<p>So, we can draw at least two conclusions immediately. From a data scientist perspective, the data looks clean: only values <code>M</code> and <code>F</code>. From a researcher perspective: there are slightly more men. Nothing we didn’t 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>
<p>Finally, we will apply <ahref="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST rules</a> on our antimicrobial results. In Europe, most medical microbiological laboratories already apply these rules. Our package features their latest insights on intrinsic resistance and exceptional phenotypes. Moreover, the <code><ahref="../reference/eucast_rules.html">eucast_rules()</a></code> function can also apply additional rules, like forcing <helptitle="ATC: J01CA01">ampicillin</help> = R when <helptitle="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p>
<p>Because the amoxicillin (column <code>amox</code>) and amoxicillin/clavulanic acid (column <code>amcl</code>) in our data were generated randomly, some rows will undoubtedly contain amox = S and amcl = R, which is technically impossible. The <code><ahref="../reference/eucast_rules.html">eucast_rules()</a></code> fixes this:</p>
<aclass="sourceLine"id="cb14-3"title="3"><spanclass="co">#>Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)</span></a>
<aclass="sourceLine"id="cb14-22"title="22"><spanclass="co">#> Table 1: Intrinsic resistance in Enterobacteriaceae (1334 changes)</span></a>
<aclass="sourceLine"id="cb14-23"title="23"><spanclass="co">#> Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></a>
<aclass="sourceLine"id="cb14-24"title="24"><spanclass="co">#> Table 3: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></a>
<aclass="sourceLine"id="cb14-25"title="25"><spanclass="co">#> Table 4: Intrinsic resistance in Gram-positive bacteria (2731 changes)</span></a>
<aclass="sourceLine"id="cb14-26"title="26"><spanclass="co">#> Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></a>
<aclass="sourceLine"id="cb14-27"title="27"><spanclass="co">#> Table 9: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></a>
<aclass="sourceLine"id="cb14-28"title="28"><spanclass="co">#> Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria (no changes)</span></a>
<aclass="sourceLine"id="cb14-29"title="29"><spanclass="co">#> Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)</span></a>
<aclass="sourceLine"id="cb14-30"title="30"><spanclass="co">#> Table 12: Interpretive rules for aminoglycosides (no changes)</span></a>
<aclass="sourceLine"id="cb14-31"title="31"><spanclass="co">#> Table 13: Interpretive rules for quinolones (no changes)</span></a>
<aclass="sourceLine"id="cb14-33"title="33"><spanclass="co">#> Other rules</span></a>
<aclass="sourceLine"id="cb14-34"title="34"><spanclass="co">#> Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (no changes)</span></a>
<aclass="sourceLine"id="cb14-35"title="35"><spanclass="co">#> Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no changes)</span></a>
<aclass="sourceLine"id="cb14-36"title="36"><spanclass="co">#> Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no changes)</span></a>
<aclass="sourceLine"id="cb14-37"title="37"><spanclass="co">#> Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (no changes)</span></a>
<aclass="sourceLine"id="cb14-38"title="38"><spanclass="co">#> Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)</span></a>
<aclass="sourceLine"id="cb14-39"title="39"><spanclass="co">#> Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)</span></a>
<aclass="sourceLine"id="cb14-41"title="41"><spanclass="co">#> => EUCAST rules affected 7,419 out of 20,000 rows</span></a>
<aclass="sourceLine"id="cb14-42"title="42"><spanclass="co">#> -> added 0 test results</span></a>
<aclass="sourceLine"id="cb14-43"title="43"><spanclass="co">#> -> changed 4,065 test results (0 to S; 0 to I; 4,065 to R)</span></a></code></pre></div>
<aclass="sourceLine"id="cb14-5"title="5"><spanclass="co">#> Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)</span></a>
<aclass="sourceLine"id="cb14-24"title="24"><spanclass="co">#> Table 1: Intrinsic resistance in Enterobacteriaceae (1230 changes)</span></a>
