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@ -325,70 +325,70 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-10-03</td>
<td align="center">E4</td>
<td align="center">Hospital B</td>
<td align="center">2010-07-04</td>
<td align="center">N1</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-05-08</td>
<td align="center">U7</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">2014-02-09</td>
<td align="center">T10</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2017-03-19</td>
<td align="center">T10</td>
<td align="center">Hospital C</td>
<td align="center">2017-03-28</td>
<td align="center">P6</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-07-20</td>
<td align="center">Y4</td>
<td align="center">2016-05-18</td>
<td align="center">E5</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-10-10</td>
<td align="center">A2</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">2016-10-13</td>
<td align="center">F4</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">2016-06-07</td>
<td align="center">H6</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">2013-09-14</td>
<td align="center">Y9</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
@ -422,16 +422,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,433</td>
<td align="right">52.16%</td>
<td align="right">10,433</td>
<td align="right">52.16%</td>
<td align="right">10,377</td>
<td align="right">51.89%</td>
<td align="right">10,377</td>
<td align="right">51.89%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,567</td>
<td align="right">47.84%</td>
<td align="right">9,623</td>
<td align="right">48.12%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -488,7 +488,7 @@ Longest: 1</p>
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,659 'phenotype-based' first isolates (53.3% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,663 'phenotype-based' first isolates (53.3% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.3% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
@ -499,7 +499,7 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,659 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,663 isolates for analysis. Now our data looks like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
<table style="width:100%;" class="table">
@ -537,92 +537,76 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2017-10-03</td>
<td align="center">E4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2015-05-08</td>
<td align="center">U7</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">2017-03-19</td>
<td align="center">2014-02-09</td>
<td align="center">T10</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-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">2016-10-10</td>
<td align="center">A2</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">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="odd">
<td align="left">9</td>
<td align="center">2011-08-27</td>
<td align="center">E1</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">TRUE</td>
</tr>
<tr class="even">
<td align="left">14</td>
<td align="center">2016-07-02</td>
<td align="center">D8</td>
<td align="left">3</td>
<td align="center">2017-03-28</td>
<td align="center">P6</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">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">5</td>
<td align="center">2016-10-13</td>
<td align="center">F4</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>
<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">2013-09-14</td>
<td align="center">Y9</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2016-09-03</td>
<td align="center">A7</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -632,6 +616,22 @@ Longest: 1</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">11</td>
<td align="center">2012-12-21</td>
<td align="center">O1</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -653,8 +653,8 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,659<br>
Available: 10,659 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,663<br>
Available: 10,663 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -671,33 +671,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,656</td>
<td align="right">43.68%</td>
<td align="right">4,656</td>
<td align="right">43.68%</td>
<td align="right">4,612</td>
<td align="right">43.25%</td>
<td align="right">4,612</td>
<td align="right">43.25%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,663</td>
<td align="right">24.98%</td>
<td align="right">7,319</td>
<td align="right">68.66%</td>
<td align="right">2,732</td>
<td align="right">25.62%</td>
<td align="right">7,344</td>
<td align="right">68.87%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,150</td>
<td align="right">2,151</td>
<td align="right">20.17%</td>
<td align="right">9,469</td>
<td align="right">88.84%</td>
<td align="right">9,495</td>
<td align="right">89.05%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,190</td>
<td align="right">11.16%</td>
<td align="right">10,659</td>
<td align="right">1,168</td>
<td align="right">10.95%</td>
<td align="right">10,663</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -716,14 +716,14 @@ Longest: 24</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="10%">
<col width="11%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@ -744,9 +744,69 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-03-19</td>
