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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="">1.8.2.9066</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9067</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">
@ -380,12 +380,12 @@ data set:</p>
<col width="13%">
<col width="13%">
<col width="13%">
<col width="26%">
<col width="28%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="9%">
<col width="8%">
</colgroup>
<thead><tr class="header">
<th align="center">date</th>
@ -400,68 +400,68 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-12-25</td>
<td align="center">G9</td>
<td align="center">Hospital C</td>
<td align="center">2011-06-10</td>
<td align="center">S6</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</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">M</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-09-15</td>
<td align="center">Q1</td>
<td align="center">2015-08-04</td>
<td align="center">O3</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2011-04-26</td>
<td align="center">V1</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</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="odd">
<td align="center">2010-12-29</td>
<td align="center">J7</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-01-07</td>
<td align="center">D5</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">2011-07-18</td>
<td align="center">I6</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2015-05-08</td>
<td align="center">H8</td>
<td align="center">2016-09-19</td>
<td align="center">D3</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">M</td>
</tr>
<tr class="even">
<td align="center">2012-01-28</td>
<td align="center">S8</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-05-26</td>
<td align="center">P3</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
@ -499,16 +499,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,511</td>
<td align="right">52.56%</td>
<td align="right">10,511</td>
<td align="right">52.56%</td>
<td align="right">10,438</td>
<td align="right">52.19%</td>
<td align="right">10,438</td>
<td align="right">52.19%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,489</td>
<td align="right">47.45%</td>
<td align="right">9,562</td>
<td align="right">47.81%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -621,9 +621,9 @@ 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 10,638 'phenotype-based' first isolates (53.2% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,551 'phenotype-based' first isolates (52.8% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.2% is suitable for resistance analysis! We can now filter
<p>So only 52.8% 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">
@ -634,7 +634,7 @@ 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 10,638 isolates for analysis. Now our data looks
<p>So we end up with 10,551 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>
@ -673,94 +673,94 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">3</td>
<td align="center">2010-12-29</td>
<td align="center">J7</td>
<td align="center">Hospital D</td>
<td align="left">1</td>
<td align="center">2011-06-10</td>
<td align="center">S6</td>
<td align="center">Hospital B</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">S</td>
<td align="center">M</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">10</td>
<td align="center">2010-01-25</td>
<td align="center">M8</td>
<td align="left">2</td>
<td align="center">2015-08-04</td>
<td align="center">O3</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">B_STRPT_PNMN</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">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="left">12</td>
<td align="center">2012-01-18</td>
<td align="center">J5</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="left">3</td>
<td align="center">2011-04-26</td>
<td align="center">V1</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">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">13</td>
<td align="center">2011-08-17</td>
<td align="center">S4</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">14</td>
<td align="center">2016-12-27</td>
<td align="center">H6</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">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">16</td>
<td align="center">2017-10-23</td>
<td align="center">D6</td>
<td align="center">Hospital C</td>
<td align="left">4</td>
<td align="center">2011-07-18</td>
<td align="center">I6</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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">5</td>
<td align="center">2016-09-19</td>
<td align="center">D3</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2014-07-28</td>
<td align="center">F6</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
@ -801,8 +801,8 @@ 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: 10,638<br>
Available: 10,638 (100%, NA: 0 = 0%)<br>
Length: 10,551<br>
Available: 10,551 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -827,33 +827,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,659</td>
