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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="">1.8.2.9135</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</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">
@ -408,69 +408,69 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-03-07</td>
<td align="center">S9</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">2015-08-25</td>
<td align="center">Z2</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-12-05</td>
<td align="center">2011-07-03</td>
<td align="center">F3</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2015-06-20</td>
<td align="center">R4</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">F</td>
</tr>
<tr class="even">
<td align="center">2012-08-20</td>
<td align="center">U4</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">I</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">J7</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2010-02-20</td>
<td align="center">C1</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-06-02</td>
<td align="center">N3</td>
<td align="center">Hospital C</td>
<td align="center">2015-10-22</td>
<td align="center">H6</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2013-01-12</td>
<td align="center">R6</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-02-28</td>
<td align="center">B3</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
</tbody>
@ -507,15 +507,15 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,347</td>
<td align="right">51.74%</td>
<td align="right">10,347</td>
<td align="right">51.74%</td>
<td align="right">10,346</td>
<td align="right">51.73%</td>
<td align="right">10,346</td>
<td align="right">51.73%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,653</td>
<td align="right">9,654</td>
<td align="right">48.27%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
@ -629,9 +629,9 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co">#&gt; Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co">#&gt; 2</span></span>
<span><span class="co">#&gt; Including isolates from ICU.</span></span>
<span><span class="co">#&gt; =&gt; Found 12,281 'phenotype-based' first isolates (61.4% of total where a</span></span>
<span><span class="co">#&gt; =&gt; Found 12,322 'phenotype-based' first isolates (61.6% of total where a</span></span>
<span><span class="co">#&gt; microbial ID was available)</span></span></code></pre></div>
<p>So only 61.4% is suitable for resistance analysis! We can now filter
<p>So only 61.6% is suitable for resistance analysis! We can now filter
on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
<code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
@ -641,11 +641,11 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>So we end up with 12 281 isolates for analysis. Now our data looks
<p>So we end up with 12 322 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%">
@ -658,7 +658,7 @@ like:</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@ -680,29 +680,13 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2013-03-07</td>
<td align="center">S9</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="even">
<td align="left">2</td>
<td align="center">2016-12-05</td>
<td align="center">2011-07-03</td>
<td align="center">F3</td>
<td align="center">Hospital A</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
@ -711,30 +695,30 @@ like:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<tr class="even">
<td align="left">3</td>
<td align="center">2010-02-20</td>
<td align="center">C1</td>
<td align="center">Hospital D</td>
<td align="center">2015-06-20</td>
<td align="center">R4</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</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">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="left">5</td>
<td align="center">2013-01-12</td>
<td align="center">R6</td>
<tr class="odd">
<td align="left">4</td>
<td align="center">2012-08-20</td>
<td align="center">U4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">F</td>
@ -743,32 +727,48 @@ like:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">2017-02-28</td>
<td align="center">B3</td>
<tr class="even">
<td align="left">7</td>
<td align="center">2017-10-28</td>
<td align="center">J6</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</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="odd">
<td align="left">8</td>
<td align="center">2017-08-19</td>
<td align="center">I1</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2014-07-31</td>
<td align="center">Y4</td>
<td align="center">2017-07-16</td>
<td align="center">S8</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
@ -808,8 +808,8 @@ readable:</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 12,281<br>
Available: 12,281 (100%, NA: 0 = 0%)<br>
Length: 12,322<br>
Available: 12,322 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -835,32 +835,32 @@ Longest: 24</p>
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">5,843</td>
<td align="right">47.58%</td>
<td align="right">47.42%</td>
<td align="right">5,843</td>
<td align="right">47.58%</td>
<td align="right">47.42%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,269</td>