<td align="center">2014-02-09</td>
<td align="center">T10</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-09-14</td>
<td align="center">Y9</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-12-21</td>
<td align="center">O1</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-07-03</td>
<td align="center">S2</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">S</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="center">2010-04-27</td>
<td align="center">Y1</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -759,78 +819,18 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-08-27</td>
<td align="center">E1</td>
<td align="center">2017-06-16</td>
<td align="center">V4</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</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-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-07-28</td>
<td align="center">L7</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-02-23</td>
<td align="center">O8</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">2015-07-29</td>
<td align="center">V3</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">2011-04-12</td>
<td align="center">B4</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -854,50 +854,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2234</td>
<td align="center">119</td>
<td align="center">2303</td>
<td align="center">4656</td>
<td align="center">2181</td>
<td align="center">134</td>
<td align="center">2297</td>
<td align="center">4612</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3425</td>
<td align="center">159</td>
<td align="center">1072</td>
<td align="center">4656</td>
<td align="center">3388</td>
<td align="center">167</td>
<td align="center">1057</td>
<td align="center">4612</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3372</td>
<td align="center">3355</td>
<td align="center">0</td>
<td align="center">1284</td>
<td align="center">4656</td>
<td align="center">1257</td>
<td align="center">4612</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4049</td>
<td align="center">4036</td>
<td align="center">0</td>
<td align="center">607</td>
<td align="center">4656</td>
<td align="center">576</td>
<td align="center">4612</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">1190</td>
<td align="center">1190</td>
<td align="center">1168</td>
<td align="center">1168</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">914</td>
<td align="center">41</td>
<td align="center">235</td>
<td align="center">1190</td>
<td align="center">912</td>
<td align="center">43</td>
<td align="center">213</td>
<td align="center">1168</td>
</tr>
</tbody>
</table>
@ -920,34 +920,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4049</td>
<td align="center">4036</td>
<td align="center">0</td>
<td align="center">607</td>
<td align="center">4656</td>
<td align="center">576</td>
<td align="center">4612</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1059</td>
<td align="center">1042</td>
<td align="center">0</td>
<td align="center">131</td>
<td align="center">1190</td>
<td align="center">126</td>
<td align="center">1168</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2365</td>
<td align="center">2433</td>
<td align="center">0</td>
<td align="center">298</td>
<td align="center">2663</td>
<td align="center">299</td>
<td align="center">2732</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">2150</td>
<td align="center">2150</td>
<td align="center">2151</td>
<td align="center">2151</td>
</tr>
</tbody>
</table>
@ -961,7 +961,7 @@ Longest: 24</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5378553</span></span></code></pre></div>
<span><span class="co"># [1] 0.5430929</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@ -975,19 +975,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5398944</td>
<td align="center">0.5517885</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5323505</td>
<td align="center">0.5364807</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5494168</td>
<td align="center">0.5249089</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5354147</td>
<td align="center">0.5559306</td>
</tr>
</tbody>
</table>
@ -1008,23 +1008,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5398944</td>
<td align="center">3221</td>
<td align="center">0.5517885</td>
<td align="center">3215</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5323505</td>
<td align="center">3663</td>
<td align="center">0.5364807</td>
<td align="center">3728</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5494168</td>
<td align="center">1629</td>
<td align="center">0.5249089</td>
<td align="center">1646</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5354147</td>
<td align="center">2146</td>
<td align="center">0.5559306</td>
<td align="center">2074</td>
</tr>
</tbody>
</table>
@ -1047,27 +1047,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7697595</td>
<td align="center">0.8696306</td>
<td align="center">0.9765893</td>
<td align="center">0.7708153</td>
<td align="center">0.8751084</td>
<td align="center">0.9754987</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8025210</td>
<td align="center">0.8899160</td>
<td align="center">0.9781513</td>
<td align="center">0.8176370</td>
<td align="center">0.8921233</td>
