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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="">1.8.2.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9029</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">
@ -325,70 +325,70 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-07-10</td>
<td align="center">Q3</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-09-20</td>
<td align="center">I5</td>
<td align="center">2014-05-24</td>
<td align="center">T2</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2010-04-28</td>
<td align="center">D3</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-08-23</td>
<td align="center">J6</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-02-07</td>
<td align="center">T8</td>
<td align="center">Hospital A</td>
<tr class="odd">
<td align="center">2014-10-30</td>
<td align="center">X10</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">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-07-15</td>
<td align="center">X5</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="odd">
<td align="center">2014-04-29</td>
<td align="center">L4</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">2015-07-31</td>
<td align="center">P4</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-05-12</td>
<td align="center">C6</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">2016-10-06</td>
<td align="center">S3</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</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>
<td align="center">F</td>
</tr>
</tbody>
</table>
@ -422,16 +422,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,372</td>
<td align="right">51.86%</td>
<td align="right">10,372</td>
<td align="right">51.86%</td>
<td align="right">10,307</td>
<td align="right">51.54%</td>
<td align="right">10,307</td>
<td align="right">51.54%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,628</td>
<td align="right">48.14%</td>
<td align="right">9,693</td>
<td align="right">48.47%</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 10,687 'phenotype-based' first isolates (53.4% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,557 'phenotype-based' first isolates (52.8% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.4% 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 52.8% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<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 10,687 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,557 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 class="table">
<table style="width:100%;" 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="10%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@ -537,42 +537,10 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">4</td>
<td align="center">2010-02-07</td>
<td align="center">T8</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">5</td>
<td align="center">2014-04-29</td>
<td align="center">L4</td>
<td align="left">1</td>
<td align="center">2014-05-24</td>
<td align="center">T2</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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="left">7</td>
<td align="center">2016-10-13</td>
<td align="center">Z2</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
@ -585,30 +553,62 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2015-02-02</td>
<td align="center">C3</td>
<td align="left">2</td>
<td align="center">2013-08-23</td>
<td align="center">J6</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</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-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</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">15</td>
<td align="center">2015-09-15</td>
<td align="center">G10</td>
<td align="left">5</td>
<td align="center">2015-07-31</td>
<td align="center">P4</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">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="even">
<td align="left">6</td>
<td align="center">2016-10-06</td>
<td align="center">S3</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">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">2014-11-19</td>
<td align="center">L6</td>
<td align="center">Hospital C</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">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
@ -617,19 +617,19 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">17</td>
<td align="center">2010-01-19</td>
<td align="center">M3</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="left">10</td>
<td align="center">2016-07-01</td>
<td align="center">Y10</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">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">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>
</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: 10,687<br>
Available: 10,687 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,557<br>
Available: 10,557 (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">4,688</td>
<td align="right">43.87%</td>
<td align="right">4,688</td>
<td align="right">43.87%</td>
<td align="right">4,550</td>
<td align="right">43.10%</td>
<td align="right">4,550</td>
