center">hospital</th>
@ -789,28 +791,14 @@ Unique: 2</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2015-12-27</td>
-<td align="center">Y9</td>
-<td align="center">Hospital A</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">F</td>
-<td align="center">Gram-negative</td>
-<td align="center">Escherichia</td>
-<td align="center">coli</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="even">
-<td align="center">2014-01-17</td>
-<td align="center">X10</td>
+<td>1</td>
+<td align="center">2013-06-23</td>
+<td align="center">V9</td>
 <td align="center">Hospital C</td>
 <td align="center">B_STPHY_AURS</td>
-<td align="center">R</td>
 <td align="center">S</td>
-<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 <td align="center">Gram-positive</td>
@ -818,43 +806,30 @@ Unique: 2</p>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
+<tr class="even">
+<td>2</td>
+<td align="center">2016-12-25</td>
+<td align="center">S10</td>
+<td align="center">Hospital D</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">F</td>
+<td align="center">Gram-negative</td>
+<td align="center">Escherichia</td>
+<td align="center">coli</td>
+<td align="center">TRUE</td>
+</tr>
 <tr class="odd">
-<td align="center">2015-10-31</td>
-<td align="center">I3</td>
+<td>3</td>
+<td align="center">2011-01-27</td>
+<td align="center">Z10</td>
 <td align="center">Hospital B</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="center">2014-10-30</td>
-<td align="center">D9</td>
-<td align="center">Hospital A</td>
-<td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">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="center">2011-02-15</td>
-<td align="center">P6</td>
-<td align="center">Hospital D</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">S</td>
 <td align="center">F</td>
@ -864,18 +839,51 @@ Unique: 2</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="center">2011-10-07</td>
-<td align="center">G2</td>
-<td align="center">Hospital C</td>
-<td align="center">B_STPHY_AURS</td>
-<td align="center">S</td>
-<td align="center">S</td>
+<td>4</td>
+<td align="center">2010-09-14</td>
+<td align="center">N1</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">R</td>
+<td align="center">R</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">Gram-negative</td>
+<td align="center">Escherichia</td>
+<td align="center">coli</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="odd">
+<td>5</td>
+<td align="center">2017-10-31</td>
+<td align="center">W1</td>
+<td align="center">Hospital D</td>
+<td align="center">B_KLBSL_PNMN</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">F</td>
+<td align="center">Gram-negative</td>
+<td align="center">Klebsiella</td>
+<td align="center">pneumoniae</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="even">
+<td>7</td>
+<td align="center">2010-03-02</td>
+<td align="center">W2</td>
+<td align="center">Hospital B</td>
+<td align="center">B_ESCHR_COLI</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">F</td>
+<td align="center">Gram-negative</td>
+<td align="center">Escherichia</td>
+<td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 </tbody>
@ -897,8 +905,8 @@ Unique: 2</p>
 <div class="sourceCode" id="cb23"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">genus</span>, <span class="no">species</span>)</pre></body></html></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: character<br>
-Length: 15,034<br>
-Available: 15,034 (100%, NA: 0 = 0%)<br>
+Length: 15,085<br>
+Available: 15,085 (100%, NA: 0 = 0%)<br>
 Unique: 4</p>
 <p>Shortest: 16<br>
 Longest: 24</p>
@ -915,33 +923,33 @@ Longest: 24</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Escherichia coli</td>
-<td align="right">7,486</td>
-<td align="right">49.79%</td>
-<td align="right">7,486</td>
-<td align="right">49.79%</td>
+<td align="right">7,418</td>
+<td align="right">49.17%</td>
+<td align="right">7,418</td>
+<td align="right">49.17%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Staphylococcus aureus</td>
-<td align="right">3,727</td>
-<td align="right">24.79%</td>
-<td align="right">11,213</td>
-<td align="right">74.58%</td>
+<td align="right">3,716</td>
+<td align="right">24.63%</td>
+<td align="right">11,134</td>
