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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="">1.8.2.9022</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -325,67 +325,67 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-10-19</td>
<td align="center">O1</td>
<td align="center">2010-03-04</td>
<td align="center">Q1</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella 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="even">
<td align="center">2016-12-24</td>
<td align="center">I6</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-04-30</td>
<td align="center">K3</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">M</td>
</tr>
<tr class="even">
<td align="center">2014-02-16</td>
<td align="center">W5</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>
</tr>
<tr class="odd">
<td align="center">2012-07-09</td>
<td align="center">J8</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-10-29</td>
<td align="center">R7</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-02-04</td>
<td align="center">F5</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-05-11</td>
<td align="center">A2</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</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="odd">
<td align="center">2015-09-26</td>
<td align="center">L5</td>
<td align="center">Hospital B</td>
<td align="center">2011-07-03</td>
<td align="center">J2</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-09-20</td>
<td align="center">N4</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">S</td>
<td align="center">M</td>
@ -422,16 +422,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,418</td>
<td align="right">52.09%</td>
<td align="right">10,418</td>
<td align="right">52.09%</td>
<td align="right">10,463</td>
<td align="right">52.32%</td>
<td align="right">10,463</td>
<td align="right">52.32%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,582</td>
<td align="right">47.91%</td>
<td align="right">9,537</td>
<td align="right">47.69%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -488,9 +488,9 @@ Longest: 1</p>
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,708 'phenotype-based' first isolates (53.5% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,669 'phenotype-based' first isolates (53.3% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.5% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<p>So only 53.3% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
@ -499,10 +499,10 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,708 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,669 isolates for analysis. Now our data looks like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
<table style="width:100%;" class="table">
<table class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -515,7 +515,7 @@ Longest: 1</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@ -538,29 +538,13 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2017-10-19</td>
<td align="center">O1</td>
<td align="center">2010-03-04</td>
<td align="center">Q1</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">R</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">2</td>
<td align="center">2013-10-29</td>
<td align="center">R7</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
@ -568,26 +552,10 @@ Longest: 1</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">2015-02-04</td>
<td align="center">F5</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>
<tr class="even">
<td align="left">5</td>
<td align="center">2015-09-26</td>
<td align="center">L5</td>
<td align="left">2</td>
<td align="center">2016-12-24</td>
<td align="center">I6</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
@ -602,9 +570,25 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">2012-09-20</td>
<td align="center">N4</td>
<td align="center">Hospital D</td>
<td align="center">2011-07-03</td>
<td align="center">J2</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>
<tr class="even">
<td align="left">7</td>
<td align="center">2011-05-07</td>
<td align="center">F3</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -616,20 +600,36 @@ Longest: 1</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2012-10-23</td>
<td align="center">M3</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<tr class="odd">
<td align="left">9</td>
<td align="center">2017-04-03</td>
<td align="center">O7</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">S</td>
<td align="center">M</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">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2012-08-29</td>
<td align="center">O9</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">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -653,8 +653,8 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,708<br>
Available: 10,708 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,669<br>
Available: 10,669 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -671,33 +671,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,622</td>
<td align="right">43.16%</td>
