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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="">1.8.2.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9041</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">
@@ -395,70 +395,70 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-05-31</td>
<td align="center">N10</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia 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>
</tr>
<tr class="even">
<td align="center">2015-04-26</td>
<td align="center">I4</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">2010-04-13</td>
<td align="center">B10</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-07-16</td>
<td align="center">V10</td>
<td align="center">Hospital D</td>
<tr class="even">
<td align="center">2014-01-20</td>
<td align="center">K9</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-01-31</td>
<td align="center">N7</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus 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">2017-02-09</td>
<td align="center">W1</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-09-11</td>
<td align="center">V5</td>
<td align="center">2012-03-04</td>
<td align="center">E5</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2011-08-21</td>
<td align="center">N6</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-08-24</td>
<td align="center">V1</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">2011-10-21</td>
<td align="center">F6</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
@@ -494,16 +494,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,447</td>
<td align="right">52.24%</td>
<td align="right">10,447</td>
<td align="right">52.24%</td>
<td align="right">10,278</td>
<td align="right">51.39%</td>
<td align="right">10,278</td>
<td align="right">51.39%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,553</td>
<td align="right">47.77%</td>
<td align="right">9,722</td>
<td align="right">48.61%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@@ -616,9 +616,9 @@ takes into account the antimicrobial susceptibility test results using
<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 10,679 'phenotype-based' first isolates (53.4% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,616 'phenotype-based' first isolates (53.1% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.4% is suitable for resistance analysis! We can now filter
<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>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
@@ -629,7 +629,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<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 10,679 isolates for analysis. Now our data looks
<p>So we end up with 10,616 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>
@@ -669,45 +669,45 @@ like:</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2012-05-31</td>
<td align="center">N10</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">2010-04-13</td>
<td align="center">B10</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">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">2016-09-11</td>
<td align="center">V5</td>
<td align="center">Hospital B</td>
<td align="left">2</td>
<td align="center">2014-01-20</td>
<td align="center">K9</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">R</td>
<td align="center">S</td>
<td align="center">F</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">7</td>
<td align="center">2012-07-11</td>
<td align="center">V1</td>
<td align="center">Hospital C</td>
<td align="left">3</td>
<td align="center">2016-01-31</td>
<td align="center">N7</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">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@@ -716,51 +716,51 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2017-09-04</td>
<td align="center">G4</td>
<td align="left">4</td>
<td align="center">2012-03-04</td>
<td align="center">E5</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</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">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">6</td>
<td align="center">2011-10-21</td>
<td align="center">F6</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</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>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">10</td>
<td align="center">2010-08-06</td>
<td align="center">V2</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">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">14</td>
<td align="center">2012-06-25</td>
<td align="center">J2</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="left">7</td>
<td align="center">2014-06-01</td>
<td align="center">G3</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@@ -796,8 +796,8 @@ readable:</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://msberends.github.io/cleaner/reference/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: 10,679<br>
Available: 10,679 (100%, NA: 0 = 0%)<br>
Length: 10,616<br>
Available: 10,616 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@@ -822,33 +822,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,629</td>
<td align="right">43.35%</td>
<td align="right">4,629</td>
<td align="right">43.35%</td>
<td align="right">4,668</td>
<td align="right">43.97%</td>
<td align="right">4,668</td>
<td align="right">43.97%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,722</td>
<td align="right">25.49%</td>
