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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="">1.8.2.9143</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9144</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">
@ -408,71 +408,71 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-07-25</td>
<td align="center">2013-12-05</td>
<td align="center">E7</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-10-24</td>
<td align="center">Y9</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-05-31</td>
<td align="center">N6</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</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">2012-12-23</td>
<td align="center">N3</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-09-03</td>
<td align="center">J8</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-06-18</td>
<td align="center">L8</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">2012-12-08</td>
<td align="center">T9</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-04-10</td>
<td align="center">K10</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">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-05-27</td>
<td align="center">W3</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">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2017-07-16</td>
<td align="center">M3</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</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>
</tr>
<tr class="even">
<td align="center">2014-10-13</td>
<td align="center">U3</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -507,16 +507,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,443</td>
<td align="right">52.22%</td>
<td align="right">10,443</td>
<td align="right">52.22%</td>
<td align="right">10,401</td>
<td align="right">52.01%</td>
<td align="right">10,401</td>
<td align="right">52.01%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,557</td>
<td align="right">47.79%</td>
<td align="right">9,599</td>
<td align="right">48.00%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -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 12,276 'phenotype-based' first isolates (61.4% of total where a</span></span>
<span><span class="co">#&gt; =&gt; Found 12,354 'phenotype-based' first isolates (61.8% 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 61.8% 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">
@ -641,7 +641,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>So we end up with 12 276 isolates for analysis. Now our data looks
<p>So we end up with 12 354 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>
@ -680,62 +680,14 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">2</td>
<td align="center">2011-10-24</td>
<td align="center">Y9</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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">4</td>
<td align="center">2012-12-23</td>
<td align="center">N3</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">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">5</td>
<td align="center">2012-09-03</td>
<td align="center">J8</td>
<td align="left">1</td>
<td align="center">2013-12-05</td>
<td align="center">E7</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="center">2012-06-18</td>
<td align="center">L8</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">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -743,15 +695,47 @@ like:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2017-07-20</td>
<td align="center">K10</td>
<tr class="even">
<td align="left">2</td>
<td align="center">2012-12-08</td>
<td align="center">T9</td>
<td align="center">Hospital A</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">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2014-05-27</td>
<td align="center">W3</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">R</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="left">5</td>
<td align="center">2017-07-16</td>
<td align="center">M3</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">M</td>
<td align="center">Gram-negative</td>
@ -759,17 +743,33 @@ like:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2015-09-17</td>
<td align="center">Z10</td>
<tr class="odd">
<td align="left">6</td>
<td align="center">2014-10-13</td>
<td align="center">U3</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</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">I</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2016-10-22</td>
<td align="center">K10</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">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
@ -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: 12,276<br>
Available: 12,276 (100%, NA: 0 = 0%)<br>
Length: 12,354<br>
Available: 12,354 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -834,33 +834,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">5,930</td>
