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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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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">
@ -400,71 +400,71 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-11-17</td>
<td align="center">D4</td>
<td align="center">2017-09-27</td>
<td align="center">K9</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-12-24</td>
<td align="center">S2</td>
<td align="center">Hospital B</td>
<td align="center">2012-09-19</td>
<td align="center">M7</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">M</td>
</tr>
<tr class="odd">
<td align="center">2010-01-21</td>
<td align="center">Q3</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-11-24</td>
<td align="center">N1</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2014-08-31</td>
<td align="center">Q4</td>
<td align="center">2016-07-29</td>
<td align="center">J7</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-08-04</td>
<td align="center">N10</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">F</td>
</tr>
<tr class="odd">
<td align="center">2016-03-16</td>
<td align="center">D5</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2016-06-19</td>
<td align="center">E7</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-10-07</td>
<td align="center">O7</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -499,16 +499,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,466</td>
<td align="right">52.33%</td>
<td align="right">10,466</td>
<td align="right">52.33%</td>
<td align="right">10,357</td>
<td align="right">51.79%</td>
<td align="right">10,357</td>
<td align="right">51.79%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,534</td>
<td align="right">47.67%</td>
<td align="right">9,643</td>
<td align="right">48.22%</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 10,633 'phenotype-based' first isolates (53.2% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,726 'phenotype-based' first isolates (53.6% 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 53.6% 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 10,633 isolates for analysis. Now our data looks
<p>So we end up with 10,726 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>
@ -673,14 +673,14 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2013-11-17</td>
<td align="center">D4</td>
<td align="left">2</td>
<td align="center">2012-09-19</td>
<td align="center">M7</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">M</td>
<td align="center">Gram-positive</td>
@ -689,29 +689,13 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2014-12-24</td>
<td align="center">S2</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">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">5</td>
<td align="center">2016-03-16</td>
<td align="center">D5</td>
<td align="left">4</td>
<td align="center">2016-11-24</td>
<td align="center">N1</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">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
@ -720,42 +704,10 @@ like:</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2011-09-05</td>
<td align="center">Z1</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">8</td>
<td align="center">2015-09-14</td>
<td align="center">B4</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="left">9</td>
<td align="center">2013-09-14</td>
<td align="center">G4</td>
<td align="left">10</td>
<td align="center">2013-06-30</td>
<td align="center">M8</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
@ -768,6 +720,54 @@ like:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">11</td>
<td align="center">2017-03-10</td>
<td align="center">N8</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">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">12</td>
<td align="center">2016-12-09</td>
<td align="center">T3</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">2014-04-02</td>
<td align="center">I2</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -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: 10,633<br>
Available: 10,633 (100%, NA: 0 = 0%)<br>
Length: 10,726<br>
Available: 10,726 (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">4,608</td>
<td align="right">43.34%</td>
<td align="right">4,608</td>
<td align="right">43.34%</td>
<td align="right">4,697</td>
<td align="right">43.79%</td>
<td align="right">4,697</td>
<td align="right">43.79%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,724</td>
<td align="right">25.62%</td>
<td align="right">7,332</td>
<td align="right">68.96%</td>
<td align="right">2,746</td>
<td align="right">25.60%</td>
<td align="right">7,443</td>
<td align="right">69.39%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,080</td>
<td align="right">19.56%</td>
<td align="right">9,412</td>
<td align="right">88.52%</td>
<td align="right">2,106</td>
<td align="right">19.63%</td>
<td align="right">9,549</td>
<td align="right">89.03%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,221</td>
<td align="right">11.48%</td>
<td align="right">10,633</td>
<td align="right">1,177</td>
<td align="right">10.97%</td>
<td align="right">10,726</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -874,14 +874,14 @@ antibiotic class they are in:</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="11%">
<col width="10%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@ -902,13 +902,13 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-11-17</td>
<td align="center">D4</td>
<td align="center">2012-09-19</td>
<td align="center">M7</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">M</td>
<td align="center">Gram-positive</td>
@ -917,39 +917,69 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-12-24</td>
<td align="center">S2</td>
<td align="center">Hospital B</td>
<td align="center">2010-02-14</td>