<td align="right">43.80%</td>
<td align="right">4,659</td>
<td align="right">43.80%</td>
<td align="right">4,601</td>
<td align="right">43.61%</td>
<td align="right">4,601</td>
<td align="right">43.61%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,645</td>
<td align="right">24.86%</td>
<td align="right">7,304</td>
<td align="right">68.66%</td>
<td align="right">2,724</td>
<td align="right">25.82%</td>
<td align="right">7,325</td>
<td align="right">69.42%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,119</td>
<td align="right">19.92%</td>
<td align="right">9,423</td>
<td align="right">88.58%</td>
<td align="right">2,023</td>
<td align="right">19.17%</td>
<td align="right">9,348</td>
<td align="right">88.60%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,215</td>
<td align="right">11.42%</td>
<td align="right">10,638</td>
<td align="right">1,203</td>
<td align="right">11.40%</td>
<td align="right">10,551</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -902,28 +902,13 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-02-06</td>
<td align="center">W3</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_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-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-10-05</td>
<td align="center">W7</td>
<td align="center">2015-08-04</td>
<td align="center">O3</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">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@ -931,42 +916,12 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-08-06</td>
<td align="center">V1</td>
<td align="center">Hospital B</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">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-05-13</td>
<td align="center">I2</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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">2015-09-18</td>
<td align="center">I5</td>
<td align="center">Hospital A</td>
<td align="center">2016-09-19</td>
<td align="center">D3</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
@ -976,13 +931,58 @@ antibiotic class they are in:</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-10-13</td>
<td align="center">N3</td>
<td align="center">Hospital D</td>
<tr class="odd">
<td align="center">2015-03-03</td>
<td align="center">C9</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">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">2011-09-04</td>
<td align="center">W10</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">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">2010-05-05</td>
<td align="center">D4</td>
<td align="center">Hospital A</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">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-03-20</td>
<td align="center">M6</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">R</td>
<td align="center">M</td>
@ -1013,50 +1013,50 @@ 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">2200</td>
<td align="center">119</td>
<td align="center">2340</td>
<td align="center">4659</td>
<td align="center">2150</td>
<td align="center">145</td>
<td align="center">2306</td>
<td align="center">4601</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3418</td>
<td align="center">146</td>
<td align="center">1095</td>
<td align="center">4659</td>
<td align="center">3387</td>
<td align="center">165</td>
<td align="center">1049</td>
<td align="center">4601</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3409</td>
<td align="center">3386</td>
<td align="center">0</td>
<td align="center">1250</td>
<td align="center">4659</td>
<td align="center">1215</td>
<td align="center">4601</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4110</td>
<td align="center">4022</td>
<td align="center">0</td>
<td align="center">549</td>
<td align="center">4659</td>
<td align="center">579</td>
<td align="center">4601</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">1215</td>
<td align="center">1215</td>
<td align="center">1203</td>
<td align="center">1203</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">963</td>
<td align="center">50</td>
<td align="center">202</td>
<td align="center">1215</td>
<td align="center">922</td>
<td align="center">49</td>
<td align="center">232</td>
<td align="center">1203</td>
</tr>
</tbody>
</table>
@ -1078,34 +1078,34 @@ 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">4110</td>
<td align="center">4022</td>
<td align="center">0</td>
<td align="center">549</td>
<td align="center">4659</td>
<td align="center">579</td>
<td align="center">4601</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1070</td>
<td align="center">1082</td>
<td align="center">0</td>
<td align="center">145</td>
<td align="center">1215</td>
<td align="center">121</td>
<td align="center">1203</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2366</td>
<td align="center">2442</td>
<td align="center">0</td>
<td align="center">279</td>
<td align="center">2645</td>
<td align="center">282</td>
