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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="">1.8.2.9132</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9133</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">
@ -411,70 +411,70 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-03-23</td>
<td align="center">C3</td>
<td align="center">2010-08-29</td>
<td align="center">Y2</td>
<td align="center">Hospital D</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">I</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-06-18</td>
<td align="center">M9</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">I</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2013-10-07</td>
<td align="center">M10</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-03-21</td>
<td align="center">C9</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2014-12-29</td>
<td align="center">Q10</td>
<td align="center">2013-03-01</td>
<td align="center">F4</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</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">M</td>
</tr>
<tr class="odd">
<td align="center">2011-09-11</td>
<td align="center">A6</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">S</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-04-12</td>
<td align="center">W1</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2010-01-07</td>
<td align="center">X4</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2015-08-23</td>
<td align="center">W8</td>
<td align="center">Hospital A</td>
<td align="center">2012-07-13</td>
<td align="center">N3</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
@ -510,16 +510,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,408</td>
<td align="right">52.04%</td>
<td align="right">10,408</td>
<td align="right">52.04%</td>
<td align="right">10,414</td>
<td align="right">52.07%</td>
<td align="right">10,414</td>
<td align="right">52.07%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,592</td>
<td align="right">47.96%</td>
<td align="right">9,586</td>
<td align="right">47.93%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -632,9 +632,9 @@ 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 12,380 'phenotype-based' first isolates (61.9% of total where a</span></span>
<span><span class="co"># =&gt; Found 12,221 'phenotype-based' first isolates (61.1% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 61.9% is suitable for resistance analysis! We can now filter
<p>So only 61.1% 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">
@ -644,7 +644,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<div class="sourceCode" id="cb16"><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="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>So we end up with 12 380 isolates for analysis. Now our data looks
<p>So we end up with 12 221 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>
@ -683,47 +683,15 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2013-03-23</td>
<td align="center">C3</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">I</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">2</td>
<td align="center">2017-06-18</td>
<td align="center">M9</td>
<td align="left">3</td>
<td align="center">2011-09-11</td>
<td align="center">A6</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="odd">
<td align="left">4</td>
<td align="center">2013-03-21</td>
<td align="center">C9</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">I</td>
<td align="center">I</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>
@ -732,13 +700,13 @@ like:</p>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">2014-12-29</td>
<td align="center">Q10</td>
<td align="center">Hospital A</td>
<td align="center">2010-01-07</td>
<td align="center">X4</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@ -748,15 +716,15 @@ like:</p>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">2015-08-23</td>
<td align="center">W8</td>
<td align="center">Hospital A</td>
<td align="center">2012-07-13</td>
<td align="center">N3</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">I</td>
<td align="center">I</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>
@ -764,14 +732,46 @@ like:</p>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2014-08-05</td>
<td align="center">R2</td>
<td align="center">Hospital D</td>
<td align="center">2015-06-25</td>
<td align="center">E2</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</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">8</td>
<td align="center">2016-05-25</td>
<td align="center">L3</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">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">10</td>
<td align="center">2014-02-22</td>
<td align="center">V1</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
@ -811,8 +811,8 @@ 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: 12,380<br>
Available: 12,380 (100%, NA: 0 = 0%)<br>
