<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 November 2019.</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 11 December 2019.</p>
<p>So, we can draw at least two conclusions immediately. From a data scientists perspective, the data looks clean: only values <code>M</code> and <code>F</code>. From a researchers perspective: there are slightly more men. Nothing we didnโt already know.</p>
<p>The data is already quite clean, but we still need to transform some variables. The <code>bacteria</code> column now consists of text, and we want to add more variables based on microbial IDs later on. So, we will transform this column to valid IDs. The <code><ahref="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> function of the <code>dplyr</code> package makes this really easy:</p>
<aclass="sourceLine"id="cb14-3"data-line-number="3"><spanclass="co"># Other rules by this AMR package</span></a>
<aclass="sourceLine"id="cb14-4"data-line-number="4"><spanclass="co"># Non-EUCAST: inherit amoxicillin results for unavailable ampicillin (no changes)</span></a>
<aclass="sourceLine"id="cb14-5"data-line-number="5"><spanclass="co"># Non-EUCAST: inherit ampicillin results for unavailable amoxicillin (no changes)</span></a>
<aclass="sourceLine"id="cb14-6"data-line-number="6"><spanclass="co"># Non-EUCAST: set amoxicillin/clav acid = S where ampicillin = S (2,960 values changed)</span></a>
<aclass="sourceLine"id="cb14-7"data-line-number="7"><spanclass="co"># Non-EUCAST: set ampicillin = R where amoxicillin/clav acid = R (144 values changed)</span></a>
<aclass="sourceLine"id="cb14-6"data-line-number="6"><spanclass="co"># Non-EUCAST: set amoxicillin/clav acid = S where ampicillin = S (2,997 values changed)</span></a>
<aclass="sourceLine"id="cb14-7"data-line-number="7"><spanclass="co"># Non-EUCAST: set ampicillin = R where amoxicillin/clav acid = R (165 values changed)</span></a>
<aclass="sourceLine"id="cb14-8"data-line-number="8"><spanclass="co"># Non-EUCAST: set piperacillin = R where piperacillin/tazobactam = R (no changes)</span></a>
<aclass="sourceLine"id="cb14-9"data-line-number="9"><spanclass="co"># Non-EUCAST: set piperacillin/tazobactam = S where piperacillin = S (no changes)</span></a>
<aclass="sourceLine"id="cb14-10"data-line-number="10"><spanclass="co"># Non-EUCAST: set trimethoprim = R where trimethoprim/sulfa = R (no changes)</span></a>
@ -448,14 +448,14 @@
@@ -448,14 +448,14 @@
<aclass="sourceLine"id="cb14-29"data-line-number="29"><spanclass="co"># Pasteurella multocida (no changes)</span></a>
<aclass="sourceLine"id="cb14-30"data-line-number="30"><spanclass="co"># Staphylococcus (no changes)</span></a>
<aclass="sourceLine"id="cb14-31"data-line-number="31"><spanclass="co"># Streptococcus groups A, B, C, G (no changes)</span></a>
<aclass="sourceLine"id="cb14-36"data-line-number="36"><spanclass="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,331 values changed)</span></a>
<aclass="sourceLine"id="cb14-36"data-line-number="36"><spanclass="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,242 values changed)</span></a>
<aclass="sourceLine"id="cb14-37"data-line-number="37"><spanclass="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></a>
<aclass="sourceLine"id="cb14-38"data-line-number="38"><spanclass="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></a>
<aclass="sourceLine"id="cb14-40"data-line-number="40"><spanclass="co"># Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></a>
<aclass="sourceLine"id="cb14-41"data-line-number="41"><spanclass="co"># Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></a>
<aclass="sourceLine"id="cb14-42"data-line-number="42"><spanclass="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)</span></a>
@ -463,15 +463,15 @@
@@ -463,15 +463,15 @@
<aclass="sourceLine"id="cb14-44"data-line-number="44"><spanclass="co"># Table 13: Interpretive rules for quinolones (no changes)</span></a>
<aclass="sourceLine"id="cb14-47"data-line-number="47"><spanclass="co"># EUCAST rules affected 6,481 out of 20,000 rows, making a total of 8,137 edits</span></a>