<td align="right">48.31%</td>
<td align="right">5,930</td>
<td align="right">48.31%</td>
<td align="right">5,962</td>
<td align="right">48.26%</td>
<td align="right">5,962</td>
<td align="right">48.26%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,288</td>
<td align="right">26.78%</td>
<td align="right">9,218</td>
<td align="right">75.09%</td>
<td align="right">3,321</td>
<td align="right">26.88%</td>
<td align="right">9,283</td>
<td align="right">75.14%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,744</td>
<td align="right">14.21%</td>
<td align="right">10,962</td>
<td align="right">89.30%</td>
<td align="right">1,785</td>
<td align="right">14.45%</td>
<td align="right">11,068</td>
<td align="right">89.59%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,314</td>
<td align="right">10.70%</td>
<td align="right">12,276</td>
<td align="right">1,286</td>
<td align="right">10.41%</td>
<td align="right">12,354</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -909,13 +909,13 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-06-18</td>
<td align="center">L8</td>
<td align="center">Hospital C</td>
<td align="center">2013-12-05</td>
<td align="center">E7</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">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -924,42 +924,12 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-10-16</td>
<td align="center">H9</td>
<td align="center">2012-12-08</td>
<td align="center">T9</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-02-22</td>
<td align="center">O1</td>
<td align="center">Hospital B</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="even">
<td align="center">2015-10-31</td>
<td align="center">X3</td>
<td align="center">Hospital D</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">R</td>
<td align="center">R</td>
<td align="center">F</td>
@ -969,33 +939,63 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-12-30</td>
<td align="center">G1</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">2014-05-27</td>
<td align="center">W3</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">R</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">2014-10-13</td>
<td align="center">U3</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">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">2016-10-22</td>
<td align="center">K10</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">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-06-14</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">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">2015-11-07</td>
<td align="center">D3</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">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">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>
@ -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">2798</td>
<td align="center">1114</td>
<td align="center">2018</td>
<td align="center">5930</td>
<td align="center">2824</td>
<td align="center">1209</td>
<td align="center">1929</td>
<td align="center">5962</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">1504</td>
<td align="center">1245</td>
<td align="center">3181</td>
<td align="center">5930</td>
<td align="center">1538</td>
<td align="center">1294</td>
<td align="center">3130</td>
<td align="center">5962</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">2027</td>
<td align="center">1808</td>
<td align="center">2095</td>
<td align="center">5930</td>
<td align="center">2046</td>
<td align="center">1862</td>
<td align="center">2054</td>
<td align="center">5962</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2054</td>
<td align="center">1817</td>
<td align="center">2059</td>
<td align="center">5930</td>
<td align="center">2049</td>
<td align="center">1812</td>
<td align="center">2101</td>
<td align="center">5962</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">582</td>
<td align="center">275</td>
<td align="center">457</td>
<td align="center">1314</td>
<td align="center">560</td>
<td align="center">278</td>
<td align="center">448</td>
<td align="center">1286</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">1314</td>
<td align="center">1314</td>
<td align="center">1286</td>
<td align="center">1286</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">2054</td>
<td align="center">1817</td>
<td align="center">2059</td>
<td align="center">5930</td>
<td align="center">2049</td>
<td align="center">1812</td>
<td align="center">2101</td>
<td align="center">5962</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">464</td>
<td align="center">407</td>
<td align="center">443</td>
<td align="center">1314</td>
<td align="center">451</td>
<td align="center">389</td>
<td align="center">446</td>