<td align="center">B5</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">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">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">2015-09-14</td>
<td align="center">B4</td>
<td align="center">2016-09-23</td>
<td align="center">O10</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">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="even">
<td align="center">2015-05-01</td>
<td align="center">W1</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-08-13</td>
<td align="center">I9</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-02-25</td>
<td align="center">P4</td>
<td align="center">Hospital C</td>
<td align="center">2014-05-21</td>
<td align="center">O10</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
@ -961,36 +991,6 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-04-27</td>
<td align="center">C10</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="even">
<td align="center">2011-03-11</td>
<td align="center">J4</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">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
@ -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">2140</td>
<td align="center">128</td>
<td align="center">2340</td>
<td align="center">4608</td>
<td align="center">2194</td>
<td align="center">130</td>
<td align="center">2373</td>
<td align="center">4697</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3336</td>
<td align="center">178</td>
<td align="center">1094</td>
<td align="center">4608</td>
<td align="center">3459</td>
<td align="center">180</td>
<td align="center">1058</td>
<td align="center">4697</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3373</td>
<td align="center">3421</td>
<td align="center">0</td>
<td align="center">1235</td>
<td align="center">4608</td>
<td align="center">1276</td>
<td align="center">4697</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4042</td>
<td align="center">4111</td>
<td align="center">0</td>
<td align="center">566</td>
<td align="center">4608</td>
<td align="center">586</td>
<td align="center">4697</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">1221</td>
<td align="center">1221</td>
<td align="center">1177</td>
<td align="center">1177</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">951</td>
<td align="center">51</td>
<td align="center">219</td>
<td align="center">1221</td>
<td align="center">938</td>
<td align="center">48</td>
<td align="center">191</td>
<td align="center">1177</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">4042</td>
<td align="center">4111</td>
<td align="center">0</td>
<td align="center">566</td>
<td align="center">4608</td>
<td align="center">586</td>
<td align="center">4697</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1121</td>
<td align="center">1045</td>
<td align="center">0</td>
<td align="center">100</td>
<td align="center">1221</td>
<td align="center">132</td>
<td align="center">1177</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2432</td>
<td align="center">2430</td>
<td align="center">0</td>
<td align="center">292</td>
<td align="center">2724</td>
<td align="center">316</td>
<td align="center">2746</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">2080</td>
<td align="center">2080</td>
<td align="center">2106</td>
<td align="center">2106</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] 0.5483871</span></span></code></pre></div>
<span><span class="co"># [1] 0.5466157</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">0.5436433</td>
<td align="center">0.5586592</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5441137</td>
<td align="center">0.5431104</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5588420</td>
<td align="center">0.5266836</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5550395</td>
<td align="center">0.5491618</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">0.5436433</td>
<td align="center">3162</td>
<td align="center">0.5586592</td>
<td align="center">3222</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5441137</td>
<td align="center">3729</td>
<td align="center">0.5431104</td>
<td align="center">3723</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5588420</td>
<td align="center">1589</td>
<td align="center">0.5266836</td>
<td align="center">1574</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5550395</td>
<td align="center">2153</td>
<td align="center">0.5491618</td>
<td align="center">2207</td>
</tr>
</tbody>
</table>
@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7625868</td>
<td align="center">0.8771701</td>
<td align="center">0.9743924</td>
<td align="center">0.7747498</td>
<td align="center">0.8752395</td>
<td align="center">0.9774324</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8206388</td>
<td align="center">0.9180999</td>
<td align="center">0.9844390</td>
<td align="center">0.8377230</td>
<td align="center">0.8878505</td>
<td align="center">0.9770603</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7830396</td>
<td align="center">0.8928047</td>
<td align="center">0.9805433</td>
<td align="center">0.7760379</td>
<td align="center">0.8849235</td>
<td align="center">0.9756009</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5447115</td>
<td align="center">0.5394112</td>
<td align="center">0.0000000</td>
<td align="center">0.5447115</td>
<td align="center">0.5394112</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">54.4%</td>
<td align="right">25.9%</td>
<td align="right">55.9%</td>
<td align="right">26.0%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.4%</td>
<td align="right">27.1%</td>
<td align="right">54.3%</td>
<td align="right">25.9%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">55.9%</td>
<td align="right">28.1%</td>
<td align="right">52.7%</td>
<td align="right">25.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">55.5%</td>
<td align="right">26.6%</td>
<td align="right">54.9%</td>
<td align="right">28.3%</td>
</tr>
</tbody>
</table>