<aclass="sourceLine"id="cb14-47"data-line-number="47"><spanclass="co"># EUCAST rules affected 6,564 out of 20,000 rows, making a total of 8,249 edits</span></a>
<aclass="sourceLine"id="cb14-48"data-line-number="48"><spanclass="co"># => added 0 test results</span></a>
<aclass="sourceLine"id="cb14-58"data-line-number="58"><spanclass="co"># Use eucast_rules(..., verbose = TRUE) (on your original data) to get a data.frame with all specified edits instead.</span></a></code></pre></div>
@ -499,7 +499,7 @@
@@ -499,7 +499,7 @@
<aclass="sourceLine"id="cb16-3"data-line-number="3"><spanclass="co"># </span><spanclass="al">NOTE</span><spanclass="co">: Using column `bacteria` as input for `col_mo`.</span></a>
<aclass="sourceLine"id="cb16-4"data-line-number="4"><spanclass="co"># </span><spanclass="al">NOTE</span><spanclass="co">: Using column `date` as input for `col_date`.</span></a>
<aclass="sourceLine"id="cb16-5"data-line-number="5"><spanclass="co"># </span><spanclass="al">NOTE</span><spanclass="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<aclass="sourceLine"id="cb16-6"data-line-number="6"><spanclass="co"># => Found 5,667 first isolates (28.3% of total)</span></a></code></pre></div>
<aclass="sourceLine"id="cb16-6"data-line-number="6"><spanclass="co"># => Found 5,656 first isolates (28.3% of total)</span></a></code></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>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 E9, 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 D2, sorted on date:</p>
<tableclass="table">
<thead><trclass="header">
<thalign="center">isolate</th>
@ -526,52 +526,52 @@
@@ -526,52 +526,52 @@
<tbody>
<trclass="odd">
<tdalign="center">1</td>
<tdalign="center">2010-07-16</td>
<tdalign="center">E9</td>
<tdalign="center">2010-02-23</td>
<tdalign="center">D2</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">2010-07-22</td>
<tdalign="center">E9</td>
<tdalign="center">2010-03-20</td>
<tdalign="center">D2</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>
</tr>
<trclass="odd">
<tdalign="center">3</td>
<tdalign="center">2010-08-26</td>
<tdalign="center">E9</td>
<tdalign="center">2010-04-13</td>
<tdalign="center">D2</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">4</td>
<tdalign="center">2010-10-17</td>
<tdalign="center">E9</td>
<tdalign="center">2010-07-22</td>
<tdalign="center">D2</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="odd">
<tdalign="center">5</td>
<tdalign="center">2010-10-25</td>
<tdalign="center">E9</td>
<tdalign="center">2010-07-22</td>
<tdalign="center">D2</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
@ -581,10 +581,10 @@
@@ -581,10 +581,10 @@
</tr>
<trclass="even">
<tdalign="center">6</td>
<tdalign="center">2011-02-27</td>
<tdalign="center">E9</td>
<tdalign="center">2010-08-04</td>
<tdalign="center">D2</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>
@ -592,8 +592,8 @@
@@ -592,8 +592,8 @@
</tr>
<trclass="odd">
<tdalign="center">7</td>
<tdalign="center">2011-03-15</td>
<tdalign="center">E9</td>
<tdalign="center">2010-08-19</td>
<tdalign="center">D2</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
@ -603,40 +603,40 @@
@@ -603,40 +603,40 @@
</tr>
<trclass="even">
<tdalign="center">8</td>
<tdalign="center">2011-03-19</td>
<tdalign="center">E9</td>
<tdalign="center">2010-09-02</td>
<tdalign="center">D2</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">R</td>
<tdalign="center">R</td>
<tdalign="center">I</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
</tr>
<trclass="odd">
<tdalign="center">9</td>
<tdalign="center">2011-06-20</td>
<tdalign="center">E9</td>
<tdalign="center">2010-09-04</td>
<tdalign="center">D2</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">10</td>
<tdalign="center">2011-12-03</td>
<tdalign="center">E9</td>
<tdalign="center">2010-09-18</td>
<tdalign="center">D2</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">TRUE</td>
<tdalign="center">FALSE</td>
</tr>
</tbody>
</table>
