Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!
<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 21 August 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 03 September 2020.</p>
<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></div>
<p>So only 28.3% 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 28.6% 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>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 C8, 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 M8, sorted on date:</p>
<tableclass="table">
<thead><trclass="header">
<thalign="center">isolate</th>
@ -548,21 +548,21 @@ Longest: 1</p>
<tbody>
<trclass="odd">
<tdalign="center">1</td>
<tdalign="center">2010-01-13</td>
<tdalign="center">C8</td>
<tdalign="center">2010-01-28</td>
<tdalign="center">M8</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">TRUE</td>
</tr>
<trclass="even">
<tdalign="center">2</td>
<tdalign="center">2010-02-19</td>
<tdalign="center">C8</td>
<tdalign="center">2010-05-23</td>
<tdalign="center">M8</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>
@ -570,10 +570,10 @@ Longest: 1</p>
</tr>
<trclass="odd">
<tdalign="center">3</td>
<tdalign="center">2010-03-12</td>
<tdalign="center">C8</td>
<tdalign="center">2010-07-11</td>
<tdalign="center">M8</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>
@ -581,30 +581,30 @@ Longest: 1</p>
</tr>
<trclass="even">
<tdalign="center">4</td>
<tdalign="center">2010-03-25</td>
<tdalign="center">C8</td>
<tdalign="center">2010-10-01</td>
<tdalign="center">M8</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
</tr>
<trclass="odd">
<tdalign="center">5</td>
<tdalign="center">2010-04-28</td>
<tdalign="center">C8</td>
<tdalign="center">2010-12-02</td>
<tdalign="center">M8</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">FALSE</td>
</tr>
<trclass="even">
<tdalign="center">6</td>
<tdalign="center">2010-07-22</td>
<tdalign="center">C8</td>
<tdalign="center">2010-12-23</td>
<tdalign="center">M8</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
@ -614,8 +614,8 @@ Longest: 1</p>
</tr>
<trclass="odd">
<tdalign="center">7</td>
<tdalign="center">2010-12-05</td>
<tdalign="center">C8</td>
<tdalign="center">2011-01-16</td>
<tdalign="center">M8</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
@ -625,33 +625,33 @@ Longest: 1</p>
</tr>
<trclass="even">
<tdalign="center">8</td>
<tdalign="center">2011-01-18</td>
<tdalign="center">C8</td>
<tdalign="center">2011-03-14</td>
<tdalign="center">M8</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">S</td>
<tdalign="center">S</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="odd">
<tdalign="center">9</td>
<tdalign="center">2011-05-24</td>
<tdalign="center">C8</td>
<tdalign="center">2011-04-02</td>
<tdalign="center">M8</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">R</td>
<tdalign="center">I</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>
</tr>
<trclass="even">
<tdalign="center">10</td>
<tdalign="center">2011-06-24</td>
<tdalign="center">C8</td>
<tdalign="center">2011-04-05</td>
<tdalign="center">M8</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
@ -686,34 +686,34 @@ Longest: 1</p>
<tbody>
<trclass="odd">
<tdalign="center">1</td>
<tdalign="center">2010-01-13</td>
<tdalign="center">C8</td>
<tdalign="center">2010-01-28</td>
<tdalign="center">M8</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">TRUE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="even">
<tdalign="center">2</td>
<tdalign="center">2010-02-19</td>
<tdalign="center">C8</td>
<tdalign="center">2010-05-23</td>
<tdalign="center">M8</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>
<tdalign="center">FALSE</td>
<tdalign="center">FALSE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="odd">
<tdalign="center">3</td>
<tdalign="center">2010-03-12</td>
<tdalign="center">C8</td>
<tdalign="center">2010-07-11</td>
<tdalign="center">M8</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>
@ -722,32 +722,32 @@ Longest: 1</p>
</tr>
<trclass="even">
<tdalign="center">4</td>
<tdalign="center">2010-03-25</td>
<tdalign="center">C8</td>
<tdalign="center">2010-10-01</td>
<tdalign="center">M8</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="odd">
<tdalign="center">5</td>
<tdalign="center">2010-04-28</td>
<tdalign="center">C8</td>
<tdalign="center">2010-12-02</td>
<tdalign="center">M8</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">FALSE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="even">
<tdalign="center">6</td>
<tdalign="center">2010-07-22</td>
<tdalign="center">C8</td>
<tdalign="center">2010-12-23</td>
<tdalign="center">M8</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
@ -758,8 +758,8 @@ Longest: 1</p>
</tr>
<trclass="odd">
<tdalign="center">7</td>
<tdalign="center">2010-12-05</td>
<tdalign="center">C8</td>
<tdalign="center">2011-01-16</td>
<tdalign="center">M8</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
@ -770,11 +770,11 @@ Longest: 1</p>
</tr>
<trclass="even">
<tdalign="center">8</td>
<tdalign="center">2011-01-18</td>
<tdalign="center">C8</td>
<tdalign="center">2011-03-14</td>
<tdalign="center">M8</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">S</td>
<tdalign="center">S</td>
<tdalign="center">TRUE</td>
@ -782,23 +782,23 @@ Longest: 1</p>
</tr>
<trclass="odd">
<tdalign="center">9</td>
<tdalign="center">2011-05-24</td>
<tdalign="center">C8</td>
<tdalign="center">2011-04-02</td>
<tdalign="center">M8</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">R</td>
<tdalign="center">I</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>
<tdalign="center">FALSE</td>
</tr>
<trclass="even">
<tdalign="center">10</td>
<tdalign="center">2011-06-24</td>
<tdalign="center">C8</td>
<tdalign="center">2011-04-05</td>
<tdalign="center">M8</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
@ -806,13 +806,13 @@ Longest: 1</p>
</tr>
</tbody>
</table>
<p>Instead of 2, now 8 isolates are flagged. In total, 78.4% of all isolates are marked ‘first weighted’ - 50.1% 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 8 isolates are flagged. In total, 79.1% of all isolates are marked ‘first weighted’ - 50.5% 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>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>