<td align="right">7,351</td>
<td align="right">68.84%</td>
<td align="right">2,697</td>
<td align="right">25.41%</td>
<td align="right">7,365</td>
<td align="right">69.38%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,112</td>
<td align="right">19.78%</td>
<td align="right">9,463</td>
<td align="right">88.61%</td>
<td align="right">2,067</td>
<td align="right">19.47%</td>
<td align="right">9,432</td>
<td align="right">88.85%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,216</td>
<td align="right">11.39%</td>
<td align="right">10,679</td>
<td align="right">1,184</td>
<td align="right">11.15%</td>
<td align="right">10,616</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@@ -869,14 +869,14 @@ antibiotic class they are in:</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="10%">
<col width="11%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@@ -897,73 +897,88 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-07-11</td>
<td align="center">V1</td>
<td align="center">Hospital C</td>
<td align="center">2010-04-13</td>
<td align="center">B10</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">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">2016-01-31</td>
<td align="center">N7</td>
<td align="center">Hospital D</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">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="odd">
<td align="center">2016-12-09</td>
<td align="center">H8</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-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-05-21</td>
<td align="center">O5</td>
<td align="center">Hospital D</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">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">2010-11-11</td>
<td align="center">A2</td>
<tr class="odd">
<td align="center">2011-03-11</td>
<td align="center">A3</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">R</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">2015-04-22</td>
<td align="center">X9</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</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">2017-04-02</td>
<td align="center">G5</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-04-01</td>
<td align="center">S1</td>
<td align="center">2017-02-09</td>
<td align="center">Q3</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">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@@ -971,21 +986,6 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-05-06</td>
<td align="center">D1</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">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in
@@ -1009,50 +1009,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2177</td>
<td align="center">124</td>
<td align="center">2328</td>
<td align="center">4629</td>
<td align="center">2238</td>
<td align="center">132</td>
<td align="center">2298</td>
<td align="center">4668</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3412</td>
<td align="center">170</td>
<td align="center">1047</td>
<td align="center">4629</td>
<td align="center">3403</td>
<td align="center">152</td>
<td align="center">1113</td>
<td align="center">4668</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3331</td>
<td align="center">3452</td>
<td align="center">0</td>
<td align="center">1298</td>
<td align="center">4629</td>
<td align="center">1216</td>
<td align="center">4668</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4046</td>
<td align="center">4097</td>
<td align="center">0</td>
<td align="center">583</td>
<td align="center">4629</td>
<td align="center">571</td>
<td align="center">4668</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">1216</td>
<td align="center">1216</td>
<td align="center">1184</td>
<td align="center">1184</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">943</td>
<td align="center">52</td>
<td align="center">221</td>
<td align="center">1216</td>
<td align="center">926</td>
<td align="center">58</td>
<td align="center">200</td>
<td align="center">1184</td>
</tr>
</tbody>
</table>
@@ -1075,34 +1075,34 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4046</td>
<td align="center">4097</td>
<td align="center">0</td>
<td align="center">583</td>
<td align="center">4629</td>
<td align="center">571</td>
<td align="center">4668</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1095</td>
<td align="center">1055</td>
<td align="center">0</td>
<td align="center">121</td>
<td align="center">1216</td>
<td align="center">129</td>
<td align="center">1184</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2420</td>
<td align="center">2375</td>
<td align="center">0</td>
<td align="center">302</td>
<td align="center">2722</td>
<td align="center">322</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">2112</td>
<td align="center">2112</td>
<td align="center">2067</td>
<td align="center">2067</td>
</tr>
</tbody>
</table>
@@ -1134,7 +1134,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
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] 0.549396</span></span></code></pre></div>
<span><span class="co"># [1] 0.5417295</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">
@@ -1149,19 +1149,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5496112</td>
<td align="center">0.5468395</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5540966</td>
<td align="center">0.5509504</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5353956</td>