<td align="right">4,622</td>
<td align="right">43.16%</td>
<td align="right">4,646</td>
<td align="right">43.55%</td>
<td align="right">4,646</td>
<td align="right">43.55%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,777</td>
<td align="right">25.93%</td>
<td align="right">7,399</td>
<td align="right">69.10%</td>
<td align="right">2,725</td>
<td align="right">25.54%</td>
<td align="right">7,371</td>
<td align="right">69.09%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,130</td>
<td align="right">19.89%</td>
<td align="right">9,529</td>
<td align="right">88.99%</td>
<td align="right">2,140</td>
<td align="right">20.06%</td>
<td align="right">9,511</td>
<td align="right">89.15%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,179</td>
<td align="right">11.01%</td>
<td align="right">10,708</td>
<td align="right">1,158</td>
<td align="right">10.85%</td>
<td align="right">10,669</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -744,8 +744,8 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-09-26</td>
<td align="center">L5</td>
<td align="center">2016-12-24</td>
<td align="center">I6</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
@ -759,44 +759,14 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-05-20</td>
<td align="center">U6</td>
<td align="center">Hospital B</td>
<td align="center">2011-07-03</td>
<td align="center">J2</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">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">2014-02-08</td>
<td align="center">Y8</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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-07-24</td>
<td align="center">L9</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>
@ -804,13 +774,13 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-02-06</td>
<td align="center">V4</td>
<td align="center">Hospital D</td>
<td align="center">2017-04-03</td>
<td align="center">O7</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">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>
@ -819,12 +789,42 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-12-31</td>
<td align="center">R10</td>
<td align="center">Hospital D</td>
<td align="center">2014-08-04</td>
<td align="center">H1</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</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>
<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">2010-04-30</td>
<td align="center">J8</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">2010-07-17</td>
<td align="center">Y3</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">R</td>
<td align="center">F</td>
@ -854,50 +854,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2187</td>
<td align="center">142</td>
<td align="center">2293</td>
<td align="center">4622</td>
<td align="center">2135</td>
<td align="center">140</td>
<td align="center">2371</td>
<td align="center">4646</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3411</td>
<td align="center">152</td>
<td align="center">1059</td>
<td align="center">4622</td>
<td align="center">3388</td>
<td align="center">166</td>
<td align="center">1092</td>
<td align="center">4646</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3398</td>
<td align="center">3397</td>
<td align="center">0</td>
<td align="center">1224</td>
<td align="center">4622</td>
<td align="center">1249</td>
<td align="center">4646</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4049</td>
<td align="center">4031</td>
<td align="center">0</td>
<td align="center">573</td>
<td align="center">4622</td>
<td align="center">615</td>
<td align="center">4646</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">1179</td>
<td align="center">1179</td>
<td align="center">1158</td>
<td align="center">1158</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">921</td>
<td align="center">44</td>
<td align="center">214</td>
<td align="center">1179</td>
<td align="center">918</td>
<td align="center">42</td>
<td align="center">198</td>
<td align="center">1158</td>
</tr>
</tbody>
</table>
@ -920,34 +920,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4049</td>
<td align="center">4031</td>
<td align="center">0</td>
<td align="center">573</td>
<td align="center">4622</td>
<td align="center">615</td>
<td align="center">4646</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1062</td>
<td align="center">1057</td>
<td align="center">0</td>
<td align="center">117</td>
<td align="center">1179</td>
<td align="center">101</td>
<td align="center">1158</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2443</td>
<td align="center">2431</td>
<td align="center">0</td>
<td align="center">334</td>
<td align="center">2777</td>
<td align="center">294</td>
<td align="center">2725</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">2130</td>
<td align="center">2130</td>
<td align="center">2140</td>
<td align="center">2140</td>
</tr>
</tbody>
</table>
@ -961,7 +961,7 @@ Longest: 24</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5418379</span></span></code></pre></div>