<aclass="sourceLine"id="cb14-25"title="25"><spanclass="co">#> Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></a>
<aclass="sourceLine"id="cb14-26"title="26"><spanclass="co">#> Table 3: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></a>
<aclass="sourceLine"id="cb14-27"title="27"><spanclass="co">#> Table 4: Intrinsic resistance in Gram-positive bacteria (2700 changes)</span></a>
<aclass="sourceLine"id="cb14-28"title="28"><spanclass="co">#> Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></a>
<aclass="sourceLine"id="cb14-29"title="29"><spanclass="co">#> Table 9: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></a>
<aclass="sourceLine"id="cb14-30"title="30"><spanclass="co">#> Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria (no changes)</span></a>
<aclass="sourceLine"id="cb14-31"title="31"><spanclass="co">#> Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)</span></a>
<aclass="sourceLine"id="cb14-32"title="32"><spanclass="co">#> Table 12: Interpretive rules for aminoglycosides (no changes)</span></a>
<aclass="sourceLine"id="cb14-33"title="33"><spanclass="co">#> Table 13: Interpretive rules for quinolones (no changes)</span></a>
<aclass="sourceLine"id="cb14-35"title="35"><spanclass="co">#> Other rules</span></a>
<aclass="sourceLine"id="cb14-36"title="36"><spanclass="co">#> Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (no changes)</span></a>
<aclass="sourceLine"id="cb14-37"title="37"><spanclass="co">#> Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no changes)</span></a>
<aclass="sourceLine"id="cb14-38"title="38"><spanclass="co">#> Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no changes)</span></a>
<aclass="sourceLine"id="cb14-39"title="39"><spanclass="co">#> Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (no changes)</span></a>
<aclass="sourceLine"id="cb14-40"title="40"><spanclass="co">#> Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)</span></a>
<aclass="sourceLine"id="cb14-41"title="41"><spanclass="co">#> Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)</span></a>
<aclass="sourceLine"id="cb14-43"title="43"><spanclass="co">#> => EUCAST rules affected 7,267 out of 20,000 rows</span></a>
<aclass="sourceLine"id="cb14-44"title="44"><spanclass="co">#> -> added 0 test results</span></a>
<aclass="sourceLine"id="cb14-45"title="45"><spanclass="co">#> -> changed 3,930 test results (0 to S; 0 to I; 3,930 to R)</span></a></code></pre></div>
<aclass="sourceLine"id="cb16-3"title="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"title="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"title="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"title="6"><spanclass="co">#> => Found 5,667 first isolates (28.3% of total)</span></a></code></pre></div>
<aclass="sourceLine"id="cb16-6"title="6"><spanclass="co">#> => Found 5,663 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>
<aclass="sourceLine"id="cb19-4"title="4"><spanclass="co">#></span><spanclass="al">NOTE</span><spanclass="co">: Using column `bacteria` as input for `col_mo`.</span></a>
<aclass="sourceLine"id="cb19-5"title="5"><spanclass="co">#></span><spanclass="al">NOTE</span><spanclass="co">: Using column `bacteria` as input for `col_mo`.</span></a>
<aclass="sourceLine"id="cb19-6"title="6"><spanclass="co">#></span><spanclass="al">NOTE</span><spanclass="co">: Using column `date` as input for `col_date`.</span></a>
<aclass="sourceLine"id="cb19-7"title="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"title="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"title="9"><spanclass="co">#> [Criterion] Inclusion based on key antibiotics, ignoring I.</span></a>
<aclass="sourceLine"id="cb19-10"title="10"><spanclass="co">#> => Found 15,851 first weighted isolates (79.3% of total)</span></a></code></pre></div>
<aclass="sourceLine"id="cb19-7"title="7"><spanclass="co">#></span><spanclass="al">NOTE</span><spanclass="co">: Using column `bacteria` as input for `col_mo`.</span></a>
