<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <ahref="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 24 July 2020.</p>
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <ahref="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 30 July 2020.</p>
<spanclass="co"># NOTE: Using column `bacteria` as input for `col_mo`.</span>
<spanclass="co"># NOTE: Using column `date` as input for `col_date`.</span>
<spanclass="co"># NOTE: Using column `patient_id` as input for `col_patient_id`.</span></pre></body></html></div>
<p>So only 28.4% is suitable for resistance analysis! We can now filter on it with the <code><ahref="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<p>So only 28.2% is suitable for resistance analysis! We can now filter on it with the <code><ahref="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<p>For future use, the above two syntaxes can be shortened with the <code><ahref="../reference/first_isolate.html">filter_first_isolate()</a></code> function:</p>
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient J1, sorted on date:</p>
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient Q3, sorted on date:</p>
<tableclass="table">
<thead><trclass="header">
<thalign="center">isolate</th>
@ -507,19 +507,19 @@ Longest: 1</p>
<tbody>
<trclass="odd">
<tdalign="center">1</td>
<tdalign="center">2010-04-08</td>
<tdalign="center">J1</td>
<tdalign="center">2010-02-06</td>
<tdalign="center">Q3</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">R</td>
<tdalign="center">I</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="even">
<tdalign="center">2</td>
<tdalign="center">2010-06-01</td>
<tdalign="center">J1</td>
<tdalign="center">2010-04-09</td>
<tdalign="center">Q3</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
@ -529,76 +529,76 @@ Longest: 1</p>
</tr>
<trclass="odd">
<tdalign="center">3</td>
<tdalign="center">2010-06-21</td>
<tdalign="center">J1</td>
<tdalign="center">2010-07-03</td>
<tdalign="center">Q3</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
</tr>
<trclass="even">
<tdalign="center">4</td>
<tdalign="center">2010-07-08</td>
<tdalign="center">J1</td>
<tdalign="center">2010-07-31</td>
<tdalign="center">Q3</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">FALSE</td>
</tr>
<trclass="odd">
<tdalign="center">5</td>
<tdalign="center">2011-01-29</td>
<tdalign="center">J1</td>
<tdalign="center">2010-10-26</td>
<tdalign="center">Q3</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
</tr>
<trclass="even">
<tdalign="center">6</td>
<tdalign="center">2011-02-23</td>
<tdalign="center">J1</td>
<tdalign="center">2010-12-11</td>
<tdalign="center">Q3</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">FALSE</td>
</tr>
<trclass="odd">
<tdalign="center">7</td>
<tdalign="center">2011-02-23</td>
<tdalign="center">J1</td>
<tdalign="center">2011-03-20</td>
<tdalign="center">Q3</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="even">
<tdalign="center">8</td>
<tdalign="center">2011-02-28</td>
<tdalign="center">J1</td>
<tdalign="center">2011-04-08</td>
<tdalign="center">Q3</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
</tr>
<trclass="odd">
<tdalign="center">9</td>
<tdalign="center">2011-03-13</td>
<tdalign="center">J1</td>
<tdalign="center">2011-04-24</td>
<tdalign="center">Q3</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
@ -606,14 +606,14 @@ Longest: 1</p>
</tr>
<trclass="even">
<tdalign="center">10</td>
<tdalign="center">2011-05-14</td>
<tdalign="center">J1</td>
<tdalign="center">2011-05-08</td>
<tdalign="center">Q3</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">R</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">TRUE</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
</tr>
</tbody>
</table>
@ -644,106 +644,106 @@ Longest: 1</p>
<tbody>
<trclass="odd">
<tdalign="center">1</td>
<tdalign="center">2010-04-08</td>
<tdalign="center">J1</td>
<tdalign="center">2010-02-06</td>
<tdalign="center">Q3</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">R</td>
<tdalign="center">I</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">TRUE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="even">
<tdalign="center">2</td>
<tdalign="center">2010-06-01</td>
<tdalign="center">J1</td>
<tdalign="center">2010-04-09</td>
<tdalign="center">Q3</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
<tdalign="center">TRUE</td>
<tdalign="center">FALSE</td>
</tr>
<trclass="odd">
<tdalign="center">3</td>
<tdalign="center">2010-06-21</td>
<tdalign="center">J1</td>
<tdalign="center">2010-07-03</td>
<tdalign="center">Q3</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
<tdalign="center">FALSE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="even">
<tdalign="center">4</td>
<tdalign="center">2010-07-08</td>
<tdalign="center">J1</td>
<tdalign="center">2010-07-31</td>
<tdalign="center">Q3</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
<tdalign="center">R</td>
<tdalign="center">FALSE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="odd">
<tdalign="center">5</td>
<tdalign="center">2011-01-29</td>
<tdalign="center">J1</td>
<tdalign="center">2010-10-26</td>
<tdalign="center">Q3</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="even">
<tdalign="center">6</td>
<tdalign="center">2011-02-23</td>
<tdalign="center">J1</td>
<tdalign="center">2010-12-11</td>
<tdalign="center">Q3</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">FALSE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="odd">
<tdalign="center">7</td>
<tdalign="center">2011-02-23</td>
<tdalign="center">J1</td>
<tdalign="center">2011-03-20</td>
<tdalign="center">Q3</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
<tdalign="center">FALSE</td>
<tdalign="center">TRUE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="even">
<tdalign="center">8</td>
<tdalign="center">2011-02-28</td>
<tdalign="center">J1</td>
<tdalign="center">2011-04-08</td>
<tdalign="center">Q3</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="odd">
<tdalign="center">9</td>
<tdalign="center">2011-03-13</td>
<tdalign="center">J1</td>
<tdalign="center">2011-04-24</td>
<tdalign="center">Q3</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
@ -752,23 +752,23 @@ Longest: 1</p>
</tr>
<trclass="even">
<tdalign="center">10</td>
<tdalign="center">2011-05-14</td>
<tdalign="center">J1</td>
<tdalign="center">2011-05-08</td>
<tdalign="center">Q3</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">R</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">TRUE</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
<tdalign="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Instead of 2, now 7 isolates are flagged. In total, 78.6% of all isolates are marked ‘first weighted’ - 50.2% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>Instead of 2, now 9 isolates are flagged. In total, 78.8% of all isolates are marked ‘first weighted’ - 50.6% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>As with <code><ahref="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
<p>The functions <code><ahref="../reference/proportion.html">resistance()</a></code> and <code><ahref="../reference/proportion.html">susceptibility()</a></code> can be used to calculate antimicrobial resistance or susceptibility. For more specific analyses, the functions <code><ahref="../reference/proportion.html">proportion_S()</a></code>, <code><ahref="../reference/proportion.html">proportion_SI()</a></code>, <code><ahref="../reference/proportion.html">proportion_I()</a></code>, <code><ahref="../reference/proportion.html">proportion_IR()</a></code> and <code><ahref="../reference/proportion.html">proportion_R()</a></code> can be used to determine the proportion of a specific antimicrobial outcome.</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><ahref="../reference/proportion.html">proportion_R()</a></code>, equal to <code><ahref="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><ahref="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><ahref="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<p>Or can be used in conjuction with <code><ahref="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><ahref="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>