+<td align="right">73.81%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Streptococcus pneumoniae</td>
-<td align="right">2,273</td>
-<td align="right">15.12%</td>
-<td align="right">13,486</td>
-<td align="right">89.70%</td>
+<td align="right">2,404</td>
+<td align="right">15.94%</td>
+<td align="right">13,538</td>
+<td align="right">89.74%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Klebsiella pneumoniae</td>
-<td align="right">1,548</td>
-<td align="right">10.30%</td>
-<td align="right">15,034</td>
+<td align="right">1,547</td>
+<td align="right">10.26%</td>
+<td align="right">15,085</td>
 <td align="right">100.00%</td>
 </tr>
 </tbody>
@ -953,7 +961,7 @@ Longest: 24</p>
 <p>The functions <code><a href="../reference/proportion.html">resistance()</a></code> and <code><a href="../reference/proportion.html">susceptibility()</a></code> can be used to calculate antimicrobial resistance or susceptibility. For more specific analyses, the functions <code><a href="../reference/proportion.html">proportion_S()</a></code>, <code><a href="../reference/proportion.html">proportion_SI()</a></code>, <code><a href="../reference/proportion.html">proportion_I()</a></code>, <code><a href="../reference/proportion.html">proportion_IR()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code> can be used to determine the proportion of a specific antimicrobial outcome.</p>
 <p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
 <div class="sourceCode" id="cb24"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="no">AMX</span>)
-<span class="co"># [1] 0.4703339</span></pre></body></html></div>
+<span class="co"># [1] 0.4658933</span></pre></body></html></div>
 <p>Or can be used in conjuction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb25"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="no">hospital</span>) <span class="kw">%&gt;%</span>
@ -966,19 +974,19 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.4760956</td>
+<td align="center">0.4701310</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.4711409</td>
+<td align="center">0.4702970</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.4700967</td>
+<td align="center">0.4575579</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.4605220</td>
+<td align="center">0.4574359</td>
 </tr>
 </tbody>
 </table>
@ -996,23 +1004,23 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.4760956</td>
-<td align="center">4518</td>
+<td align="center">0.4701310</td>
+<td align="center">4503</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.4711409</td>
-<td align="center">5215</td>
+<td align="center">0.4702970</td>
+<td align="center">5454</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.4700967</td>
-<td align="center">2274</td>
+<td align="center">0.4575579</td>
+<td align="center">2203</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.4605220</td>
-<td align="center">3027</td>
+<td align="center">0.4574359</td>
+<td align="center">2925</td>
 </tr>
 </tbody>
 </table>
@ -1032,27 +1040,27 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Escherichia</td>
-<td align="center">0.9181138</td>
-<td align="center">0.8947368</td>
-<td align="center">0.9927865</td>
+<td align="center">0.9207334</td>
+<td align="center">0.8959288</td>
+<td align="center">0.9936641</td>
 </tr>
 <tr class="even">
 <td align="center">Klebsiella</td>
-<td align="center">0.9153747</td>
-<td align="center">0.8959948</td>
-<td align="center">0.9948320</td>
+<td align="center">0.9198449</td>
+<td align="center">0.9004525</td>
+<td align="center">0.9974144</td>
 </tr>
 <tr class="odd">
 <td align="center">Staphylococcus</td>
-<td align="center">0.9246042</td>
-<td align="center">0.9203112</td>
-<td align="center">0.9946338</td>
+<td align="center">0.9203445</td>
+<td align="center">0.9233046</td>
+<td align="center">0.9938105</td>
 </tr>
 <tr class="even">
 <td align="center">Streptococcus</td>
-<td align="center">0.6159261</td>
+<td align="center">0.6110649</td>
 <td align="center">0.0000000</td>
-<td align="center">0.6159261</td>
+<td align="center">0.6110649</td>
 </tr>
 </tbody>
 </table>
@ -1180,7 +1188,7 @@ Longest: 24</p>
 </div>

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-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
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