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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="">1.8.2.9102</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9103</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">
@ -386,12 +386,12 @@ data set:</p>
<col width="13%">
<col width="13%">
<col width="13%">
<col width="26%">
<col width="28%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="9%">
<col width="8%">
</colgroup>
<thead><tr class="header">
<th align="center">date</th>
@ -406,70 +406,70 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-09-21</td>
<td align="center">J4</td>
<td align="center">Hospital A</td>
<td align="center">2018-01-01</td>
<td align="center">Y10</td>
<td align="center">Hospital B</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">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-03-19</td>
<td align="center">M7</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">I</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-02-22</td>
<td align="center">D10</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2010-03-04</td>
<td align="center">G5</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">2015-12-24</td>
<td align="center">H3</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</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">M</td>
</tr>
<tr class="even">
<td align="center">2013-03-28</td>
<td align="center">V6</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">2017-07-13</td>
<td align="center">U7</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</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="odd">
<td align="center">2010-09-26</td>
<td align="center">L5</td>
<td align="center">2016-02-29</td>
<td align="center">O4</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">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-09-16</td>
<td align="center">M4</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">2016-02-09</td>
<td align="center">S1</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella 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>
<td align="center">F</td>
</tr>
</tbody>
</table>
@ -505,16 +505,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,477</td>
<td align="right">52.39%</td>
<td align="right">10,477</td>
<td align="right">52.39%</td>
<td align="right">10,349</td>
<td align="right">51.75%</td>
<td align="right">10,349</td>
<td align="right">51.75%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,523</td>
<td align="right">47.62%</td>
<td align="right">9,651</td>
<td align="right">48.26%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -627,9 +627,9 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 12,316 'phenotype-based' first isolates (61.6% of total where a</span></span>
<span><span class="co"># =&gt; Found 12,429 'phenotype-based' first isolates (62.1% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 61.6% is suitable for resistance analysis! We can now filter
<p>So only 62.1% 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">
@ -640,7 +640,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 12,316 isolates for analysis. Now our data looks
<p>So we end up with 12,429 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>
@ -679,30 +679,30 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">2</td>
<td align="center">2011-03-19</td>
<td align="center">M7</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="left">1</td>
<td align="center">2018-01-01</td>
<td align="center">Y10</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">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</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">3</td>
<td align="center">2010-03-04</td>
<td align="center">G5</td>
<td align="left">2</td>
<td align="center">2012-02-22</td>
<td align="center">D10</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">I</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>
@ -711,14 +711,30 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2016-01-22</td>
<td align="center">Z1</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="left">5</td>
<td align="center">2016-02-29</td>
<td align="center">O4</td>
<td align="center">Hospital B</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">I</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">6</td>
<td align="center">2016-02-09</td>
<td align="center">S1</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
@ -726,32 +742,16 @@ like:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2011-10-25</td>
<td align="center">W6</td>
<tr class="odd">
<td align="left">7</td>
<td align="center">2013-02-22</td>
<td align="center">S5</td>
<td align="center">Hospital D</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">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">10</td>
<td align="center">2013-07-04</td>
<td align="center">W5</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</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>
@ -759,19 +759,19 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">13</td>