<td align="center">0.5332103</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5518987</td>
<td align="center">0.5243269</td>
</tr>
</tbody>
</table>
@@ -1186,23 +1186,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5496112</td>
<td align="center">3215</td>
<td align="center">0.5468395</td>
<td align="center">3085</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5540966</td>
<td align="center">3808</td>
<td align="center">0.5509504</td>
<td align="center">3788</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5353956</td>
<td align="center">1681</td>
<td align="center">0.5332103</td>
<td align="center">1626</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5518987</td>
<td align="center">1975</td>
<td align="center">0.5243269</td>
<td align="center">2117</td>
</tr>
</tbody>
</table>
@@ -1227,27 +1227,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7738172</td>
<td align="center">0.8740549</td>
<td align="center">0.9758047</td>
<td align="center">0.7615681</td>
<td align="center">0.8776778</td>
<td align="center">0.9768638</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8182566</td>
<td align="center">0.9004934</td>
<td align="center">0.9851974</td>
<td align="center">0.8310811</td>
<td align="center">0.8910473</td>
<td align="center">0.9805743</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7883909</td>
<td align="center">0.8890522</td>
<td align="center">0.9783248</td>
<td align="center">0.7897664</td>
<td align="center">0.8806081</td>
<td align="center">0.9762699</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5298295</td>
<td align="center">0.5365264</td>
<td align="center">0.0000000</td>
<td align="center">0.5298295</td>
<td align="center">0.5365264</td>
</tr>
</tbody>
</table>
@@ -1275,23 +1275,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">55.0%</td>
<td align="right">27.0%</td>
<td align="right">54.7%</td>
<td align="right">26.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">55.4%</td>
<td align="right">25.8%</td>
<td align="right">55.1%</td>
<td align="right">27.6%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">53.5%</td>
<td align="right">25.3%</td>
<td align="right">53.3%</td>
<td align="right">26.8%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">55.2%</td>
<td align="right">28.5%</td>
<td align="right">52.4%</td>
<td align="right">25.9%</td>
</tr>
</tbody>
</table>
@@ -1407,18 +1407,16 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</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] 64 16 0.01 0.01 32 1 0.25 2 &lt;=0.001</span></span>
<span><span class="co"># [10] 0.025 0.002 0.002 0.005 128 0.5 0.125 0.0625 4 </span></span>
<span><span class="co"># [19] 0.01 2 0.25 32 128 0.005 0.0625 0.005 0.01 </span></span>
<span><span class="co"># [28] 8 &lt;=0.001 0.002 &lt;=0.001 0.0625 &lt;=0.001 1 0.01 0.025 </span></span>
<span><span class="co"># [37] 0.0625 1 2 64 32 0.125 16 32 1 </span></span>
<span><span class="co"># [46] 16 8 0.002 4 0.0625 0.0625 4 0.01 0.0625 </span></span>
<span><span class="co"># [55] 0.25 0.0625 4 8 0.5 16 128 0.01 256 </span></span>
<span><span class="co"># [64] 1 8 32 0.002 2 2 4 8 8 </span></span>
<span><span class="co"># [73] 64 128 0.005 256 256 128 0.025 1 128 </span></span>
<span><span class="co"># [82] 0.01 0.002 0.5 0.002 0.5 0.002 2 &lt;=0.001 128 </span></span>
<span><span class="co"># [91] 256 0.005 8 0.125 256 64 0.025 32 0.002 </span></span>
<span><span class="co"># [100] 0.5</span></span></code></pre></div>
<span><span class="co"># [1] 0.125 16 64 0.0625 0.01 4 0.5 1 0.5 1 </span></span>
<span><span class="co"># [11] 0.001 16 0.0625 0.025 0.5 0.025 0.025 16 0.5 32 </span></span>
<span><span class="co"># [21] 1 0.025 0.5 64 0.25 0.5 0.001 0.5 0.25 0.001 </span></span>
<span><span class="co"># [31] 0.0625 2 0.002 0.025 64 1 1 64 0.01 0.001 </span></span>
<span><span class="co"># [41] 0.025 0.002 0.01 64 0.01 1 0.005 16 64 0.0625</span></span>
<span><span class="co"># [51] 0.002 128 0.5 32 0.25 0.002 0.01 0.025 8 128 </span></span>
<span><span class="co"># [61] 0.025 64 0.25 2 4 0.025 2 16 0.25 0.25 </span></span>
<span><span class="co"># [71] 64 32 1 0.125 0.125 32 16 128 2 0.0625</span></span>
<span><span class="co"># [81] 0.01 0.125 0.01 16 32 0.01 2 16 4 0.002 </span></span>
<span><span class="co"># [91] 32 8 0.25 0.025 0.005 0.01 8 16 0.005 8</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>
@@ -1452,10 +1450,10 @@ plotting:</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] 25 24 24 22 25 22 25 30 24 19 19 31 19 19 26 22 23 30 25 30 21 26 31 21 23</span></span>
<span><span class="co"># [26] 21 27 22 17 22 25 18 28 25 17 28 25 22 30 29 27 24 20 24 28 24 19 21 26 25</span></span>
<span><span class="co"># [51] 21 19 31 21 26 21 25 26 18 20 24 24 19 23 18 25 28 27 30 29 21 29 19 31 19</span></span>
<span><span class="co"># [76] 21 17 29 28 26 20 29 29 26 27 30 19 21 23 28 19 21 25 31 17 20 26 20 19 29</span></span></code></pre></div>
<span><span class="co"># [1] 28 17 23 21 20 24 23 26 17 17 24 20 29 17 20 24 17 17 27 20 28 21 17 18 30</span></span>
<span><span class="co"># [26] 28 26 20 20 30 26 29 18 28 23 20 23 19 28 22 29 29 19 25 31 26 24 21 23 22</span></span>
<span><span class="co"># [51] 25 25 25 18 28 17 31 29 25 26 27 23 17 24 17 28 25 29 29 24 29 29 18 20 27</span></span>
<span><span class="co"># [76] 26 18 22 25 28 30 31 27 25 21 26 29 18 18 26 22 30 29 29 29 22 24 28 17 27</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>