@ -1410,16 +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] 0.025 2 128 0.0625 0.005 16 0.125 0.5 0.5 64 </span></span>
<span><span class="co"># [11] 0.002 0.025 16 0.0625 2 2 1 0.01 4 0.002 </span></span>
<span><span class="co"># [21] 128 1 0.025 64 128 16 0.01 0.002 2 0.5 </span></span>
<span><span class="co"># [31] 2 8 0.125 0.125 0.005 0.001 0.01 2 0.0625 4 </span></span>
<span><span class="co"># [41] 0.01 32 0.01 32 32 0.25 1 0.25 64 0.5 </span></span>
<span><span class="co"># [51] 2 128 0.005 1 0.0625 64 0.125 1 0.5 0.5 </span></span>
<span><span class="co"># [61] 0.5 2 0.125 256 128 16 64 0.25 2 0.01 </span></span>
<span><span class="co"># [71] 0.025 0.125 0.005 16 1 8 0.001 0.125 32 256 </span></span>
<span><span class="co"># [81] 0.5 16 0.005 4 1 16 256 8 0.25 0.01 </span></span>
<span><span class="co"># [91] 0.5 16 0.002 32 128 16 1 0.001 16 32</span></span></code></pre></div>
<span><span class="co"># [1] 0.0625 0.005 16 0.005 0.0625 8 1 0.25 0.01 </span></span>
<span><span class="co"># [10] &gt;=256 0.01 0.0625 0.0625 128 0.025 0.01 1 4 </span></span>
<span><span class="co"># [19] 0.01 128 0.125 0.025 16 &lt;=0.001 &lt;=0.001 8 0.125 </span></span>
<span><span class="co"># [28] 0.25 0.25 0.125 0.025 0.01 0.0625 16 0.002 8 </span></span>
<span><span class="co"># [37] 2 128 128 &lt;=0.001 0.0625 0.125 0.002 &lt;=0.001 0.025 </span></span>
<span><span class="co"># [46] 0.5 0.0625 128 0.5 64 0.5 0.005 0.5 16 </span></span>
<span><span class="co"># [55] 0.125 0.002 0.5 2 &gt;=256 &gt;=256 0.125 64 0.005 </span></span>
<span><span class="co"># [64] 64 32 16 4 16 8 8 0.125 0.5 </span></span>
<span><span class="co"># [73] 32 0.025 1 64 1 0.125 0.125 0.025 32 </span></span>
<span><span class="co"># [82] 64 0.01 0.25 2 0.125 0.0625 8 2 0.01 </span></span>
<span><span class="co"># [91] 64 0.005 8 0.25 0.125 8 128 0.5 &lt;=0.001</span></span>
<span><span class="co"># [100] 0.0625</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>
@ -1453,10 +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] 21 18 31 26 31 22 21 22 22 27 21 28 24 29 30 27 31 22 30 31 25 29 30 22 22</span></span>
<span><span class="co"># [26] 20 29 18 31 28 18 19 18 25 30 28 25 20 22 20 17 20 21 24 19 23 25 19 30 30</span></span>
<span><span class="co"># [51] 23 24 23 17 17 17 25 24 26 17 24 19 31 27 24 21 27 21 25 31 22 24 22 19 24</span></span>
<span><span class="co"># [76] 23 24 18 29 24 21 28 19 26 23 24 18 20 31 31 26 19 24 17 18 27 25 26 28 25</span></span></code></pre></div>
<span><span class="co"># [1] 27 19 29 18 21 24 23 21 17 28 17 27 23 22 23 18 30 30 22 24 22 22 20 26 17</span></span>
<span><span class="co"># [26] 17 29 22 23 19 24 28 27 28 17 17 27 28 17 23 28 18 28 23 21 22 22 19 29 27</span></span>
<span><span class="co"># [51] 17 18 22 22 24 19 30 24 31 29 26 17 28 26 27 17 17 27 22 20 28 25 17 20 30</span></span>
<span><span class="co"># [76] 25 31 25 28 27 27 20 31 25 23 24 22 20 18 26 29 18 25 31 20 22 26 29 20 31</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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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">

58
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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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">
@ -375,18 +375,18 @@ 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 S R S</span></span>
<span><span class="co"># 2 S S R S R S</span></span>
<span><span class="co"># 3 I R S I R I</span></span>
<span><span class="co"># 4 R R S S R S</span></span>
<span><span class="co"># 5 S R R S I R</span></span>
<span><span class="co"># 6 I I I S I I</span></span>
<span><span class="co"># 1 R S R S I S</span></span>
<span><span class="co"># 2 R S S S I R</span></span>
<span><span class="co"># 3 R R R S I S</span></span>
<span><span class="co"># 4 S S I S I R</span></span>
<span><span class="co"># 5 R S I I R R</span></span>
<span><span class="co"># 6 R R 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 S</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 R</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
@ -428,40 +428,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3194</td>
<td align="right">63.88%</td>
<td align="right">3194</td>
<td align="right">63.88%</td>
<td align="right">3249</td>
<td align="right">64.98%</td>
<td align="right">3249</td>
<td align="right">64.98%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">983</td>
<td align="right">19.66%</td>
<td align="right">4177</td>
<td align="right">83.54%</td>
<td align="right">936</td>
<td align="right">18.72%</td>
<td align="right">4185</td>
<td align="right">83.70%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">492</td>
<td align="right">9.84%</td>
<td align="right">4669</td>
<td align="right">93.38%</td>
<td align="right">465</td>
<td align="right">9.30%</td>
<td align="right">4650</td>
<td align="right">93.00%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">235</td>
<td align="right">4.70%</td>
<td align="right">4904</td>
<td align="right">98.08%</td>
<td align="right">249</td>
<td align="right">4.98%</td>
<td align="right">4899</td>
<td align="right">97.98%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">96</td>
<td align="right">1.92%</td>
<td align="right">101</td>
<td align="right">2.02%</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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</small>
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2
articles/WHONET.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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</small>
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2
articles/resistance_predict.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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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="">1.8.2.9082</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9083</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">