<span><span class="co"># [1] 0.5476614</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@ -975,19 +975,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5446373</td>
<td align="center">0.5541245</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5459846</td>
<td align="center">0.5501455</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5303218</td>
<td align="center">0.5269306</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5389393</td>
<td align="center">0.5483716</td>
</tr>
</tbody>
</table>
@ -1008,23 +1008,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5446373</td>
<td align="center">3226</td>
<td align="center">0.5541245</td>
<td align="center">3261</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5459846</td>
<td align="center">3773</td>
<td align="center">0.5501455</td>
<td align="center">3779</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5303218</td>
<td align="center">1616</td>
<td align="center">0.5269306</td>
<td align="center">1541</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5389393</td>
<td align="center">2093</td>
<td align="center">0.5483716</td>
<td align="center">2088</td>
</tr>
</tbody>
</table>
@ -1047,27 +1047,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7708784</td>
<td align="center">0.8760277</td>
<td align="center">0.9757681</td>
<td align="center">0.7649591</td>
<td align="center">0.8676281</td>
<td align="center">0.9750323</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8184902</td>
<td align="center">0.9007634</td>
<td align="center">0.9813401</td>
<td align="center">0.8290155</td>
<td align="center">0.9127807</td>
<td align="center">0.9818653</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8030248</td>
<td align="center">0.8797263</td>
<td align="center">0.9773136</td>
<td align="center">0.7893578</td>
<td align="center">0.8921101</td>
<td align="center">0.9809174</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5384977</td>
<td align="center">0.5341121</td>
<td align="center">0.0000000</td>
<td align="center">0.5384977</td>
<td align="center">0.5341121</td>
</tr>
</tbody>
</table>
@ -1092,23 +1092,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.5%</td>
<td align="right">26.0%</td>
<td align="right">55.4%</td>
<td align="right">27.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.6%</td>
<td align="right">26.5%</td>
<td align="right">55.0%</td>
<td align="right">26.8%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">53.0%</td>
<td align="right">26.8%</td>
<td align="right">52.7%</td>
<td align="right">27.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">53.9%</td>
<td align="right">25.4%</td>
<td align="right">54.8%</td>
<td align="right">25.9%</td>
</tr>
</tbody>
</table>
@ -1205,17 +1205,17 @@ Longest: 24</p>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<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 &lt;mic&gt;</span></span>
<span><span class="co"># [1] 32 0.002 1 0.125 8 16 256 0.25 32 32 </span></span>
<span><span class="co"># [11] 1 0.001 2 2 64 64 1 0.025 128 64 </span></span>
<span><span class="co"># [21] 128 0.001 8 4 0.0625 0.025 32 32 0.005 256 </span></span>
<span><span class="co"># [31] 256 128 0.025 0.002 0.125 4 0.001 0.125 0.001 1 </span></span>
<span><span class="co"># [41] 4 64 0.005 0.0625 0.01 0.01 2 0.002 0.002 16 </span></span>
<span><span class="co"># [51] 256 0.0625 32 8 256 256 0.005 128 0.125 0.001 </span></span>
<span><span class="co"># [61] 0.0625 4 4 0.5 0.01 2 0.125 64 4 16 </span></span>
<span><span class="co"># [71] 16 1 0.025 0.005 0.0625 0.001 0.001 128 2 1 </span></span>
<span><span class="co"># [81] 32 32 0.25 0.5 0.0625 8 64 0.005 0.005 256 </span></span>
<span><span class="co"># [91] 128 0.001 256 256 0.005 0.01 128 8 0.01 2</span></span></code></pre></div>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 0.01 128 0.005 2 0.002 0.025 128 0.001 4 128 </span></span>
<span><span class="co"># [11] 32 128 0.002 0.025 2 128 8 16 0.002 0.005 </span></span>
<span><span class="co"># [21] 0.005 0.0625 0.0625 2 0.5 0.25 0.001 4 32 &gt;=256 </span></span>
<span><span class="co"># [31] 0.25 &gt;=256 0.125 4 0.001 32 16 0.25 0.025 0.002 </span></span>
<span><span class="co"># [41] 32 128 64 16 0.001 64 0.025 0.125 0.025 &gt;=256 </span></span>
<span><span class="co"># [51] &gt;=256 1 0.0625 32 0.025 16 8 0.025 0.025 &gt;=256 </span></span>
<span><span class="co"># [61] 0.0625 0.01 0.002 0.025 0.002 0.002 0.5 64 0.25 0.5 </span></span>
<span><span class="co"># [71] 64 0.0625 1 0.0625 2 0.0625 0.25 0.25 32 1 </span></span>
<span><span class="co"># [81] 4 0.005 128 0.5 0.001 16 0.25 16 0.5 &gt;=256 </span></span>
<span><span class="co"># [91] 0.002 32 0.005 16 16 128 0.025 0.0625 128 0.001</span></span></code></pre></div>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1241,11 +1241,11 @@ Longest: 24</p>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<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 &lt;disk&gt;</span></span>
<span><span class="co"># [1] 20 18 21 23 29 24 24 23 24 19 22 27 19 23 22 21 29 18 17 25 29 25 31 18 28</span></span>