<td align="center">0.9803082</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7972212</td>
<td align="center">0.8880961</td>
<td align="center">0.9831018</td>
<td align="center">0.7877013</td>
<td align="center">0.8905564</td>
<td align="center">0.9802343</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5530233</td>
<td align="center">0.5281265</td>
<td align="center">0.0000000</td>
<td align="center">0.5530233</td>
<td align="center">0.5281265</td>
</tr>
</tbody>
</table>
@ -1092,23 +1092,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.0%</td>
<td align="right">25.8%</td>
<td align="right">55.2%</td>
<td align="right">28.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">53.2%</td>
<td align="right">26.7%</td>
<td align="right">53.6%</td>
<td align="right">25.4%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">54.9%</td>
<td align="right">26.8%</td>
<td align="right">52.5%</td>
<td align="right">26.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">53.5%</td>
<td align="right">26.2%</td>
<td align="right">55.6%</td>
<td align="right">27.4%</td>
</tr>
</tbody>
</table>
@ -1206,18 +1206,18 @@ Longest: 24</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 0.01 0.025 128 0.25 0.01 0.025 8 0.005 0.01 </span></span>
<span><span class="co"># [10] 0.5 0.01 0.025 &lt;=0.001 128 0.0625 0.5 0.005 4 </span></span>
<span><span class="co"># [19] 0.5 0.25 16 0.005 16 16 0.5 &lt;=0.001 4 </span></span>
<span><span class="co"># [28] 8 0.0625 16 2 4 &lt;=0.001 0.125 0.002 32 </span></span>
<span><span class="co"># [37] 0.0625 0.5 0.5 0.5 0.125 4 0.01 4 8 </span></span>
<span><span class="co"># [46] 64 128 256 128 2 1 256 2 8 </span></span>
<span><span class="co"># [55] 0.01 &lt;=0.001 0.01 0.25 32 &lt;=0.001 2 1 0.005 </span></span>
<span><span class="co"># [64] 4 256 0.025 32 2 64 128 32 &lt;=0.001</span></span>
<span><span class="co"># [73] 16 0.005 0.5 0.25 4 2 0.5 32 64 </span></span>
<span><span class="co"># [82] 0.005 64 256 0.005 256 0.0625 256 0.005 64 </span></span>
<span><span class="co"># [91] 0.005 0.005 0.005 0.002 0.25 8 32 4 1 </span></span>
<span><span class="co"># [100] 0.0625</span></span></code></pre></div>
<span><span class="co"># [1] 32 0.025 4 0.01 32 &lt;=0.001 0.0625 0.002 0.125 </span></span>
<span><span class="co"># [10] 4 64 64 0.01 0.005 64 0.125 8 1 </span></span>
<span><span class="co"># [19] 0.25 0.002 0.01 16 0.01 256 32 2 0.005 </span></span>
<span><span class="co"># [28] 8 0.002 0.125 0.025 0.005 1 0.025 4 0.005 </span></span>
<span><span class="co"># [37] 4 &lt;=0.001 64 32 0.025 0.125 1 64 0.002 </span></span>
<span><span class="co"># [46] 0.005 0.5 0.005 0.0625 0.5 0.125 1 0.25 0.025 </span></span>
<span><span class="co"># [55] 1 0.005 0.002 0.0625 2 32 0.01 0.0625 16 </span></span>
<span><span class="co"># [64] 0.005 0.125 0.01 4 0.5 4 2 0.01 0.25 </span></span>
<span><span class="co"># [73] 16 &lt;=0.001 0.0625 0.0625 64 16 0.0625 0.25 0.01 </span></span>
<span><span class="co"># [82] 256 128 64 16 0.25 8 64 0.002 &lt;=0.001</span></span>
<span><span class="co"># [91] 256 &lt;=0.001 32 0.5 16 &lt;=0.001 0.5 16 0.5 </span></span>
<span><span class="co"># [100] 16</span></span></code></pre></div>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1244,10 +1244,10 @@ Longest: 24</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 20 22 22 23 28 28 28 22 21 18 27 22 21 21 29 19 24 24 26 22 28 21 17 30 22</span></span>
<span><span class="co"># [26] 27 28 23 31 18 25 17 23 25 26 28 24 18 29 29 17 18 20 21 23 26 27 28 18 17</span></span>
<span><span class="co"># [51] 18 24 23 23 17 31 24 19 23 19 27 28 30 30 28 21 19 24 29 26 19 19 18 20 25</span></span>
<span><span class="co"># [76] 26 27 31 27 20 31 31 18 30 23 18 19 26 19 31 28 30 18 21 18 17 21 30 20 28</span></span></code></pre></div>
<span><span class="co"># [1] 28 27 22 29 26 26 28 22 31 20 23 18 26 31 28 18 17 19 17 23 19 21 27 28 24</span></span>
<span><span class="co"># [26] 30 27 22 21 24 28 28 24 18 31 31 17 17 30 30 17 30 26 27 21 17 28 20 21 27</span></span>
<span><span class="co"># [51] 31 28 23 24 30 19 27 30 24 29 23 26 22 24 17 17 31 20 27 20 22 29 27 28 30</span></span>
<span><span class="co"># [76] 20 31 25 29 20 29 27 28 29 20 30 27 21 23 24 24 26 18 26 27 19 25 26 28 24</span></span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>

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52
articles/MDR.html
View File

@ -314,19 +314,19 @@ Unique: 2</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 S R I I I R</span></span>
<span><span class="co"># 2 I S R R R R</span></span>
<span><span class="co"># 3 R I I S I S</span></span>
<span><span class="co"># 4 R R R R I S</span></span>
<span><span class="co"># 5 I S I R I R</span></span>
<span><span class="co"># 6 R S R S S I</span></span>
<span><span class="co"># 1 S I I S I S</span></span>
<span><span class="co"># 2 R I I R R R</span></span>
<span><span class="co"># 3 S I S S S R</span></span>
<span><span class="co"># 4 R S R I R S</span></span>
<span><span class="co"># 5 I R I I R I</span></span>
<span><span class="co"># 6 S I I S I S</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 2 I</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 I</span></span></code></pre></div>
<span><span class="co"># 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>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></span></code></pre></div>