<td align="center">2724</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">2119</td>
<td align="center">2119</td>
<td align="center">2023</td>
<td align="center">2023</td>
</tr>
</tbody>
</table>
@ -1137,7 +1137,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb25"><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] 0.5423952</span></span></code></pre></div>
<span><span class="co"># [1] 0.5440243</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="cb26"><pre class="downlit sourceCode r">
@ -1152,19 +1152,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5512821</td>
<td align="center">0.5401168</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5344323</td>
<td align="center">0.5521811</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5549206</td>
<td align="center">0.5381703</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5337452</td>
<td align="center">0.5404113</td>
</tr>
</tbody>
</table>
@ -1189,23 +1189,23 @@ 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">0.5512821</td>
<td align="center">3198</td>
<td align="center">0.5401168</td>
<td align="center">3253</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5344323</td>
<td align="center">3761</td>
<td align="center">0.5521811</td>
<td align="center">3622</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5549206</td>
<td align="center">1575</td>
<td align="center">0.5381703</td>
<td align="center">1585</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5337452</td>
<td align="center">2104</td>
<td align="center">0.5404113</td>
<td align="center">2091</td>
</tr>
</tbody>
</table>
@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7649710</td>
<td align="center">0.8821636</td>
<td align="center">0.9778923</td>
<td align="center">0.7720061</td>
<td align="center">0.8741578</td>
<td align="center">0.9793523</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8337449</td>
<td align="center">0.8806584</td>
<td align="center">0.9777778</td>
<td align="center">0.8071488</td>
<td align="center">0.8994181</td>
<td align="center">0.9800499</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8003781</td>
<td align="center">0.8945180</td>
<td align="center">0.9826087</td>
<td align="center">0.7907489</td>
<td align="center">0.8964758</td>
<td align="center">0.9842144</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5450684</td>
<td align="center">0.5353435</td>
<td align="center">0.0000000</td>
<td align="center">0.5450684</td>
<td align="center">0.5353435</td>
</tr>
</tbody>
</table>
@ -1278,23 +1278,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">55.1%</td>
<td align="right">26.5%</td>
<td align="right">54.0%</td>
<td align="right">26.6%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">53.4%</td>
<td align="right">26.3%</td>
<td align="right">55.2%</td>
<td align="right">26.2%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">55.5%</td>
<td align="right">25.6%</td>
<td align="right">53.8%</td>
<td align="right">26.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">53.4%</td>
<td align="right">26.0%</td>
<td align="right">54.0%</td>
<td align="right">26.3%</td>
</tr>
</tbody>
</table>
@ -1410,18 +1410,18 @@ 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] 128 32 0.01 &lt;=0.001 0.125 0.125 64 0.025 8 </span></span>
<span><span class="co"># [10] 8 32 8 0.002 1 0.125 0.125 0.002 0.01 </span></span>
<span><span class="co"># [19] 128 1 &lt;=0.001 8 0.005 0.01 0.002 64 1 </span></span>
<span><span class="co"># [28] 0.125 0.5 256 256 2 1 0.025 4 8 </span></span>
<span><span class="co"># [37] 0.025 1 0.5 &lt;=0.001 0.0625 0.002 64 0.002 0.005 </span></span>
<span><span class="co"># [46] 256 0.01 0.0625 &lt;=0.001 0.025 2 1 256 1 </span></span>
<span><span class="co"># [55] 2 32 0.25 32 64 0.5 &lt;=0.001 0.005 0.5 </span></span>
<span><span class="co"># [64] 0.5 32 0.25 4 16 0.025 0.5 &lt;=0.001 16 </span></span>
<span><span class="co"># [73] 2 0.0625 128 4 2 2 0.005 256 0.125 </span></span>
<span><span class="co"># [82] 0.002 256 8 &lt;=0.001 0.0625 64 &lt;=0.001 0.002 1 </span></span>
<span><span class="co"># [91] 64 16 0.025 16 0.025 0.002 1 0.25 32 </span></span>
<span><span class="co"># [100] 64</span></span></code></pre></div>
<span><span class="co"># [1] 128 4 4 64 0.125 0.5 1 4 128 </span></span>
<span><span class="co"># [10] 0.125 0.0625 0.025 64 0.025 0.01 4 16 32 </span></span>
<span><span class="co"># [19] 256 &lt;=0.001 64 64 8 256 1 0.002 0.01 </span></span>
<span><span class="co"># [28] 0.005 64 0.125 16 128 2 4 32 8 </span></span>
<span><span class="co"># [37] 256 256 128 0.0625 16 32 32 256 0.002 </span></span>
<span><span class="co"># [46] 0.25 &lt;=0.001 2 128 &lt;=0.001 &lt;=0.001 256 0.0625 4 </span></span>
<span><span class="co"># [55] 0.25 64 16 0.125 1 0.5 0.002 16 128 </span></span>
<span><span class="co"># [64] 0.002 0.025 128 16 0.01 64 0.025 0.125 0.01 </span></span>
<span><span class="co"># [73] 0.25 0.25 1 16 1 2 0.25 32 0.25 </span></span>
<span><span class="co"># [82] 16 0.01 0.01 1 1 128 128 2 0.125 </span></span>
