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(v0.7.1.9030) eucast_rules() fix

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@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9029</span>
</span>
</div>
@ -185,7 +185,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">07 August 2019</h4>
<h4 class="date">08 August 2019</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -194,7 +194,7 @@
<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 <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 07 August 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 <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 08 August 2019.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -210,21 +210,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2019-08-07</td>
<td align="center">2019-08-08</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2019-08-07</td>
<td align="center">2019-08-08</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2019-08-07</td>
<td align="center">2019-08-08</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -320,69 +320,69 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-01-02</td>
<td align="center">V8</td>
<td align="center">Hospital A</td>
<td align="center">2017-01-03</td>
<td align="center">T3</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</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="even">
<td align="center">2012-11-05</td>
<td align="center">F9</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>
</tr>
<tr class="odd">
<td align="center">2011-12-06</td>
<td align="center">I5</td>
<td align="center">Hospital C</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-05-08</td>
<td align="center">W2</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-08-15</td>
<td align="center">R1</td>
<td align="center">Hospital B</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">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-01-09</td>
<td align="center">X9</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-06-18</td>
<td align="center">Z7</td>
<td align="center">2011-03-10</td>
<td align="center">B9</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">R</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">F</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-02-18</td>
<td align="center">F4</td>
<td align="center">Hospital A</td>
<tr class="odd">
<td align="center">2010-06-27</td>
<td align="center">A2</td>
<td align="center">Hospital D</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">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-12-11</td>
<td align="center">F8</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
</tbody>
@ -406,8 +406,8 @@
#
# Item Count Percent Cum. Count Cum. Percent
# --- ----- ------- -------- ----------- -------------
# 1 M 10,401 52.0% 10,401 52.0%
# 2 F 9,599 48.0% 20,000 100.0%</code></pre>
# 1 M 10,468 52.3% 10,468 52.3%
# 2 F 9,532 47.7% 20,000 100.0%</code></pre>
<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 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><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> function of the <code>dplyr</code> package makes this really easy:</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span></a>
@ -437,14 +437,14 @@
<a class="sourceLine" id="cb15-18" data-line-number="18"><span class="co"># Pasteurella multocida (no values changed)</span></a>
<a class="sourceLine" id="cb15-19" data-line-number="19"><span class="co"># Staphylococcus (no values changed)</span></a>
<a class="sourceLine" id="cb15-20" data-line-number="20"><span class="co"># Streptococcus groups A, B, C, G (no values changed)</span></a>
<a class="sourceLine" id="cb15-21" data-line-number="21"><span class="co"># Streptococcus pneumoniae (1,456 values changed)</span></a>
<a class="sourceLine" id="cb15-21" data-line-number="21"><span class="co"># Streptococcus pneumoniae (1,480 values changed)</span></a>
<a class="sourceLine" id="cb15-22" data-line-number="22"><span class="co"># Viridans group streptococci (no values changed)</span></a>
<a class="sourceLine" id="cb15-23" data-line-number="23"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-24" data-line-number="24"><span class="co"># EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
<a class="sourceLine" id="cb15-25" data-line-number="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,287 values changed)</span></a>
<a class="sourceLine" id="cb15-25" data-line-number="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,293 values changed)</span></a>
<a class="sourceLine" id="cb15-26" data-line-number="26"><span class="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no values changed)</span></a>
<a class="sourceLine" id="cb15-27" data-line-number="27"><span class="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no values changed)</span></a>
<a class="sourceLine" id="cb15-28" data-line-number="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,759 values changed)</span></a>
<a class="sourceLine" id="cb15-28" data-line-number="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,772 values changed)</span></a>
<a class="sourceLine" id="cb15-29" data-line-number="29"><span class="co"># Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no values changed)</span></a>
<a class="sourceLine" id="cb15-30" data-line-number="30"><span class="co"># Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no values changed)</span></a>
<a class="sourceLine" id="cb15-31" data-line-number="31"><span class="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no values changed)</span></a>
@ -452,24 +452,24 @@
<a class="sourceLine" id="cb15-33" data-line-number="33"><span class="co"># Table 13: Interpretive rules for quinolones (no values changed)</span></a>
<a class="sourceLine" id="cb15-34" data-line-number="34"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-35" data-line-number="35"><span class="co"># Other rules</span></a>