Length: 12,221<br>
Available: 12,221 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -837,33 +837,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">5,922</td>
<td align="right">47.84%</td>
<td align="right">5,922</td>
<td align="right">47.84%</td>
<td align="right">5,791</td>
<td align="right">47.39%</td>
<td align="right">5,791</td>
<td align="right">47.39%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,262</td>
<td align="right">26.35%</td>
<td align="right">9,184</td>
<td align="right">74.18%</td>
<td align="right">3,265</td>
<td align="right">26.72%</td>
<td align="right">9,056</td>
<td align="right">74.10%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,854</td>
<td align="right">14.98%</td>
<td align="right">11,038</td>
<td align="right">89.16%</td>
<td align="right">1,847</td>
<td align="right">15.11%</td>
<td align="right">10,903</td>
<td align="right">89.22%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,342</td>
<td align="right">10.84%</td>
<td align="right">12,380</td>
<td align="right">1,318</td>
<td align="right">10.78%</td>
<td align="right">12,221</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -912,13 +912,43 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-06-18</td>
<td align="center">M9</td>
<td align="center">2011-09-11</td>
<td align="center">A6</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">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">2012-07-13</td>
<td align="center">N3</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="odd">
<td align="center">2016-05-25</td>
<td align="center">L3</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">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -927,75 +957,45 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-08-05</td>
<td align="center">R2</td>
<td align="center">2014-06-30</td>
<td align="center">F10</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">I</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-08-22</td>
<td align="center">S8</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">I</td>
<td align="center">R</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="even">
<td align="center">2013-07-23</td>
<td align="center">C7</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<tr class="odd">
<td align="center">2015-10-02</td>
<td align="center">Z1</td>
<td align="center">Hospital C</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">R</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="odd">
<td align="center">2012-03-19</td>
<td align="center">H6</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">I</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2010-03-15</td>
<td align="center">A3</td>
<td align="center">Hospital B</td>
<td align="center">2014-03-03</td>
<td align="center">P2</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">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</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>
@ -1025,46 +1025,46 @@ different bug/drug combinations, you can use the
<td align="left">2</td>
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">2776</td>
<td align="center">1183</td>
<td align="center">1963</td>
<td align="center">5922</td>
<td align="center">2701</td>
<td align="center">1149</td>
<td align="center">1941</td>
<td align="center">5791</td>
</tr>
<tr class="even">
<td align="left">1</td>
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">1534</td>
<td align="center">1264</td>
<td align="center">3124</td>
<td align="center">5922</td>
<td align="center">1437</td>
<td align="center">1241</td>
<td align="center">3113</td>
<td align="center">5791</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">2035</td>
<td align="center">1845</td>
<td align="center">2042</td>
<td align="center">5922</td>
<td align="center">1994</td>
<td align="center">1821</td>
<td align="center">1976</td>
<td align="center">5791</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2048</td>
<td align="center">1829</td>
<td align="center">2045</td>
<td align="center">5922</td>
<td align="center">2001</td>
<td align="center">1735</td>
<td align="center">2055</td>
<td align="center">5791</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">595</td>
<td align="center">583</td>
<td align="center">281</td>
<td align="center">466</td>
<td align="center">1342</td>
<td align="center">454</td>
<td align="center">1318</td>
</tr>
<tr class="even">
<td align="left">5</td>
@ -1072,8 +1072,8 @@ different bug/drug combinations, you can use the
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1342</td>
<td align="center">1342</td>
<td align="center">1318</td>
<td align="center">1318</td>
</tr>
</tbody>
</table>
@ -1095,34 +1095,34 @@ 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">2048</td>
<td align="center">1829</td>
<td align="center">2045</td>
<td align="center">5922</td>
<td align="center">2001</td>
<td align="center">1735</td>
<td align="center">2055</td>