@ -357,40 +357,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3227</td>
<td align="right">64.54%</td>
<td align="right">3227</td>
<td align="right">64.54%</td>
<td align="right">3202</td>
<td align="right">64.04%</td>
<td align="right">3202</td>
<td align="right">64.04%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">945</td>
<td align="right">18.90%</td>
<td align="right">4172</td>
<td align="right">83.44%</td>
<td align="right">995</td>
<td align="right">19.90%</td>
<td align="right">4197</td>
<td align="right">83.94%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">459</td>
<td align="right">9.18%</td>
<td align="right">4631</td>
<td align="right">92.62%</td>
<td align="right">443</td>
<td align="right">8.86%</td>
<td align="right">4640</td>
<td align="right">92.80%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">260</td>
<td align="right">5.20%</td>
<td align="right">4891</td>
<td align="right">97.82%</td>
<td align="right">4900</td>
<td align="right">98.00%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">109</td>
<td align="right">2.18%</td>
<td align="right">100</td>
<td align="right">2.00%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

16
articles/datasets.html
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@ -177,7 +177,7 @@
</h2>
<p>A data set with 48,787 rows and 22 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>source</em>, <em>lpsn</em>, <em>lpsn_parent</em>, <em>lpsn_renamed_to</em>, <em>gbif</em>, <em>gbif_parent</em>, <em>gbif_renamed_to</em>, <em>prevalence</em> and <em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 20 October 2022 14:08:59 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p>It was last updated on 20 October 2022 17:39:59 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">original R Data Structure (RDS) file</a> (1.1 MB)<br>
@ -449,7 +449,7 @@
</h2>
<p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 20 October 2022 14:08:59 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 20 October 2022 17:39:59 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">original R Data Structure (RDS) file</a> (36 kB)<br>
@ -622,7 +622,7 @@
</h2>
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 20 October 2022 14:08:59 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 20 October 2022 17:39:59 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">original R Data Structure (RDS) file</a> (4 kB)<br>
@ -754,7 +754,7 @@
</h2>
<p>A data set with 20,369 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 20 October 2022 14:08:59 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p>It was last updated on 20 October 2022 17:39:59 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">original R Data Structure (RDS) file</a> (49 kB)<br>
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</h2>
<p>A data set with 134,659 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 20 October 2022 14:08:59 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p>It was last updated on 20 October 2022 17:39:59 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">original R Data Structure (RDS) file</a> (78 kB)<br>
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</h2>
<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 20 October 2022 14:08:59 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p>It was last updated on 20 October 2022 17:39:59 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">original R Data Structure (RDS) file</a> (3 kB)<br>
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</h2>
<p>A data set with 2,000 rows and 46 columns, containing the following column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>, <em>ward</em>, <em>mo</em>, <em>PEN</em>, <em>OXA</em>, <em>FLC</em>, <em>AMX</em>, <em>AMC</em>, <em>AMP</em>, <em>TZP</em>, <em>CZO</em>, <em>FEP</em>, <em>CXM</em>, <em>FOX</em>, <em>CTX</em>, <em>CAZ</em>, <em>CRO</em>, <em>GEN</em>, <em>TOB</em>, <em>AMK</em>, <em>KAN</em>, <em>TMP</em>, <em>SXT</em>, <em>NIT</em>, <em>FOS</em>, <em>LNZ</em>, <em>CIP</em>, <em>MFX</em>, <em>VAN</em>, <em>TEC</em>, <em>TCY</em>, <em>TGC</em>, <em>DOX</em>, <em>ERY</em>, <em>CLI</em>, <em>AZM</em>, <em>IPM</em>, <em>MEM</em>, <em>MTR</em>, <em>CHL</em>, <em>COL</em>, <em>MUP</em> and <em>RIF</em>.</p>
<p>This data set is in R available as <code>example_isolates</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 20 October 2022 14:08:59 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
<p>It was last updated on 20 October 2022 17:39:59 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
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<p>A data set with 3,000 rows and 8 columns, containing the following column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>, <em>bacteria</em>, <em>AMX</em>, <em>AMC</em>, <em>CIP</em> and <em>GEN</em>.</p>
<p>This data set is in R available as <code>example_isolates_unclean</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 20 October 2022 14:08:59 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
<p>It was last updated on 20 October 2022 17:39:59 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
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<h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>
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