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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9024</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9027</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -325,53 +325,31 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-10-24</td>
<td align="center">Z2</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">2015-07-10</td>
<td align="center">Q3</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus 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="even">
<td align="center">2013-05-29</td>
<td align="center">G1</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">2016-09-20</td>
<td align="center">I5</td>
<td align="center">Hospital D</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">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-08-07</td>
<td align="center">U2</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-05-20</td>
<td align="center">V3</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-06-18</td>
<td align="center">M1</td>
<td align="center">Hospital D</td>
<td align="center">2010-04-28</td>
<td align="center">D3</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
@ -380,16 +358,38 @@
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-02-29</td>
<td align="center">V8</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2010-02-07</td>
<td align="center">T8</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">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-04-29</td>
<td align="center">L4</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">S</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-05-12</td>
<td align="center">C6</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -422,16 +422,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,349</td>
<td align="right">51.75%</td>
<td align="right">10,349</td>
<td align="right">51.75%</td>
<td align="right">10,372</td>
<td align="right">51.86%</td>
<td align="right">10,372</td>
<td align="right">51.86%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,651</td>
<td align="right">48.26%</td>
<td align="right">9,628</td>
<td align="right">48.14%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -488,9 +488,9 @@ Longest: 1</p>
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,623 'phenotype-based' first isolates (53.1% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,687 'phenotype-based' first isolates (53.4% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.1% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<p>So only 53.4% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">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></span></code></pre></div>
@ -499,10 +499,10 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,623 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,687 isolates for analysis. Now our data looks like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
<table style="width:100%;" class="table">
<table class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -515,7 +515,7 @@ Longest: 1</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="10%">
<col width="9%">
<col width="5%">
</colgroup>
@ -537,25 +537,9 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">2</td>
<td align="center">2013-05-29</td>
<td align="center">G1</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">3</td>
<td align="center">2012-08-07</td>
<td align="center">U2</td>
<td align="left">4</td>
<td align="center">2010-02-07</td>
<td align="center">T8</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
@ -568,68 +552,84 @@ Longest: 1</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">2014-04-29</td>
<td align="center">L4</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">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2012-05-20</td>
<td align="center">V3</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="left">7</td>
<td align="center">2016-10-13</td>
<td align="center">Z2</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">2014-06-18</td>
<td align="center">M1</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">2016-02-29</td>
<td align="center">V8</td>
<tr class="even">
<td align="left">9</td>
<td align="center">2015-02-02</td>
<td align="center">C3</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</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">15</td>
<td align="center">2015-09-15</td>
<td align="center">G10</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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2010-05-10</td>
<td align="center">B9</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="left">17</td>
<td align="center">2010-01-19</td>
<td align="center">M3</td>
<td align="center">Hospital A</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-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -653,8 +653,8 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,623<br>
Available: 10,623 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,687<br>
Available: 10,687 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -671,33 +671,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,630</td>
<td align="right">43.58%</td>
<td align="right">4,630</td>
<td align="right">43.58%</td>
<td align="right">4,688</td>
<td align="right">43.87%</td>
<td align="right">4,688</td>