<td align="center">5791</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">472</td>
<td align="center">436</td>
<td align="center">434</td>
<td align="center">1342</td>
<td align="center">426</td>
<td align="center">454</td>
<td align="center">438</td>
<td align="center">1318</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1107</td>
<td align="center">1029</td>
<td align="center">1126</td>
<td align="center">3262</td>
<td align="center">1104</td>
<td align="center">1010</td>
<td align="center">1151</td>
<td align="center">3265</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">1854</td>
<td align="center">1854</td>
<td align="center">1847</td>
<td align="center">1847</td>
</tr>
</tbody>
</table>
@ -1154,7 +1154,7 @@ 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] 0.5808562</span></span></code></pre></div>
<span><span class="co"># [1] 0.584813</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">
@ -1169,19 +1169,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5816024</td>
<td align="center">0.5930677</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5940042</td>
<td align="center">0.5801668</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5499199</td>
<td align="center">0.6017699</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5802964</td>
<td align="center">0.5680230</td>
</tr>
</tbody>
</table>
@ -1206,23 +1206,23 @@ 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">0.5816024</td>
<td align="center">3707</td>
<td align="center">0.5930677</td>
<td align="center">3664</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5940042</td>
<td align="center">4303</td>
<td align="center">0.5801668</td>
<td align="center">4316</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5499199</td>
<td align="center">1873</td>
<td align="center">0.6017699</td>
<td align="center">1808</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5802964</td>
<td align="center">2497</td>
<td align="center">0.5680230</td>
<td align="center">2433</td>
</tr>
</tbody>
</table>
@ -1247,27 +1247,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6685241</td>
<td align="center">0.6546775</td>
<td align="center">0.8850051</td>
<td align="center">0.6648247</td>
<td align="center">0.6451390</td>
<td align="center">0.8791228</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6527571</td>
<td align="center">0.6766021</td>
<td align="center">0.8971684</td>
<td align="center">0.6555387</td>
<td align="center">0.6676783</td>
<td align="center">0.8945372</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6686082</td>
<td align="center">0.6548130</td>
<td align="center">0.8868792</td>
<td align="center">0.6771822</td>
<td align="center">0.6474732</td>
<td align="center">0.8885145</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4778857</td>
<td align="center">0.4683270</td>
<td align="center">0.0000000</td>
<td align="center">0.4778857</td>
<td align="center">0.4683270</td>
</tr>
</tbody>
</table>
@ -1295,23 +1295,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">58.2%</td>
<td align="right">35.3%</td>
<td align="right">59.3%</td>
<td align="right">35.6%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">59.4%</td>
<td align="right">37.5%</td>
<td align="right">58.0%</td>
<td align="right">36.7%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">55.0%</td>
<td align="right">34.5%</td>
<td align="right">60.2%</td>
<td align="right">37.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">58.0%</td>
<td align="right">36.5%</td>
<td align="right">56.8%</td>
<td align="right">35.5%</td>
</tr>
</tbody>
</table>
@ -1427,16 +1427,16 @@ 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] 32 64 0.002 2 16 8 128 0.025 0.0625 0.001 </span></span>
<span><span class="co"># [11] 0.0625 0.005 16 128 4 0.025 0.01 128 0.001 16 </span></span>
<span><span class="co"># [21] 128 0.025 4 0.002 0.01 64 4 0.125 &gt;=256 128 </span></span>
<span><span class="co"># [31] 1 0.002 0.005 64 0.25 0.025 16 32 32 1 </span></span>
<span><span class="co"># [41] 8 2 32 16 0.0625 16 8 &gt;=256 &gt;=256 0.25 </span></span>
<span><span class="co"># [51] 64 0.25 128 16 0.0625 0.001 4 0.0625 0.005 0.5 </span></span>
<span><span class="co"># [61] 64 0.0625 0.025 0.001 0.001 0.005 0.0625 0.025 0.25 1 </span></span>
<span><span class="co"># [71] 0.125 0.002 8 0.125 0.001 0.001 0.01 16 8 32 </span></span>
<span><span class="co"># [81] 0.002 0.01 1 0.01 1 0.0625 0.025 0.01 1 1 </span></span>
<span><span class="co"># [91] 0.025 0.125 8 4 32 &gt;=256 4 0.001 4 0.005</span></span></code></pre></div>
<span><span class="co"># [1] 4 0.0625 256 0.0625 0.0625 2 0.025 0.001 0.001 256 </span></span>
<span><span class="co"># [11] 16 16 0.25 32 2 0.005 8 0.025 1 32 </span></span>
<span><span class="co"># [21] 32 0.005 8 0.5 0.025 32 8 0.025 0.025 1 </span></span>
<span><span class="co"># [31] 8 0.0625 0.002 16 16 0.0625 128 4 0.125 0.01 </span></span>