<td align="right">26.62%</td>
<td align="right">9,112</td>
<td align="right">74.20%</td>
<td align="right">3,319</td>
<td align="right">26.94%</td>
<td align="right">9,162</td>
<td align="right">74.35%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,832</td>
<td align="right">14.92%</td>
<td align="right">10,944</td>
<td align="right">89.11%</td>
<td align="right">1,857</td>
<td align="right">15.07%</td>
<td align="right">11,019</td>
<td align="right">89.43%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,337</td>
<td align="right">10.89%</td>
<td align="right">12,281</td>
<td align="right">1,303</td>
<td align="right">10.57%</td>
<td align="right">12,322</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -881,14 +881,14 @@ antibiotic class they are in:</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="11%">
<col width="10%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@ -909,42 +909,12 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-03-07</td>
<td align="center">S9</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="even">
<td align="center">2010-02-20</td>
<td align="center">C1</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2013-12-08</td>
<td align="center">S8</td>
<td align="center">2015-06-20</td>
<td align="center">R4</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</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>
@ -954,13 +924,43 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-07-08</td>
<td align="center">C6</td>
<td align="center">Hospital D</td>
<td align="center">2014-01-08</td>
<td align="center">V3</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2013-07-30</td>
<td align="center">Y4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-03-23</td>
<td align="center">E6</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">I</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -969,33 +969,33 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-06-17</td>
<td align="center">G10</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">2013-12-04</td>
<td align="center">S8</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">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">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-06-11</td>
<td align="center">N7</td>
<td align="center">2013-02-27</td>
<td align="center">Z2</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -1020,50 +1020,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">2674</td>
<td align="center">1181</td>
<td align="center">1988</td>
<td align="center">2759</td>
<td align="center">1167</td>
<td align="center">1917</td>
<td align="center">5843</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">1496</td>
<td align="center">1187</td>
<td align="center">3160</td>
<td align="center">1459</td>
<td align="center">1245</td>
<td align="center">3139</td>
<td align="center">5843</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">2028</td>
<td align="center">1831</td>
<td align="center">2071</td>
<td align="center">1788</td>
<td align="center">1984</td>
<td align="center">5843</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2077</td>
<td align="center">1762</td>
<td align="center">2004</td>
<td align="center">2002</td>
<td align="center">1833</td>
<td align="center">2008</td>
<td align="center">5843</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">573</td>
<td align="center">303</td>
<td align="center">461</td>
<td align="center">1337</td>
<td align="center">583</td>
<td align="center">292</td>
<td align="center">428</td>
<td align="center">1303</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1337</td>
<td align="center">1337</td>
<td align="center">1303</td>
<td align="center">1303</td>
</tr>
</tbody>
</table>
@ -1085,34 +1085,34 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2077</td>
<td align="center">1762</td>
<td align="center">2004</td>
<td align="center">2002</td>
<td align="center">1833</td>
<td align="center">2008</td>
<td align="center">5843</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">454</td>
<td align="center">434</td>
<td align="center">449</td>
<td align="center">1337</td>
<td align="center">456</td>
<td align="center">423</td>
<td align="center">424</td>
<td align="center">1303</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1138</td>
<td align="center">1010</td>
<td align="center">1121</td>
<td align="center">3269</td>
<td align="center">1144</td>
<td align="center">1045</td>
<td align="center">1130</td>
<td align="center">3319</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">1832</td>
<td align="center">1832</td>
<td align="center">1857</td>
<td align="center">1857</td>
</tr>
</tbody>
</table>
@ -1144,7 +1144,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] 0.5882257</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 0.5842396</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
@ -1159,19 +1159,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5913304</td>
<td align="center">0.5827676</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5810277</td>
<td align="center">0.5907183</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.6058002</td>