<td align="center">1286</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1122</td>
<td align="center">1047</td>
<td align="center">1119</td>
<td align="center">3288</td>
<td align="center">1163</td>
<td align="center">1016</td>
<td align="center">1142</td>
<td align="center">3321</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">1744</td>
<td align="center">1744</td>
<td align="center">1785</td>
<td align="center">1785</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] 0.5847181</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 0.5781124</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">0.5877193</td>
<td align="center">0.5903060</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5747854</td>
<td align="center">0.5759064</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5892857</td>
<td align="center">0.5773087</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5948136</td>
<td align="center">0.5644320</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">0.5877193</td>
<td align="center">3534</td>
<td align="center">0.5903060</td>
<td align="center">3693</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5747854</td>
<td align="center">4426</td>
<td align="center">0.5759064</td>
<td align="center">4275</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5892857</td>
<td align="center">1848</td>
<td align="center">0.5773087</td>
<td align="center">1895</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5948136</td>
<td align="center">2468</td>
<td align="center">0.5644320</td>
<td align="center">2491</td>
</tr>
</tbody>
</table>
@ -1237,27 +1237,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6596965</td>
<td align="center">0.6527825</td>
<td align="center">0.8831366</td>
<td align="center">0.6764509</td>
<td align="center">0.6476015</td>
<td align="center">0.8901375</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6522070</td>
<td align="center">0.6628615</td>
<td align="center">0.8896499</td>
<td align="center">0.6516330</td>
<td align="center">0.6531882</td>
<td align="center">0.8833593</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6727494</td>
<td align="center">0.6596715</td>
<td align="center">0.8892944</td>
<td align="center">0.6591388</td>
<td align="center">0.6561277</td>
<td align="center">0.8858777</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4678899</td>
<td align="center">0.4829132</td>
<td align="center">0.0000000</td>
<td align="center">0.4678899</td>
<td align="center">0.4829132</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">58.8%</td>
<td align="right">36.5%</td>
<td align="right">59.0%</td>
<td align="right">36.6%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">57.5%</td>
<td align="right">36.2%</td>
<td align="right">57.6%</td>
<td align="right">35.7%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">58.9%</td>
<td align="right">36.7%</td>
<td align="right">57.7%</td>
<td align="right">36.6%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">59.5%</td>
<td align="right">36.8%</td>
<td align="right">56.4%</td>
<td align="right">34.5%</td>
</tr>
</tbody>
</table>
@ -1417,18 +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] 0.5 0.0625 8 16 8 64 32 256 32 </span></span>
<span><span class="co">#&gt; [10] 0.025 1 0.002 16 256 0.025 2 0.01 8 </span></span>
<span><span class="co">#&gt; [19] 64 0.25 0.005 &lt;=0.001 &lt;=0.001 2 0.002 0.125 4 </span></span>
<span><span class="co">#&gt; [28] 1 2 256 4 32 0.125 1 2 0.0625 </span></span>
<span><span class="co">#&gt; [37] 0.01 0.0625 0.125 &lt;=0.001 0.01 256 256 128 32 </span></span>
<span><span class="co">#&gt; [46] 8 256 32 8 0.25 1 32 256 128 </span></span>
<span><span class="co">#&gt; [55] &lt;=0.001 16 128 0.25 0.005 0.25 8 16 0.125 </span></span>
<span><span class="co">#&gt; [64] 0.002 4 0.125 256 8 &lt;=0.001 0.005 0.025 64 </span></span>
<span><span class="co">#&gt; [73] 2 256 0.25 16 4 0.125 32 0.5 0.002 </span></span>
<span><span class="co">#&gt; [82] 0.025 256 0.025 1 64 0.5 0.01 0.01 64 </span></span>
<span><span class="co">#&gt; [91] &lt;=0.001 16 256 64 0.25 0.25 64 4 0.025 </span></span>
<span><span class="co">#&gt; [100] 0.005</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 0.0625 0.001 0.01 0.125 0.01 0.01 0.025 32 0.25 0.025 </span></span>
<span><span class="co">#&gt; [11] 0.25 4 0.01 0.001 0.005 16 2 0.01 0.025 0.025 </span></span>
<span><span class="co">#&gt; [21] 0.01 0.005 0.0625 0.01 0.005 0.001 0.01 0.002 0.01 &gt;=256 </span></span>
<span><span class="co">#&gt; [31] 0.025 0.025 0.005 4 0.005 0.001 0.5 64 0.025 4 </span></span>
<span><span class="co">#&gt; [41] 0.0625 &gt;=256 1 0.125 16 32 0.01 0.01 64 64 </span></span>
<span><span class="co">#&gt; [51] 1 0.25 0.25 0.125 128 0.002 64 0.125 16 128 </span></span>
<span><span class="co">#&gt; [61] 0.01 0.01 0.01 128 0.0625 8 0.01 0.5 16 1 </span></span>