<span><span class="co"># [41] 64 8 32 0.002 0.125 0.005 64 0.125 0.002 0.005 </span></span>
<span><span class="co"># [51] 0.002 4 0.125 4 16 8 64 0.025 8 0.001 </span></span>
<span><span class="co"># [61] 16 1 0.5 64 16 0.001 4 0.001 0.002 0.001 </span></span>
<span><span class="co"># [71] 0.01 1 0.005 1 0.5 4 0.0625 0.001 8 1 </span></span>
<span><span class="co"># [81] 0.01 0.002 0.0625 32 0.025 64 1 0.5 0.25 32 </span></span>
<span><span class="co"># [91] 2 0.01 0.025 0.01 8 0.001 0.001 1 1 256</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>
@ -1470,10 +1470,10 @@ 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] 26 25 22 31 23 25 21 17 28 29 23 26 21 19 29 21 25 27 25 28 28 30 23 26 17</span></span>
<span><span class="co"># [26] 29 27 25 28 21 26 28 24 27 31 22 21 23 18 29 26 30 30 28 18 25 20 30 29 17</span></span>
<span><span class="co"># [51] 18 21 27 24 29 21 24 22 26 27 18 25 28 31 19 18 18 28 19 22 18 27 28 31 21</span></span>
<span><span class="co"># [76] 31 18 17 27 20 26 24 17 26 23 19 20 18 25 26 26 24 24 29 30 19 19 23 31 25</span></span></code></pre></div>
<span><span class="co"># [1] 18 26 28 24 26 31 28 23 20 24 18 28 27 24 28 17 18 25 24 21 17 26 20 22 20</span></span>
<span><span class="co"># [26] 22 20 29 24 17 25 21 23 30 17 22 27 19 19 24 31 28 26 21 29 27 19 24 20 23</span></span>
<span><span class="co"># [51] 27 27 29 29 17 21 17 20 24 31 30 17 24 31 25 29 19 29 18 27 26 30 31 26 30</span></span>
<span><span class="co"># [76] 21 25 22 25 31 22 22 20 31 30 17 17 29 23 24 27 26 29 17 27 28 28 26 18 26</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="">1.8.2.9132</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9133</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">

54
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="">1.8.2.9132</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9133</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">
@ -385,19 +385,19 @@ 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 I S I I R R</span></span>
<span><span class="co"># 2 S I R S S R</span></span>
<span><span class="co"># 3 I I I R R S</span></span>
<span><span class="co"># 4 R R I R R I</span></span>
<span><span class="co"># 5 S R S R I I</span></span>
<span><span class="co"># 6 S S I R I I</span></span>
<span><span class="co"># 1 S S S R I I</span></span>
<span><span class="co"># 2 S I R R I R</span></span>
<span><span class="co"># 3 I S R S S S</span></span>
<span><span class="co"># 4 R I R S S S</span></span>
<span><span class="co"># 5 R I I R R S</span></span>
<span><span class="co"># 6 I S R S R R</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<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
use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3173</td>
<td align="right">63.46%</td>
<td align="right">3173</td>
<td align="right">63.46%</td>
<td align="right">3208</td>
<td align="right">64.16%</td>
<td align="right">3208</td>
<td align="right">64.16%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1003</td>
<td align="right">20.06%</td>
<td align="right">4176</td>
<td align="right">83.52%</td>
<td align="right">1018</td>
<td align="right">20.36%</td>
<td align="right">4226</td>
<td align="right">84.52%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">462</td>
<td align="right">9.24%</td>
<td align="right">4638</td>
<td align="right">92.76%</td>
<td align="right">447</td>
<td align="right">8.94%</td>
<td align="right">4673</td>
<td align="right">93.46%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">255</td>
<td align="right">5.10%</td>
<td align="right">4893</td>
<td align="right">97.86%</td>
<td align="right">229</td>
<td align="right">4.58%</td>
<td align="right">4902</td>
<td align="right">98.04%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">107</td>
<td align="right">2.14%</td>
<td align="right">98</td>
<td align="right">1.96%</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="">1.8.2.9132</small>
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2
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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="">1.8.2.9132</small>
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@ -38,7 +38,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9132</small>
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@ -38,7 +38,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9132</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="">1.8.2.9132</small>
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2
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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="">1.8.2.9132</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9133</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/welcome_to_AMR.html
View File

@ -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="">1.8.2.9132</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9133</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">