<td align="center">0.5845813</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5828571</td>
<td align="center">0.5747605</td>
</tr>
</tbody>
</table>
@ -1196,23 +1196,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5913304</td>
<td align="center">3668</td>
<td align="center">0.5827676</td>
<td align="center">3830</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5810277</td>
<td align="center">4301</td>
<td align="center">0.5907183</td>
<td align="center">4288</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.6058002</td>
<td align="center">1862</td>
<td align="center">0.5845813</td>
<td align="center">1803</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5828571</td>
<td align="center">2450</td>
<td align="center">0.5747605</td>
<td align="center">2401</td>
</tr>
</tbody>
</table>
@ -1237,27 +1237,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6597638</td>
<td align="center">0.6570255</td>
<td align="center">0.8873866</td>
<td align="center">0.6719151</td>
<td align="center">0.6563409</td>
<td align="center">0.8921787</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6551982</td>
<td align="center">0.6641735</td>
<td align="center">0.8840688</td>
<td align="center">0.6715272</td>
<td align="center">0.6745971</td>
<td align="center">0.8879509</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6628939</td>
<td align="center">0.6570817</td>
<td align="center">0.8877333</td>
<td align="center">0.6776137</td>
<td align="center">0.6595360</td>
<td align="center">0.8945466</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4737991</td>
<td align="center">0.4717286</td>
<td align="center">0.0000000</td>
<td align="center">0.4737991</td>
<td align="center">0.4717286</td>
</tr>
</tbody>
</table>
@ -1285,23 +1285,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">59.1%</td>
<td align="right">37.7%</td>
<td align="right">58.3%</td>
<td align="right">35.1%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">58.1%</td>
<td align="right">35.5%</td>
<td align="right">59.1%</td>
<td align="right">35.8%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">60.6%</td>
<td align="right">37.3%</td>
<td align="right">58.5%</td>
<td align="right">37.4%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">58.3%</td>
<td align="right">37.1%</td>
<td align="right">57.5%</td>
<td align="right">34.9%</td>
</tr>
</tbody>
</table>
@ -1417,16 +1417,16 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co">#&gt; Class 'mic'</span></span>
<span><span class="co">#&gt; [1] 1 8 0.01 8 0.01 0.001 1 0.0625 0.01 0.002 </span></span>
<span><span class="co">#&gt; [11] 0.0625 8 128 0.005 0.001 32 1 0.0625 64 256 </span></span>
<span><span class="co">#&gt; [21] 4 0.002 1 0.0625 0.001 0.25 4 4 0.002 8 </span></span>
<span><span class="co">#&gt; [31] 64 1 4 0.01 128 1 0.002 0.01 0.5 0.25 </span></span>
<span><span class="co">#&gt; [41] 0.0625 0.005 256 1 2 32 0.01 128 0.002 64 </span></span>
<span><span class="co">#&gt; [51] 0.5 0.5 32 16 0.002 0.5 32 0.125 0.0625 0.001 </span></span>
<span><span class="co">#&gt; [61] 32 0.125 0.002 256 2 0.0625 0.002 0.025 0.025 0.001 </span></span>
<span><span class="co">#&gt; [71] 0.0625 16 256 16 2 4 8 0.001 0.025 0.125 </span></span>
<span><span class="co">#&gt; [81] 1 0.01 8 0.125 0.5 2 128 0.005 256 0.125 </span></span>
<span><span class="co">#&gt; [91] 8 0.25 0.005 0.25 0.002 2 32 0.125 4 0.025</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 0.25 0.5 0.125 0.125 16 32 0.002 &gt;=256 0.025 1 </span></span>
<span><span class="co">#&gt; [11] 64 128 32 0.25 0.5 0.0625 128 &gt;=256 8 0.002 </span></span>
<span><span class="co">#&gt; [21] 0.005 0.002 4 0.125 0.005 0.125 0.01 4 64 0.005 </span></span>
<span><span class="co">#&gt; [31] 32 0.002 0.25 0.002 0.0625 32 16 128 0.001 128 </span></span>
<span><span class="co">#&gt; [41] 0.001 0.5 0.025 0.5 128 4 0.005 0.25 0.125 0.002 </span></span>
<span><span class="co">#&gt; [51] 16 0.025 0.005 0.0625 4 32 0.005 4 0.025 0.001 </span></span>
<span><span class="co">#&gt; [61] 128 0.125 0.025 2 4 0.0625 0.001 8 0.25 0.025 </span></span>
<span><span class="co">#&gt; [71] 1 32 &gt;=256 1 16 8 0.0625 0.01 2 0.005 </span></span>
<span><span class="co">#&gt; [81] 16 0.025 1 0.002 128 0.002 0.5 8 8 64 </span></span>
<span><span class="co">#&gt; [91] 128 0.01 0.005 16 0.002 0.005 &gt;=256 8 0.002 0.25</span></span></code></pre></div>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1460,10 +1460,10 @@ plotting:</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co">#&gt; Class 'disk'</span></span>
<span><span class="co">#&gt; [1] 23 29 25 27 30 18 31 23 27 29 30 26 26 17 24 27 22 23 28 17 27 21 31 23 31</span></span>
<span><span class="co">#&gt; [26] 28 19 23 28 22 26 25 30 20 20 23 30 31 27 22 20 28 22 28 20 20 29 20 31 22</span></span>
<span><span class="co">#&gt; [51] 24 27 19 25 31 21 17 21 29 24 27 27 31 26 17 22 26 26 26 31 20 31 23 31 21</span></span>
<span><span class="co">#&gt; [76] 18 19 31 28 25 25 31 29 29 17 23 22 29 23 30 23 23 31 19 18 28 20 31 22 19</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 28 18 29 27 31 26 27 30 31 18 30 25 17 20 20 31 22 22 30 26 24 26 23 28 28</span></span>