<span><span class="co">#&gt; [71] 0.005 128 0.002 0.125 2 16 0.01 0.25 1 2 </span></span>
<span><span class="co">#&gt; [81] 0.001 4 0.002 8 0.25 8 0.002 16 0.01 128 </span></span>
<span><span class="co">#&gt; [91] 1 128 0.125 0.5 0.01 0.025 0.5 32 0.0625 0.002</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>
@ -1462,10 +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] 27 25 28 20 31 23 27 18 23 19 25 22 21 20 18 28 27 30 18 29 31 18 21 20 23</span></span>
<span><span class="co">#&gt; [26] 27 27 30 29 27 21 18 28 27 23 31 21 30 17 20 29 20 18 18 21 26 25 26 29 20</span></span>
<span><span class="co">#&gt; [51] 21 26 21 31 19 18 21 26 22 25 22 21 20 20 31 25 24 19 20 30 19 24 28 23 23</span></span>
<span><span class="co">#&gt; [76] 20 29 22 18 26 26 27 31 27 30 29 21 31 20 17 18 19 27 29 20 19 26 17 20 21</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 27 26 31 31 27 28 21 17 30 29 22 24 19 27 22 31 19 17 23 27 18 29 24 26 19</span></span>
<span><span class="co">#&gt; [26] 30 28 22 30 24 19 27 27 20 25 22 19 19 26 17 27 29 27 26 27 27 30 19 27 21</span></span>
<span><span class="co">#&gt; [51] 24 24 19 23 21 18 30 22 28 22 26 26 21 19 31 19 17 24 30 28 25 22 23 30 24</span></span>
<span><span class="co">#&gt; [76] 23 21 26 30 23 28 24 27 22 28 31 21 30 23 30 26 17 28 17 29 19 20 28 28 27</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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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="">1.8.2.9143</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9144</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">

60
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="">1.8.2.9143</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9144</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">
@ -385,18 +385,18 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co">#&gt; rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co">#&gt; 1 R I S R S R</span></span>
<span><span class="co">#&gt; 2 R R I I R I</span></span>
<span><span class="co">#&gt; 3 I R S S I R</span></span>
<span><span class="co">#&gt; 4 R S I S R S</span></span>
<span><span class="co">#&gt; 5 S R S S S S</span></span>
<span><span class="co">#&gt; 6 S R S I S R</span></span>
<span><span class="co">#&gt; 1 I I R R S I</span></span>
<span><span class="co">#&gt; 2 R R S S R R</span></span>
<span><span class="co">#&gt; 3 R R S I I R</span></span>
<span><span class="co">#&gt; 4 I R R S I R</span></span>
<span><span class="co">#&gt; 5 I I R I R R</span></span>
<span><span class="co">#&gt; 6 R I I I S R</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 I</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 S</span></span>
<span><span class="co">#&gt; 1 R</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 S</span></span>
<span><span class="co">#&gt; 5 I</span></span>
<span><span class="co">#&gt; 6 S</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3217</td>
<td align="right">64.34%</td>
<td align="right">3217</td>
<td align="right">64.34%</td>
<td align="right">3196</td>
<td align="right">63.92%</td>
<td align="right">3196</td>
<td align="right">63.92%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">960</td>
<td align="right">19.20%</td>
<td align="right">4177</td>
<td align="right">83.54%</td>
<td align="right">959</td>
<td align="right">19.18%</td>
<td align="right">4155</td>
<td align="right">83.10%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">461</td>
<td align="right">9.22%</td>
<td align="right">4638</td>
<td align="right">92.76%</td>
<td align="right">479</td>
<td align="right">9.58%</td>
<td align="right">4634</td>
<td align="right">92.68%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">257</td>
<td align="right">5.14%</td>
<td align="right">4895</td>
<td align="right">97.90%</td>
<td align="right">256</td>
<td align="right">5.12%</td>
<td align="right">4890</td>
<td align="right">97.80%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">105</td>
<td align="right">2.10%</td>
<td align="right">110</td>
<td align="right">2.20%</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="">1.8.2.9143</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9144</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="">1.8.2.9143</small>
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2
articles/WHONET.html
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@ -38,7 +38,7 @@
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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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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -38,7 +38,7 @@
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articles/welcome_to_AMR.html
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@ -38,7 +38,7 @@
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