<td align="right">43.10%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,697</td>
<td align="right">25.24%</td>
<td align="right">7,385</td>
<td align="right">69.10%</td>
<td align="right">2,652</td>
<td align="right">25.12%</td>
<td align="right">7,202</td>
<td align="right">68.22%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,160</td>
<td align="right">20.21%</td>
<td align="right">9,545</td>
<td align="right">89.31%</td>
<td align="right">2,179</td>
<td align="right">20.64%</td>
<td align="right">9,381</td>
<td align="right">88.86%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,142</td>
<td align="right">10.69%</td>
<td align="right">10,687</td>
<td align="right">1,176</td>
<td align="right">11.14%</td>
<td align="right">10,557</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -744,58 +744,28 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-04-29</td>
<td align="center">L4</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">2013-08-23</td>
<td align="center">J6</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-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-08-22</td>
<td align="center">P8</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-10-25</td>
<td align="center">Y2</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">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">2013-03-30</td>
<td align="center">R4</td>
<td align="center">Hospital D</td>
<td align="center">2016-07-01</td>
<td align="center">Y10</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">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@ -804,10 +774,25 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-02-24</td>
<td align="center">V1</td>
<td align="center">2013-10-02</td>
<td align="center">U3</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="even">
<td align="center">2011-12-07</td>
<td align="center">R3</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
@ -818,19 +803,34 @@ Longest: 24</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-10-30</td>
<td align="center">J2</td>
<tr class="odd">
<td align="center">2011-04-13</td>
<td align="center">J9</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</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">2015-02-08</td>
<td align="center">A4</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>
@ -854,50 +854,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2172</td>
<td align="center">146</td>
<td align="center">2370</td>
<td align="center">4688</td>
<td align="center">2169</td>
<td align="center">143</td>
<td align="center">2238</td>
<td align="center">4550</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3417</td>
<td align="center">158</td>
<td align="center">1113</td>
<td align="center">4688</td>
<td align="center">3372</td>
<td align="center">155</td>
<td align="center">1023</td>
<td align="center">4550</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3458</td>
<td align="center">3371</td>
<td align="center">0</td>
<td align="center">1230</td>
<td align="center">4688</td>
<td align="center">1179</td>
<td align="center">4550</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4071</td>
<td align="center">3965</td>
<td align="center">0</td>
<td align="center">617</td>
<td align="center">4688</td>
<td align="center">585</td>
<td align="center">4550</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">1142</td>
<td align="center">1142</td>
<td align="center">1176</td>
<td align="center">1176</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">904</td>
<td align="center">40</td>
<td align="center">940</td>
<td align="center">38</td>
<td align="center">198</td>
<td align="center">1142</td>
<td align="center">1176</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">4071</td>
<td align="center">3965</td>
<td align="center">0</td>
<td align="center">617</td>
<td align="center">4688</td>
<td align="center">585</td>
<td align="center">4550</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1034</td>
<td align="center">1053</td>
<td align="center">0</td>
<td align="center">108</td>
<td align="center">1142</td>
<td align="center">123</td>
<td align="center">1176</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2386</td>
<td align="center">2362</td>
<td align="center">0</td>
<td align="center">311</td>
<td align="center">2697</td>
<td align="center">290</td>
<td align="center">2652</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">2160</td>
<td align="center">2160</td>
<td align="center">2179</td>
<td align="center">2179</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] 0.540844</span></span></code></pre></div>
<span><span class="co"># [1] 0.5391683</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">0.5347460</td>
<td align="center">0.5290698</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5486298</td>
<td align="center">0.5434023</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5512224</td>
<td align="center">0.5325670</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5274779</td>
<td align="center">0.5510580</td>
</tr>
</tbody>
</table>
@ -1008,23 +1008,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5347460</td>