<td align="center">2013-11-07</td>
<td align="center">M6</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="left">9</td>
<td align="center">2014-08-17</td>
<td align="center">J7</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">I</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">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -807,8 +807,8 @@ 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: 12,316<br>
Available: 12,316 (100%, NA: 0 = 0%)<br>
Length: 12,429<br>
Available: 12,429 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -833,33 +833,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">5,955</td>
<td align="right">48.35%</td>
<td align="right">5,955</td>
<td align="right">48.35%</td>
<td align="right">5,950</td>
<td align="right">47.87%</td>
<td align="right">5,950</td>
<td align="right">47.87%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,207</td>
<td align="right">26.04%</td>
<td align="right">9,162</td>
<td align="right">74.39%</td>
<td align="right">3,328</td>
<td align="right">26.78%</td>
<td align="right">9,278</td>
<td align="right">74.65%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,796</td>
<td align="right">14.58%</td>
<td align="right">10,958</td>
<td align="right">88.97%</td>
<td align="right">1,809</td>
<td align="right">14.55%</td>
<td align="right">11,087</td>
<td align="right">89.20%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,358</td>
<td align="right">11.03%</td>
<td align="right">12,316</td>
<td align="right">1,342</td>
<td align="right">10.80%</td>
<td align="right">12,429</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -908,13 +908,13 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-03-19</td>
<td align="center">M7</td>
<td align="center">Hospital D</td>
<td align="center">2012-02-22</td>
<td align="center">D10</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -923,28 +923,13 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2010-03-04</td>
<td align="center">G5</td>
<td align="center">2016-02-09</td>
<td align="center">S1</td>
<td align="center">Hospital B</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">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">2016-01-22</td>
<td align="center">Z1</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
@ -952,49 +937,64 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-08-17</td>
<td align="center">J7</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">S</td>
<td align="center">R</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="center">2013-07-04</td>
<td align="center">W5</td>
<td align="center">2013-05-07</td>
<td align="center">V6</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</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">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">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2013-12-25</td>
<td align="center">L2</td>
<td align="center">Hospital A</td>
<td align="center">2013-10-28</td>
<td align="center">P9</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</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">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">2015-03-12</td>
<td align="center">Q2</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">R</td>
<td align="center">2017-04-15</td>
<td align="center">V10</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</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">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -1019,50 +1019,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">1489</td>
<td align="center">1320</td>
<td align="center">3146</td>
<td align="center">5955</td>
<td align="center">1484</td>
<td align="center">1261</td>
<td align="center">3205</td>
<td align="center">5950</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">2797</td>
<td align="center">1202</td>
<td align="center">1956</td>
<td align="center">5955</td>
<td align="center">2726</td>
<td align="center">1214</td>
<td align="center">2010</td>
<td align="center">5950</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">2035</td>
<td align="center">1852</td>
<td align="center">2068</td>
<td align="center">5955</td>
<td align="center">2026</td>
<td align="center">1824</td>
<td align="center">2100</td>
<td align="center">5950</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2089</td>
<td align="center">1802</td>
<td align="center">2064</td>
<td align="center">5955</td>
<td align="center">2016</td>
<td align="center">1853</td>
<td align="center">2081</td>
<td align="center">5950</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">1358</td>
<td align="center">1358</td>
<td align="center">1342</td>
<td align="center">1342</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">607</td>
<td align="center">291</td>
<td align="center">460</td>
<td align="center">1358</td>
<td align="center">599</td>
<td align="center">262</td>
<td align="center">481</td>
<td align="center">1342</td>
</tr>
</tbody>
</table>
@ -1084,34 +1084,34 @@ 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">2089</td>