<aclass="sourceLine"id="cb19-8"title="8"><spanclass="co">#></span><spanclass="al">NOTE</span><spanclass="co">: Using column `date` as input for `col_date`.</span></a>
<aclass="sourceLine"id="cb19-9"title="9"><spanclass="co">#></span><spanclass="al">NOTE</span><spanclass="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<aclass="sourceLine"id="cb19-10"title="10"><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="cb19-11"title="11"><spanclass="co">#> [Criterion] Inclusion based on key antibiotics, ignoring I.</span></a>
<aclass="sourceLine"id="cb19-12"title="12"><spanclass="co">#> => Found 15,865 first weighted isolates (79.3% of total)</span></a></code></pre></div>
<tableclass="table">
<thead><trclass="header">
<thalign="center">isolate</th>
@ -654,8 +662,8 @@
@@ -654,8 +662,8 @@
<tbody>
<trclass="odd">
<tdalign="center">1</td>
<tdalign="center">2010-02-08</td>
<tdalign="center">H1</td>
<tdalign="center">2010-04-19</td>
<tdalign="center">S8</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
@ -666,44 +674,44 @@
@@ -666,44 +674,44 @@
</tr>
<trclass="even">
<tdalign="center">2</td>
<tdalign="center">2010-04-06</td>
<tdalign="center">H1</td>
<tdalign="center">2010-08-08</td>
<tdalign="center">S8</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">I</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">2010-04-25</td>
<tdalign="center">H1</td>
<tdalign="center">2010-10-31</td>
<tdalign="center">S8</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">I</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="even">
<tdalign="center">4</td>
<tdalign="center">2010-10-05</td>
<tdalign="center">H1</td>
<tdalign="center">2010-11-11</td>
<tdalign="center">S8</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">I</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">I</td>
<tdalign="center">R</td>
<tdalign="center">R</td>
<tdalign="center">FALSE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="odd">
<tdalign="center">5</td>
<tdalign="center">2010-11-09</td>
<tdalign="center">H1</td>
<tdalign="center">2011-04-04</td>
<tdalign="center">S8</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
@ -714,23 +722,23 @@
@@ -714,23 +722,23 @@
</tr>
<trclass="even">
<tdalign="center">6</td>
<tdalign="center">2010-11-23</td>
<tdalign="center">H1</td>
<tdalign="center">2011-05-22</td>
<tdalign="center">S8</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">TRUE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="odd">
<tdalign="center">7</td>
<tdalign="center">2010-12-26</td>
<tdalign="center">H1</td>
<tdalign="center">2011-08-15</td>
<tdalign="center">S8</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">R</td>
<tdalign="center">I</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
@ -738,23 +746,23 @@
@@ -738,23 +746,23 @@
</tr>
<trclass="even">
<tdalign="center">8</td>
<tdalign="center">2011-01-01</td>
<tdalign="center">H1</td>
<tdalign="center">2011-08-20</td>
<tdalign="center">S8</td>
<tdalign="center">B_ESCHR_COL</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">9</td>
<tdalign="center">2011-01-21</td>
<tdalign="center">H1</td>
<tdalign="center">2011-08-25</td>
<tdalign="center">S8</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">R</td>
<tdalign="center">I</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
@ -762,23 +770,23 @@
@@ -762,23 +770,23 @@
</tr>
<trclass="even">
<tdalign="center">10</td>
<tdalign="center">2011-02-28</td>
<tdalign="center">H1</td>
<tdalign="center">2011-12-16</td>
<tdalign="center">S8</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</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 10 isolates are flagged. In total, 79.3% of all isolates are marked ‘first weighted’ - 50.9% 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 2, now 9 isolates are flagged. In total, 79.3% of all isolates are marked ‘first weighted’ - 51% 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>portion_R</code>, <code>portion_RI</code>, <code>portion_I</code>, <code>portion_IS</code> and <code>portion_S</code> can be used to determine the portion of a specific antimicrobial outcome. They 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>