<td align="center">3209</td>
<td align="center">0.5290698</td>
<td align="center">3096</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5486298</td>
<td align="center">3722</td>
<td align="center">0.5434023</td>
<td align="center">3721</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5512224</td>
<td align="center">1718</td>
<td align="center">0.5325670</td>
<td align="center">1566</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5274779</td>
<td align="center">2038</td>
<td align="center">0.5510580</td>
<td align="center">2174</td>
</tr>
</tbody>
</table>
@ -1047,27 +1047,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7625853</td>
<td align="center">0.8683874</td>
<td align="center">0.9769625</td>
<td align="center">0.7751648</td>
<td align="center">0.8714286</td>
<td align="center">0.9795604</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8266200</td>
<td align="center">0.9054291</td>
<td align="center">0.9824869</td>
<td align="center">0.8316327</td>
<td align="center">0.8954082</td>
<td align="center">0.9838435</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7997775</td>
<td align="center">0.8846867</td>
<td align="center">0.9818317</td>
<td align="center">0.7993967</td>
<td align="center">0.8906486</td>
<td align="center">0.9792609</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5462963</td>
<td align="center">0.5392382</td>
<td align="center">0.0000000</td>
<td align="center">0.5462963</td>
<td align="center">0.5392382</td>
</tr>
</tbody>
</table>
@ -1092,23 +1092,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">53.5%</td>
<td align="right">26.7%</td>
<td align="right">52.9%</td>
<td align="right">24.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.9%</td>
<td align="right">27.3%</td>
<td align="right">54.3%</td>
<td align="right">27.5%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">55.1%</td>
<td align="right">24.3%</td>
<td align="right">53.3%</td>
<td align="right">26.4%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">52.7%</td>
<td align="right">26.4%</td>
<td align="right">55.1%</td>
<td align="right">25.8%</td>
</tr>
</tbody>
</table>
@ -1206,18 +1206,16 @@ Longest: 24</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] 0.125 0.005 128 0.25 16 0.5 0.002 4 256 </span></span>
<span><span class="co"># [10] 0.01 32 0.0625 64 0.5 0.005 0.125 0.01 4 </span></span>
<span><span class="co"># [19] 16 2 2 256 4 16 4 0.025 0.125 </span></span>
<span><span class="co"># [28] 2 0.0625 16 0.5 1 0.025 &lt;=0.001 0.5 0.5 </span></span>
<span><span class="co"># [37] 0.025 2 0.01 0.0625 16 8 &lt;=0.001 0.01 8 </span></span>
<span><span class="co"># [46] 0.005 0.125 0.002 0.0625 16 0.25 64 128 0.5 </span></span>
<span><span class="co"># [55] 64 2 0.125 0.0625 0.01 16 0.005 1 1 </span></span>
<span><span class="co"># [64] 64 0.002 4 16 64 0.125 0.01 0.01 8 </span></span>
<span><span class="co"># [73] 0.5 0.5 &lt;=0.001 256 256 64 0.01 4 32 </span></span>
<span><span class="co"># [82] 0.01 8 0.25 &lt;=0.001 &lt;=0.001 64 0.01 0.005 0.002 </span></span>
<span><span class="co"># [91] 2 0.01 0.002 0.5 2 0.125 1 0.5 0.0625 </span></span>
<span><span class="co"># [100] 0.005</span></span></code></pre></div>
<span><span class="co"># [1] 0.002 0.01 0.25 2 &gt;=256 8 0.002 0.025 0.25 0.125 </span></span>
<span><span class="co"># [11] 32 0.005 0.005 4 32 128 16 0.01 2 4 </span></span>
<span><span class="co"># [21] 0.005 0.002 1 0.25 0.001 8 0.025 64 0.01 &gt;=256 </span></span>
<span><span class="co"># [31] 32 0.025 2 0.025 0.002 0.005 8 1 0.25 16 </span></span>
<span><span class="co"># [41] 0.001 64 2 0.002 0.005 0.002 &gt;=256 0.5 0.002 0.002 </span></span>
<span><span class="co"># [51] 0.125 64 0.01 1 0.025 0.0625 0.002 32 32 2 </span></span>
<span><span class="co"># [61] 0.002 64 64 0.01 0.001 2 16 16 0.125 &gt;=256 </span></span>
<span><span class="co"># [71] 32 &gt;=256 16 0.005 32 0.25 0.005 1 0.25 0.125 </span></span>
<span><span class="co"># [81] 0.005 0.0625 2 8 &gt;=256 0.25 0.01 0.025 32 0.0625</span></span>
<span><span class="co"># [91] &gt;=256 0.25 &gt;=256 0.001 128 1 0.125 0.125 0.5 0.125</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>
@ -1244,10 +1242,10 @@ Longest: 24</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] 24 18 17 20 25 19 31 25 27 19 20 19 31 19 21 20 27 21 21 29 22 17 26 23 20</span></span>
<span><span class="co"># [26] 25 22 21 20 24 28 17 17 18 31 21 26 17 30 17 23 22 26 30 18 29 20 27 22 28</span></span>
<span><span class="co"># [51] 17 23 27 23 27 23 25 22 22 31 18 20 17 25 20 24 27 17 29 25 25 28 25 24 20</span></span>
<span><span class="co"># [76] 30 20 17 29 28 31 26 18 21 26 26 27 28 21 18 19 27 31 26 24 21 23 22 29 25</span></span></code></pre></div>
<span><span class="co"># [1] 30 25 27 27 22 25 26 31 26 18 18 28 23 28 22 31 21 22 28 22 21 30 31 29 31</span></span>
<span><span class="co"># [26] 19 27 22 31 25 17 25 24 27 27 27 23 21 25 20 30 30 19 30 20 29 28 29 26 27</span></span>
<span><span class="co"># [51] 17 31 31 17 21 18 25 19 23 23 19 20 24 26 26 24 30 17 25 18 24 30 29 29 21</span></span>