<td align="center">1802</td>
<td align="center">2064</td>
<td align="center">5955</td>
<td align="center">2016</td>
<td align="center">1853</td>
<td align="center">2081</td>
<td align="center">5950</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">456</td>
<td align="center">442</td>
<td align="center">460</td>
<td align="center">1358</td>
<td align="center">468</td>
<td align="center">429</td>
<td align="center">445</td>
<td align="center">1342</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1084</td>
<td align="center">1058</td>
<td align="center">1065</td>
<td align="center">3207</td>
<td align="center">1083</td>
<td align="center">1090</td>
<td align="center">1155</td>
<td align="center">3328</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">1796</td>
<td align="center">1796</td>
<td align="center">1809</td>
<td align="center">1809</td>
</tr>
</tbody>
</table>
@ -1143,7 +1143,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.583631</span></span></code></pre></div>
<span><span class="co"># [1] 0.5882211</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">
@ -1158,19 +1158,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5774648</td>
<td align="center">0.5883152</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5798359</td>
<td align="center">0.5836154</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5947678</td>
<td align="center">0.5717427</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5909091</td>
<td align="center">0.6082433</td>
</tr>
</tbody>
</table>
@ -1195,23 +1195,23 @@ 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">0.5774648</td>
<td align="center">3692</td>
<td align="center">0.5883152</td>
<td align="center">3680</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5798359</td>
<td align="center">4265</td>
<td align="center">0.5836154</td>
<td align="center">4431</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5947678</td>
<td align="center">1873</td>
<td align="center">0.5717427</td>
<td align="center">1819</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5909091</td>
<td align="center">2486</td>
<td align="center">0.6082433</td>
<td align="center">2499</td>
</tr>
</tbody>
</table>
@ -1236,27 +1236,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6715365</td>
<td align="center">0.6534005</td>
<td align="center">0.8831234</td>
<td align="center">0.6621849</td>
<td align="center">0.6502521</td>
<td align="center">0.8878992</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6612666</td>
<td align="center">0.6612666</td>
<td align="center">0.8910162</td>
<td align="center">0.6415797</td>
<td align="center">0.6684054</td>
<td align="center">0.8941878</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6719676</td>
<td align="center">0.6679139</td>
<td align="center">0.8961646</td>
<td align="center">0.6676683</td>
<td align="center">0.6529447</td>
<td align="center">0.8846154</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4732739</td>
<td align="center">0.4693201</td>
<td align="center">0.0000000</td>
<td align="center">0.4732739</td>
<td align="center">0.4693201</td>
</tr>
</tbody>
</table>
@ -1284,23 +1284,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">57.7%</td>
<td align="right">35.9%</td>
<td align="right">58.8%</td>
<td align="right">36.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">58.0%</td>
<td align="right">35.8%</td>
<td align="right">58.4%</td>
<td align="right">36.9%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">59.5%</td>
<td align="right">36.9%</td>
<td align="right">57.2%</td>
<td align="right">36.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">59.1%</td>
<td align="right">35.0%</td>
<td align="right">60.8%</td>
<td align="right">37.1%</td>
</tr>
</tbody>
</table>
@ -1416,18 +1416,16 @@ 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"># Class 'mic'</span></span>
<span><span class="co"># [1] 256 0.5 0.002 16 0.01 0.025 0.0625 0.002 0.25 </span></span>
<span><span class="co"># [10] 0.25 0.002 0.002 256 &lt;=0.001 2 4 0.025 1 </span></span>
<span><span class="co"># [19] 32 32 0.5 0.125 256 64 0.25 0.002 0.005 </span></span>
<span><span class="co"># [28] 0.01 64 0.5 0.25 8 256 0.025 8 0.025 </span></span>
<span><span class="co"># [37] 0.0625 4 0.0625 0.125 0.025 128 256 16 2 </span></span>
<span><span class="co"># [46] 32 32 0.125 16 &lt;=0.001 0.25 64 0.01 0.01 </span></span>
<span><span class="co"># [55] 128 256 0.01 256 32 0.5 0.25 16 128 </span></span>
<span><span class="co"># [64] &lt;=0.001 2 8 128 2 32 4 0.025 16 </span></span>
<span><span class="co"># [73] 4 0.002 0.025 0.125 0.125 16 16 64 0.005 </span></span>
<span><span class="co"># [82] 4 4 &lt;=0.001 0.125 4 0.025 0.25 0.25 0.025 </span></span>
<span><span class="co"># [91] 256 64 128 0.25 0.002 128 2 1 0.005 </span></span>
<span><span class="co"># [100] 0.005</span></span></code></pre></div>
<span><span class="co"># [1] 256 64 0.001 0.01 8 8 1 0.5 0.5 16 </span></span>
<span><span class="co"># [11] 0.125 256 0.5 0.002 2 0.005 1 1 256 0.002 </span></span>