<span><span class="co"># [26] 19 25 20 17 24 17 20 30 30 29 28 25 22 23 21 27 30 18 24 31 24 29 24 25 28</span></span>
<span><span class="co"># [51] 23 24 23 30 20 26 17 18 29 24 18 30 26 23 30 27 31 24 28 29 17 26 31 21 29</span></span>
<span><span class="co"># [76] 18 20 20 31 31 28 19 24 24 31 19 21 22 26 29 29 22 28 22 19 23 26 22 22 27</span></span></code></pre></div>
<span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 30 17 29 30 29 30 28 21 28 19 26 17 25 30 18 21 23 29 21 18 17 18 23 27 23</span></span>
<span><span class="co"># [26] 30 29 26 24 29 31 31 24 19 22 26 17 24 25 27 20 29 28 20 28 30 19 31 19 18</span></span>
<span><span class="co"># [51] 23 24 23 25 22 28 29 18 26 20 23 20 23 28 18 22 19 29 30 18 28 22 30 31 18</span></span>
<span><span class="co"># [76] 22 21 29 30 25 30 24 29 21 27 31 24 29 18 21 30 26 20 27 19 20 25 18 24 27</span></span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>

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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="">1.8.2.9022</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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
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="">1.8.2.9022</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
@ -226,7 +226,7 @@
<span><span class="co"># 3. Otherwise: Negative</span></span>
<span><span class="co"># </span></span>
<span><span class="co"># Unmatched rows will return NA.</span></span>
<span><span class="co"># Results will be of class &lt;factor&gt;, with ordered levels: Negative &lt; Elderly Type A &lt; Elderly Type B</span></span></code></pre></div>
<span><span class="co"># Results will be of class 'factor', with ordered levels: Negative &lt; Elderly Type A &lt; Elderly Type B</span></span></code></pre></div>
<p>The outcome of the function can be used for the <code>guideline</code> argument in the <code><a href="../reference/mdro.html">mdro()</a></code> function:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">example_isolates</span>, guideline <span class="op">=</span> <span class="va">custom</span><span class="op">)</span></span>
@ -314,19 +314,19 @@ Unique: 2</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 S I R R I R</span></span>
<span><span class="co"># 2 I S R S R I</span></span>
<span><span class="co"># 3 R I R I R S</span></span>
<span><span class="co"># 4 S R I I R R</span></span>
<span><span class="co"># 5 I I S S S R</span></span>
<span><span class="co"># 6 R R S I I R</span></span>
<span><span class="co"># 1 R S I S I S</span></span>
<span><span class="co"># 2 R R I R R I</span></span>
<span><span class="co"># 3 R I S I I I</span></span>
<span><span class="co"># 4 R R S I S S</span></span>
<span><span class="co"># 5 R R S R I R</span></span>
<span><span class="co"># 6 S S R I S S</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 1 R</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"># 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"># 6 I</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">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></span></code></pre></div>
@ -357,40 +357,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3172</td>
<td align="right">63.44%</td>
<td align="right">3172</td>
<td align="right">63.44%</td>
<td align="right">3161</td>
<td align="right">63.22%</td>
<td align="right">3161</td>
<td align="right">63.22%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">973</td>
<td align="right">19.46%</td>
<td align="right">4145</td>
<td align="right">82.90%</td>
<td align="right">1035</td>
<td align="right">20.70%</td>
<td align="right">4196</td>
<td align="right">83.92%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">489</td>
<td align="right">9.78%</td>
<td align="right">4634</td>
<td align="right">92.68%</td>
<td align="right">452</td>
<td align="right">9.04%</td>
<td align="right">4648</td>
<td align="right">92.96%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">247</td>
<td align="right">4.94%</td>
<td align="right">4881</td>
<td align="right">97.62%</td>
<td align="right">241</td>
<td align="right">4.82%</td>
<td align="right">4889</td>
<td align="right">97.78%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">119</td>
<td align="right">2.38%</td>
<td align="right">111</td>
<td align="right">2.22%</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="">1.8.2.9022</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">

6
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="">1.8.2.9022</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
@ -218,10 +218,10 @@
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># not all values are valid MIC values:</span></span>
<span><span class="fu"><a href="../reference/as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">0.125</span><span class="op">)</span></span>
<span><span class="co"># Class &lt;mic&gt;</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 0.125</span></span>
<span><span class="fu"><a href="../reference/as.mic.html">as.mic</a></span><span class="op">(</span><span class="st">"testvalue"</span><span class="op">)</span></span>