<span><span class="co"># [91] 0.01 0.0625 0.01 0.005 4 16 256 4 4 </span></span>
<span><span class="co"># [100] 1</span></span></code></pre></div>
<div class="sourceCode" id="cb36"><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>
@ -1455,10 +1455,10 @@ 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] 27 25 21 24 18 18 19 26 23 28 19 21 28 28 31 28 22 26 17 29 19 27 21 24 23</span></span>
<span><span class="co"># [26] 20 26 18 18 18 17 28 31 23 23 22 29 29 23 20 21 20 30 22 26 26 31 19 18 25</span></span>
<span><span class="co"># [51] 19 22 23 26 21 30 21 27 18 27 21 26 21 30 31 21 31 18 18 18 21 30 27 29 19</span></span>
<span><span class="co"># [76] 26 29 25 19 25 20 31 20 24 18 26 28 21 28 18 25 31 17 23 28 21 25 30 26 23</span></span></code></pre></div>
<span><span class="co"># [1] 28 17 17 21 28 19 31 28 27 19 17 31 18 19 26 31 23 29 27 26 21 28 17 28 22</span></span>
<span><span class="co"># [26] 20 24 28 28 23 20 27 19 28 30 27 19 27 18 21 24 17 21 27 28 26 22 27 30 23</span></span>
<span><span class="co"># [51] 31 28 28 31 21 21 28 31 21 26 21 18 24 20 31 22 28 25 25 21 22 25 18 18 26</span></span>
<span><span class="co"># [76] 30 23 29 24 27 19 17 21 24 27 31 17 26 21 26 22 17 24 23 21 25 22 28 22 28</span></span></code></pre></div>
<div class="sourceCode" id="cb42"><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>

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2
articles/EUCAST.html
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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="">1.8.2.9066</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9067</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">

56
articles/MDR.html
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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="">1.8.2.9066</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9067</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">
@ -375,17 +375,17 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><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">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 R R R S R S</span></span>
<span><span class="co"># 2 R I I S S I</span></span>
<span><span class="co"># 3 S S S S S S</span></span>
<span><span class="co"># 4 I I R R R R</span></span>
<span><span class="co"># 5 R S S I R S</span></span>
<span><span class="co"># 6 S R S R R I</span></span>
<span><span class="co"># 1 S S I S S R</span></span>
<span><span class="co"># 2 R S R I S S</span></span>
<span><span class="co"># 3 I R S S I R</span></span>
<span><span class="co"># 4 R R I I S R</span></span>
<span><span class="co"># 5 S R S I R S</span></span>
<span><span class="co"># 6 I I S I S S</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 I</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
@ -428,40 +428,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3190</td>
<td align="right">63.80%</td>
<td align="right">3190</td>
<td align="right">63.80%</td>
<td align="right">3192</td>
<td align="right">63.84%</td>
<td align="right">3192</td>
<td align="right">63.84%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1010</td>
<td align="right">20.20%</td>
<td align="right">4200</td>
<td align="right">84.00%</td>
<td align="right">1039</td>
<td align="right">20.78%</td>
<td align="right">4231</td>
<td align="right">84.62%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">446</td>
<td align="right">8.92%</td>
<td align="right">4646</td>
<td align="right">92.92%</td>
<td align="right">425</td>
<td align="right">8.50%</td>
<td align="right">4656</td>
<td align="right">93.12%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">267</td>
<td align="right">5.34%</td>
<td align="right">4913</td>
<td align="right">98.26%</td>
<td align="right">240</td>
<td align="right">4.80%</td>
<td align="right">4896</td>
<td align="right">97.92%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">87</td>
<td align="right">1.74%</td>
<td align="right">104</td>
<td align="right">2.08%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
articles/PCA.html
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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="">1.8.2.9066</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9067</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">

2
articles/SPSS.html
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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="">1.8.2.9066</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9067</small>
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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="">1.8.2.9066</small>
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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="">1.8.2.9066</small>
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2
articles/index.html
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@ -10,7 +10,7 @@
<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="">1.8.2.9066</small>
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