<span><span class="co"># [21] 0.002 0.01 0.25 2 256 64 0.125 128 0.001 4 </span></span>
<span><span class="co"># [31] 0.125 0.0625 1 64 256 0.25 128 0.5 0.5 32 </span></span>
<span><span class="co"># [41] 16 2 0.125 0.005 8 0.0625 0.01 0.25 0.125 0.025 </span></span>
<span><span class="co"># [51] 0.0625 4 0.125 8 0.002 0.5 0.01 0.025 0.125 0.025 </span></span>
<span><span class="co"># [61] 0.001 16 1 0.25 0.5 2 8 0.01 8 0.0625</span></span>
<span><span class="co"># [71] 2 0.025 8 0.005 0.025 8 0.002 0.002 256 2 </span></span>
<span><span class="co"># [81] 0.01 0.002 16 0.0625 64 8 0.005 32 0.125 0.001 </span></span>
<span><span class="co"># [91] 0.002 2 0.125 8 1 128 0.01 1 0.001 0.025</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>
@ -1461,10 +1459,10 @@ plotting:</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 25 30 24 29 30 26 26 18 31 21 25 20 21 29 30 18 29 28 26 24 29 23 21 19 18</span></span>
<span><span class="co"># [26] 19 30 23 22 21 28 24 30 22 24 18 27 24 20 21 30 28 27 27 30 20 30 24 21 29</span></span>
<span><span class="co"># [51] 29 20 22 24 20 28 27 30 20 24 23 19 28 29 31 28 31 30 28 31 28 27 27 25 28</span></span>
<span><span class="co"># [76] 24 18 22 22 28 22 17 30 17 27 25 24 17 29 30 19 19 18 26 23 23 18 23 19 30</span></span></code></pre></div>
<span><span class="co"># [1] 25 20 25 25 26 18 20 24 23 28 30 18 27 27 25 20 28 21 19 23 27 28 28 24 28</span></span>
<span><span class="co"># [26] 17 25 19 23 30 22 17 31 23 31 24 28 25 28 28 27 31 20 24 18 18 24 29 17 31</span></span>
<span><span class="co"># [51] 17 28 23 26 19 25 18 22 24 18 17 27 26 26 25 18 23 21 21 28 17 25 30 29 29</span></span>
<span><span class="co"># [76] 18 31 20 22 28 23 26 24 27 28 20 25 19 19 17 24 24 17 18 17 30 24 21 29 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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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="">1.8.2.9102</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9103</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">

54
articles/MDR.html
View File

@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9102</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9103</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">
@ -380,19 +380,19 @@ 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"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 I S R I I I</span></span>
<span><span class="co"># 2 I S I I S I</span></span>
<span><span class="co"># 3 S I S S I R</span></span>
<span><span class="co"># 4 R R R R I S</span></span>
<span><span class="co"># 5 R S I I R I</span></span>
<span><span class="co"># 6 I I I R R R</span></span>
<span><span class="co"># 1 S S R I I R</span></span>
<span><span class="co"># 2 R R S S I I</span></span>
<span><span class="co"># 3 S R S S I S</span></span>
<span><span class="co"># 4 R I R S S R</span></span>
<span><span class="co"># 5 R I R I S S</span></span>
<span><span class="co"># 6 I I I R S I</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 I</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 R</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div>
<span><span class="co"># 6 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -433,40 +433,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3250</td>
<td align="right">65.00%</td>
<td align="right">3250</td>
<td align="right">65.00%</td>
<td align="right">3174</td>
<td align="right">63.48%</td>
<td align="right">3174</td>
<td align="right">63.48%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">977</td>
<td align="right">19.54%</td>
<td align="right">4227</td>
<td align="right">84.54%</td>
<td align="right">1008</td>
<td align="right">20.16%</td>
<td align="right">4182</td>
<td align="right">83.64%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">433</td>
<td align="right">8.66%</td>
<td align="right">4660</td>
<td align="right">93.20%</td>
<td align="right">451</td>
<td align="right">9.02%</td>
<td align="right">4633</td>
<td align="right">92.66%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">250</td>
<td align="right">5.00%</td>
<td align="right">4910</td>
<td align="right">98.20%</td>
<td align="right">255</td>
<td align="right">5.10%</td>
<td align="right">4888</td>
<td align="right">97.76%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">90</td>
<td align="right">1.80%</td>
<td align="right">112</td>
<td align="right">2.24%</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="">1.8.2.9102</small>
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2
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9102</small>
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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="">1.8.2.9102</small>
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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="">1.8.2.9102</small>
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2
articles/index.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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