<td align="right">43.87%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,710</td>
<td align="right">25.51%</td>
<td align="right">7,340</td>
<td align="right">2,697</td>
<td align="right">25.24%</td>
<td align="right">7,385</td>
<td align="right">69.10%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,057</td>
<td align="right">19.36%</td>
<td align="right">9,397</td>
<td align="right">88.46%</td>
<td align="right">2,160</td>
<td align="right">20.21%</td>
<td align="right">9,545</td>
<td align="right">89.31%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,226</td>
<td align="right">11.54%</td>
<td align="right">10,623</td>
<td align="right">1,142</td>
<td align="right">10.69%</td>
<td align="right">10,687</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -744,41 +744,11 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-05-10</td>
<td align="center">B9</td>
<td align="center">2014-04-29</td>
<td align="center">L4</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-02-28</td>
<td align="center">B6</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-03-07</td>
<td align="center">L6</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
@ -789,24 +759,39 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-02-04</td>
<td align="center">J2</td>
<td align="center">Hospital D</td>
<td align="center">2015-08-22</td>
<td align="center">P8</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-07-22</td>
<td align="center">X8</td>
<td align="center">2012-10-25</td>
<td align="center">Y2</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-03-30</td>
<td align="center">R4</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
@ -818,14 +803,14 @@ Longest: 24</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-03-20</td>
<td align="center">P7</td>
<td align="center">Hospital D</td>
<tr class="odd">
<td align="center">2014-02-24</td>
<td align="center">V1</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_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">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@ -833,6 +818,21 @@ Longest: 24</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-10-30</td>
<td align="center">J2</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">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> function:</p>
@ -854,50 +854,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2159</td>
<td align="center">145</td>
<td align="center">2326</td>
<td align="center">4630</td>
<td align="center">2172</td>
<td align="center">146</td>
<td align="center">2370</td>
<td align="center">4688</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3398</td>
<td align="center">178</td>
<td align="center">1054</td>
<td align="center">4630</td>
<td align="center">3417</td>
<td align="center">158</td>
<td align="center">1113</td>
<td align="center">4688</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3369</td>
<td align="center">3458</td>
<td align="center">0</td>
<td align="center">1261</td>
<td align="center">4630</td>
<td align="center">1230</td>
<td align="center">4688</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4053</td>
<td align="center">4071</td>
<td align="center">0</td>
<td align="center">577</td>
<td align="center">4630</td>
<td align="center">617</td>
<td align="center">4688</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">1226</td>
<td align="center">1226</td>
<td align="center">1142</td>
<td align="center">1142</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">943</td>
<td align="center">48</td>
<td align="center">235</td>
<td align="center">1226</td>
<td align="center">904</td>
<td align="center">40</td>
<td align="center">198</td>
<td align="center">1142</td>
</tr>
</tbody>
</table>
@ -920,34 +920,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4053</td>
<td align="center">4071</td>
<td align="center">0</td>
<td align="center">577</td>
<td align="center">4630</td>
<td align="center">617</td>
<td align="center">4688</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1092</td>
<td align="center">1034</td>
<td align="center">0</td>
<td align="center">134</td>
<td align="center">1226</td>
<td align="center">108</td>
<td align="center">1142</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2400</td>
<td align="center">2386</td>
<td align="center">0</td>
<td align="center">310</td>
<td align="center">2710</td>
<td align="center">311</td>
<td align="center">2697</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">2057</td>
<td align="center">2057</td>
<td align="center">2160</td>
<td align="center">2160</td>
</tr>
</tbody>
</table>
@ -961,7 +961,7 @@ 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="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></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>
<span><span class="co"># [1] 0.5488092</span></span></code></pre></div>
<span><span class="co"># [1] 0.540844</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@ -975,19 +975,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5565721</td>
<td align="center">0.5347460</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5457235</td>
<td align="center">0.5486298</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5533546</td>
<td align="center">0.5512224</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5385735</td>
<td align="center">0.5274779</td>
</tr>