<span><span class="co">#&gt; [26] 24 27 29 20 30 25 25 25 22 23 27 27 23 29 27 23 20 19 23 23 18 29 21 31 29</span></span>
<span><span class="co">#&gt; [51] 19 31 27 27 31 20 22 28 31 19 21 30 28 21 24 21 20 20 19 27 26 30 19 24 29</span></span>
<span><span class="co">#&gt; [76] 17 26 18 27 23 19 29 24 27 27 20 25 28 17 21 29 29 17 22 20 26 24 23 17 25</span></span></code></pre></div>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>

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2
articles/EUCAST.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9135</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</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">

62
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="">1.8.2.9135</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -385,19 +385,19 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co">#&gt; rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co">#&gt; 1 R R R S I R</span></span>
<span><span class="co">#&gt; 2 R R I I S R</span></span>
<span><span class="co">#&gt; 3 I S S S S S</span></span>
<span><span class="co">#&gt; 4 S I I S I S</span></span>
<span><span class="co">#&gt; 5 R R I S I I</span></span>
<span><span class="co">#&gt; 6 R S I R S R</span></span>
<span><span class="co">#&gt; 1 S R R R S S</span></span>
<span><span class="co">#&gt; 2 I I S I R R</span></span>
<span><span class="co">#&gt; 3 S S S I R I</span></span>
<span><span class="co">#&gt; 4 I I R R R S</span></span>
<span><span class="co">#&gt; 5 I I S I R S</span></span>
<span><span class="co">#&gt; 6 S R I I R S</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 S</span></span>
<span><span class="co">#&gt; 2 I</span></span>
<span><span class="co">#&gt; 3 I</span></span>
<span><span class="co">#&gt; 4 I</span></span>
<span><span class="co">#&gt; 5 R</span></span>
<span><span class="co">#&gt; 6 S</span></span></code></pre></div>
<span><span class="co">#&gt; 1 R</span></span>
<span><span class="co">#&gt; 2 R</span></span>
<span><span class="co">#&gt; 3 S</span></span>
<span><span class="co">#&gt; 4 R</span></span>
<span><span class="co">#&gt; 5 I</span></span>
<span><span class="co">#&gt; 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">
@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3244</td>
<td align="right">64.88%</td>
<td align="right">3244</td>
<td align="right">64.88%</td>
<td align="right">3221</td>
<td align="right">64.42%</td>
<td align="right">3221</td>
<td align="right">64.42%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">993</td>
<td align="right">19.86%</td>
<td align="right">4237</td>
<td align="right">84.74%</td>
<td align="right">966</td>
<td align="right">19.32%</td>
<td align="right">4187</td>
<td align="right">83.74%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">447</td>
<td align="right">8.94%</td>
<td align="right">4684</td>
<td align="right">93.68%</td>
<td align="right">448</td>
<td align="right">8.96%</td>
<td align="right">4635</td>
<td align="right">92.70%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">214</td>
<td align="right">4.28%</td>
<td align="right">4898</td>
<td align="right">97.96%</td>
<td align="right">256</td>
<td align="right">5.12%</td>
<td align="right">4891</td>
<td align="right">97.82%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">102</td>
<td align="right">2.04%</td>
<td align="right">109</td>
<td align="right">2.18%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

4
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="">1.8.2.9135</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</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">
@ -290,7 +290,7 @@ function:</p>
<span><span class="co">#&gt; [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></span>
<span><span class="co">#&gt; Importance of components:</span></span>
<span><span class="co">#&gt; PC1 PC2 PC3 PC4 PC5 PC6 PC7</span></span>
<span><span class="co">#&gt; Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16</span></span>
<span><span class="co">#&gt; Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17</span></span>
<span><span class="co">#&gt; Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span></span>
<span><span class="co">#&gt; Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></span></code></pre></div>
<pre><code><span><span class="co">#&gt; Groups (n=4, named as 'order'):</span></span>

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="">1.8.2.9135</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</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>
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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="">1.8.2.9135</small>
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articles/index.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9135</small>
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articles/resistance_predict.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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articles/welcome_to_AMR.html
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@ -38,7 +38,7 @@
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