<p>Only 2 isolates are marked as โfirstโ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><ahref="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>Only 1 isolates are marked as โfirstโ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><ahref="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>If a column exists with a name like โkey(โฆ)abโ the <code><ahref="../reference/first_isolate.html">first_isolate()</a></code> function will automatically use it and determine the first weighted isolates. Mind the NOTEs in below output:</p>
<aclass="sourceLine"id="cb19-7"data-line-number="7"><spanclass="co"># </span><spanclass="al">NOTE</span><spanclass="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<aclass="sourceLine"id="cb19-8"data-line-number="8"><spanclass="co"># </span><spanclass="al">NOTE</span><spanclass="co">: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.</span></a>
<aclass="sourceLine"id="cb19-9"data-line-number="9"><spanclass="co"># [Criterion] Inclusion based on key antibiotics, ignoring I</span></a>
<aclass="sourceLine"id="cb19-10"data-line-number="10"><spanclass="co"># => Found 15,044 first weighted isolates (75.2% of total)</span></a></code></pre></div>
<aclass="sourceLine"id="cb19-10"data-line-number="10"><spanclass="co"># => Found 15,026 first weighted isolates (75.1% of total)</span></a></code></pre></div>
<tableclass="table">
<thead><trclass="header">
<thalign="center">isolate</th>
@ -664,131 +664,131 @@
@@ -664,131 +664,131 @@
<tbody>
<trclass="odd">
<tdalign="center">1</td>
<tdalign="center">2010-07-16</td>
<tdalign="center">E9</td>
<tdalign="center">2010-02-23</td>
<tdalign="center">D2</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">2010-07-22</td>
<tdalign="center">E9</td>
<tdalign="center">2010-03-20</td>
<tdalign="center">D2</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>
<tdalign="center">TRUE</td>
</tr>
<trclass="odd">
<tdalign="center">3</td>
<tdalign="center">2010-08-26</td>
<tdalign="center">E9</td>
<tdalign="center">2010-04-13</td>
<tdalign="center">D2</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">4</td>
<tdalign="center">2010-10-17</td>
<tdalign="center">E9</td>
<tdalign="center">2010-07-22</td>
<tdalign="center">D2</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>
<tdalign="center">TRUE</td>
</tr>
<trclass="odd">
<tdalign="center">5</td>
<tdalign="center">2010-10-25</td>
<tdalign="center">E9</td>
<tdalign="center">2010-07-22</td>
<tdalign="center">D2</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">FALSE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="even">
<tdalign="center">6</td>
<tdalign="center">2011-02-27</td>
<tdalign="center">E9</td>
<tdalign="center">2010-08-04</td>
<tdalign="center">D2</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>
</tr>
<trclass="odd">
<tdalign="center">7</td>
<tdalign="center">2011-03-15</td>
<tdalign="center">E9</td>
<tdalign="center">2010-08-19</td>
<tdalign="center">D2</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">FALSE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="even">
<tdalign="center">8</td>
<tdalign="center">2011-03-19</td>
<tdalign="center">E9</td>
<tdalign="center">2010-09-02</td>
<tdalign="center">D2</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">R</td>
<tdalign="center">R</td>
<tdalign="center">I</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="odd">
<tdalign="center">9</td>
<tdalign="center">2011-06-20</td>
<tdalign="center">E9</td>
<tdalign="center">2010-09-04</td>
<tdalign="center">D2</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>
<tdalign="center">TRUE</td>
<tdalign="center">FALSE</td>
</tr>
<trclass="even">
<tdalign="center">10</td>
<tdalign="center">2011-12-03</td>
<tdalign="center">E9</td>
<tdalign="center">2010-09-18</td>
<tdalign="center">D2</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">TRUE</td>
<tdalign="center">FALSE</td>
<tdalign="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Instead of 2, now 7 isolates are flagged. In total, 75.2% of all isolates are marked โfirst weightedโ - 46.9% 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 1, now 9 isolates are flagged. In total, 75.1% of all isolates are marked โfirst weightedโ - 46.9% 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>, thereโs 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>