<span><span class="co"># Class &lt;mic&gt;</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] &lt;NA&gt;</span></span>
<span></span>
<span><span class="co"># the Gram stain is available for all bacteria:</span></span>

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="">1.8.2.9022</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</small>
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18
articles/datasets.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="">1.8.2.9022</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</small>
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@ -177,7 +177,7 @@
</h2>
<p>A data set with 48,787 rows and 22 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>source</em>, <em>lpsn</em>, <em>lpsn_parent</em>, <em>lpsn_renamed_to</em>, <em>gbif</em>, <em>gbif_parent</em>, <em>gbif_renamed_to</em>, <em>prevalence</em> and <em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 19 October 2022 06:31:36 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p>It was last updated on 19 October 2022 09:53:44 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">original R Data Structure (RDS) file</a> (1.1 MB)<br>
@ -449,7 +449,7 @@
</h2>
<p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 19 October 2022 06:31:36 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 19 October 2022 09:53:44 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">original R Data Structure (RDS) file</a> (36 kB)<br>
@ -622,7 +622,7 @@
</h2>
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 19 October 2022 06:31:36 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 19 October 2022 09:53:44 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">original R Data Structure (RDS) file</a> (4 kB)<br>
@ -754,7 +754,7 @@
</h2>
<p>A data set with 20,369 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 19 October 2022 06:31:36 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p>It was last updated on 19 October 2022 09:53:44 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">original R Data Structure (RDS) file</a> (49 kB)<br>
@ -913,7 +913,7 @@
</h2>
<p>A data set with 134,659 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 19 October 2022 06:31:36 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p>It was last updated on 19 October 2022 09:53:44 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">original R Data Structure (RDS) file</a> (78 kB)<br>
@ -1185,7 +1185,7 @@
</h2>
<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 19 October 2022 06:31:36 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p>It was last updated on 19 October 2022 09:53:44 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">original R Data Structure (RDS) file</a> (3 kB)<br>
@ -1302,7 +1302,7 @@
</h2>
<p>A data set with 2,000 rows and 46 columns, containing the following column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>, <em>ward</em>, <em>mo</em>, <em>PEN</em>, <em>OXA</em>, <em>FLC</em>, <em>AMX</em>, <em>AMC</em>, <em>AMP</em>, <em>TZP</em>, <em>CZO</em>, <em>FEP</em>, <em>CXM</em>, <em>FOX</em>, <em>CTX</em>, <em>CAZ</em>, <em>CRO</em>, <em>GEN</em>, <em>TOB</em>, <em>AMK</em>, <em>KAN</em>, <em>TMP</em>, <em>SXT</em>, <em>NIT</em>, <em>FOS</em>, <em>LNZ</em>, <em>CIP</em>, <em>MFX</em>, <em>VAN</em>, <em>TEC</em>, <em>TCY</em>, <em>TGC</em>, <em>DOX</em>, <em>ERY</em>, <em>CLI</em>, <em>AZM</em>, <em>IPM</em>, <em>MEM</em>, <em>MTR</em>, <em>CHL</em>, <em>COL</em>, <em>MUP</em> and <em>RIF</em>.</p>
<p>This data set is in R available as <code>example_isolates</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 19 October 2022 06:31:36 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
<p>It was last updated on 19 October 2022 09:53:44 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
<div class="section level3">
<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
</h3>
@ -1707,7 +1707,7 @@
</h2>
<p>A data set with 3,000 rows and 8 columns, containing the following column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>, <em>bacteria</em>, <em>AMX</em>, <em>AMC</em>, <em>CIP</em> and <em>GEN</em>.</p>
<p>This data set is in R available as <code>example_isolates_unclean</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 19 October 2022 06:31:36 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
<p>It was last updated on 19 October 2022 09:53:44 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
<div class="section level3">
<h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>
</h3>

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>
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articles/resistance_predict.html
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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="">1.8.2.9022</small>
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articles/welcome_to_AMR.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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