<span><span class="co"># [76] 29 22 23 22 24 28 30 23 17 20 31 27 17 27 19 21 31 22 30 23 25 29 21 17 20</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="">1.8.2.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9029</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="">1.8.2.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9029</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">
@ -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 I I S S S R</span></span>
<span><span class="co"># 2 I I I I I S</span></span>
<span><span class="co"># 3 R S I I R S</span></span>
<span><span class="co"># 4 I I I S S S</span></span>
<span><span class="co"># 5 I I I S S I</span></span>
<span><span class="co"># 6 R R R R I I</span></span>
<span><span class="co"># 1 R S S I R S</span></span>
<span><span class="co"># 2 R I R S R S</span></span>
<span><span class="co"># 3 S S R S I R</span></span>
<span><span class="co"># 4 I R I R R R</span></span>
<span><span class="co"># 5 S S I I S R</span></span>
<span><span class="co"># 6 R R S S S I</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 3 I</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>
<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">3183</td>
<td align="right">63.66%</td>
<td align="right">3183</td>
<td align="right">63.66%</td>
<td align="right">3229</td>
<td align="right">64.58%</td>
<td align="right">3229</td>
<td align="right">64.58%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1007</td>
<td align="right">20.14%</td>
<td align="right">4190</td>
<td align="right">83.80%</td>
<td align="right">971</td>
<td align="right">19.42%</td>
<td align="right">4200</td>
<td align="right">84.00%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">469</td>
<td align="right">9.38%</td>
<td align="right">4659</td>
<td align="right">93.18%</td>
<td align="right">443</td>
<td align="right">8.86%</td>
<td align="right">4643</td>
<td align="right">92.86%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">241</td>
<td align="right">4.82%</td>
<td align="right">4900</td>
<td align="right">98.00%</td>
<td align="right">262</td>
<td align="right">5.24%</td>
<td align="right">4905</td>
<td align="right">98.10%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">100</td>
<td align="right">2.00%</td>
<td align="right">95</td>
<td align="right">1.90%</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="">1.8.2.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9029</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="">1.8.2.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9029</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/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="">1.8.2.9027</small>
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articles/datasets.html
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<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="">1.8.2.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9029</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 21 October 2022 13:14:53 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 21 October 2022 14:26:06 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>
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</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 21 October 2022 13:14:53 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 21 October 2022 14:26:06 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>
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</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 21 October 2022 13:14:53 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 21 October 2022 14:26:06 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>
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</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 21 October 2022 13:14:53 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 21 October 2022 14:26:06 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>
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</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 21 October 2022 13:14:53 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 21 October 2022 14:26:06 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>
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</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 21 October 2022 13:14:53 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 21 October 2022 14:26:06 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>
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</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 21 October 2022 13:14:53 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 21 October 2022 14:26:06 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>
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</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 21 October 2022 13:14:53 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 21 October 2022 14:26:06 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>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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