</tbody>
</table>
@ -1008,23 +1008,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5565721</td>
<td align="center">3279</td>
<td align="center">0.5347460</td>
<td align="center">3209</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5457235</td>
<td align="center">3718</td>
<td align="center">0.5486298</td>
<td align="center">3722</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5533546</td>
<td align="center">1565</td>
<td align="center">0.5512224</td>
<td align="center">1718</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5385735</td>
<td align="center">2061</td>
<td align="center">0.5274779</td>
<td align="center">2038</td>
</tr>
</tbody>
</table>
@ -1047,27 +1047,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7723542</td>
<td align="center">0.8753780</td>
<td align="center">0.9790497</td>
<td align="center">0.7625853</td>
<td align="center">0.8683874</td>
<td align="center">0.9769625</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8083197</td>
<td align="center">0.8907015</td>
<td align="center">0.9787928</td>
<td align="center">0.8266200</td>
<td align="center">0.9054291</td>
<td align="center">0.9824869</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7911439</td>
<td align="center">0.8856089</td>
<td align="center">0.9833948</td>
<td align="center">0.7997775</td>
<td align="center">0.8846867</td>
<td align="center">0.9818317</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5333009</td>
<td align="center">0.5462963</td>
<td align="center">0.0000000</td>
<td align="center">0.5333009</td>
<td align="center">0.5462963</td>
</tr>
</tbody>
</table>
@ -1092,23 +1092,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">55.7%</td>
<td align="right">28.5%</td>
<td align="right">53.5%</td>
<td align="right">26.7%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.6%</td>
<td align="right">25.6%</td>
<td align="right">54.9%</td>
<td align="right">27.3%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">55.3%</td>
<td align="right">26.5%</td>
<td align="right">55.1%</td>
<td align="right">24.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">53.9%</td>
<td align="right">24.8%</td>
<td align="right">52.7%</td>
<td align="right">26.4%</td>
</tr>
</tbody>
</table>
@ -1206,16 +1206,18 @@ Longest: 24</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 8 64 4 0.005 32 0.125 0.005 4 &gt;=256 0.005 </span></span>
<span><span class="co"># [11] 0.01 &gt;=256 0.01 0.5 8 0.125 0.01 4 0.125 0.5 </span></span>
<span><span class="co"># [21] 1 1 0.25 0.0625 8 128 8 64 &gt;=256 0.5 </span></span>
<span><span class="co"># [31] 0.25 8 2 32 0.125 0.0625 0.25 0.025 0.001 8 </span></span>
<span><span class="co"># [41] 128 2 64 0.25 &gt;=256 0.01 0.01 2 0.125 0.025 </span></span>
<span><span class="co"># [51] &gt;=256 0.25 0.025 8 0.005 0.125 0.025 16 0.01 0.025 </span></span>
<span><span class="co"># [61] 1 64 8 1 64 0.025 32 &gt;=256 8 2 </span></span>
<span><span class="co"># [71] 4 0.25 0.002 0.001 1 0.001 &gt;=256 16 4 2 </span></span>
<span><span class="co"># [81] 0.125 0.125 0.125 4 64 2 0.01 0.01 0.01 4 </span></span>
<span><span class="co"># [91] 16 32 0.005 0.005 4 0.0625 0.125 0.005 0.01 2</span></span></code></pre></div>
<span><span class="co"># [1] 0.125 0.005 128 0.25 16 0.5 0.002 4 256 </span></span>
<span><span class="co"># [10] 0.01 32 0.0625 64 0.5 0.005 0.125 0.01 4 </span></span>
<span><span class="co"># [19] 16 2 2 256 4 16 4 0.025 0.125 </span></span>
<span><span class="co"># [28] 2 0.0625 16 0.5 1 0.025 &lt;=0.001 0.5 0.5 </span></span>
<span><span class="co"># [37] 0.025 2 0.01 0.0625 16 8 &lt;=0.001 0.01 8 </span></span>
<span><span class="co"># [46] 0.005 0.125 0.002 0.0625 16 0.25 64 128 0.5 </span></span>
<span><span class="co"># [55] 64 2 0.125 0.0625 0.01 16 0.005 1 1 </span></span>
<span><span class="co"># [64] 64 0.002 4 16 64 0.125 0.01 0.01 8 </span></span>
<span><span class="co"># [73] 0.5 0.5 &lt;=0.001 256 256 64 0.01 4 32 </span></span>
<span><span class="co"># [82] 0.01 8 0.25 &lt;=0.001 &lt;=0.001 64 0.01 0.005 0.002 </span></span>
<span><span class="co"># [91] 2 0.01 0.002 0.5 2 0.125 1 0.5 0.0625 </span></span>
<span><span class="co"># [100] 0.005</span></span></code></pre></div>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1242,10 +1244,10 @@ Longest: 24</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 22 18 29 23 26 26 22 22 17 28 29 31 25 28 22 27 28 30 27 26 28 29 31 19 26</span></span>
<span><span class="co"># [26] 25 25 24 25 30 17 21 25 21 18 17 30 23 30 19 18 29 25 29 27 23 28 21 17 25</span></span>
<span><span class="co"># [51] 27 23 17 29 28 25 30 23 21 22 20 21 28 25 23 31 29 25 31 17 22 20 21 17 19</span></span>
<span><span class="co"># [76] 17 21 21 18 18 20 29 30 21 18 23 18 29 25 22 27 22 22 24 24 25 27 31 26 18</span></span></code></pre></div>
<span><span class="co"># [1] 24 18 17 20 25 19 31 25 27 19 20 19 31 19 21 20 27 21 21 29 22 17 26 23 20</span></span>
<span><span class="co"># [26] 25 22 21 20 24 28 17 17 18 31 21 26 17 30 17 23 22 26 30 18 29 20 27 22 28</span></span>
<span><span class="co"># [51] 17 23 27 23 27 23 25 22 22 31 18 20 17 25 20 24 27 17 29 25 25 28 25 24 20</span></span>
<span><span class="co"># [76] 30 20 17 29 28 31 26 18 21 26 26 27 28 21 18 19 27 31 26 24 21 23 22 29 25</span></span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>