<a class="sourceLine" id="cb15-36" data-line-number="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2,330 values changed)</span></a>
<a class="sourceLine" id="cb15-37" data-line-number="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (108 values changed)</span></a>
<a class="sourceLine" id="cb15-36" data-line-number="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2,251 values changed)</span></a>
<a class="sourceLine" id="cb15-37" data-line-number="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (117 values changed)</span></a>
<a class="sourceLine" id="cb15-38" data-line-number="38"><span class="co"># Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no values changed)</span></a>
<a class="sourceLine" id="cb15-39" data-line-number="39"><span class="co"># Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no values changed)</span></a>
<a class="sourceLine" id="cb15-40" data-line-number="40"><span class="co"># Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no values changed)</span></a>
<a class="sourceLine" id="cb15-41" data-line-number="41"><span class="co"># Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no values changed)</span></a>
<a class="sourceLine" id="cb15-42" data-line-number="42"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-43" data-line-number="43"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb15-44" data-line-number="44"><span class="co"># EUCAST rules affected 6,604 out of 20,000 rows, making a total of 7,940 edits</span></a>
<a class="sourceLine" id="cb15-44" data-line-number="44"><span class="co"># EUCAST rules affected 6,550 out of 20,000 rows, making a total of 7,913 edits</span></a>
<a class="sourceLine" id="cb15-45" data-line-number="45"><span class="co"># =&gt; added 0 test results</span></a>
<a class="sourceLine" id="cb15-46" data-line-number="46"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-47" data-line-number="47"><span class="co"># =&gt; changed 7,940 test results</span></a>
<a class="sourceLine" id="cb15-48" data-line-number="48"><span class="co"># * 110 test results changed from S to I</span></a>
<a class="sourceLine" id="cb15-49" data-line-number="49"><span class="co"># * 4,715 test results changed from S to R</span></a>
<a class="sourceLine" id="cb15-50" data-line-number="50"><span class="co"># * 1,119 test results changed from I to S</span></a>
<a class="sourceLine" id="cb15-51" data-line-number="51"><span class="co"># * 307 test results changed from I to R</span></a>
<a class="sourceLine" id="cb15-52" data-line-number="52"><span class="co"># * 1,664 test results changed from R to S</span></a>
<a class="sourceLine" id="cb15-53" data-line-number="53"><span class="co"># * 25 test results changed from R to I</span></a>
<a class="sourceLine" id="cb15-47" data-line-number="47"><span class="co"># =&gt; changed 7,913 test results</span></a>
<a class="sourceLine" id="cb15-48" data-line-number="48"><span class="co"># * 111 test results changed from S to I</span></a>
<a class="sourceLine" id="cb15-49" data-line-number="49"><span class="co"># * 4,763 test results changed from S to R</span></a>
<a class="sourceLine" id="cb15-50" data-line-number="50"><span class="co"># * 1,086 test results changed from I to S</span></a>
<a class="sourceLine" id="cb15-51" data-line-number="51"><span class="co"># * 349 test results changed from I to R</span></a>
<a class="sourceLine" id="cb15-52" data-line-number="52"><span class="co"># * 1,585 test results changed from R to S</span></a>
<a class="sourceLine" id="cb15-53" data-line-number="53"><span class="co"># * 19 test results changed from R to I</span></a>
<a class="sourceLine" id="cb15-54" data-line-number="54"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb15-55" data-line-number="55"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-56" data-line-number="56"><span class="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>
@ -497,7 +497,7 @@
<a class="sourceLine" id="cb17-3" data-line-number="3"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `bacteria` as input for `col_mo`.</span></a>
<a class="sourceLine" id="cb17-4" data-line-number="4"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a>
<a class="sourceLine" id="cb17-5" data-line-number="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<a class="sourceLine" id="cb17-6" data-line-number="6"><span class="co"># =&gt; Found 5,676 first isolates (28.4% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb17-6" data-line-number="6"><span class="co"># =&gt; Found 5,610 first isolates (28.0% of total)</span></a></code></pre></div>
<p>So only is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb18-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(first <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>)</a></code></pre></div>
@ -508,7 +508,7 @@
<div id="first-weighted-isolates" class="section level2">
<h2 class="hasAnchor">
<a href="#first-weighted-isolates" class="anchor"></a>First <em>weighted</em> isolates</h2>
<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 M4, 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 W2, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -524,10 +524,10 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-04-02</td>
<td align="center">M4</td>
<td align="center">2010-02-15</td>
<td align="center">W2</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
@ -535,8 +535,8 @@
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-05-26</td>
<td align="center">M4</td>
<td align="center">2010-05-10</td>
<td align="center">W2</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -546,10 +546,10 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-07-15</td>
<td align="center">M4</td>
<td align="center">2010-08-30</td>
<td align="center">W2</td>
<td align="center">B_ESCHR_COL</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>
@ -557,8 +557,8 @@
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-09-11</td>
<td align="center">M4</td>
<td align="center">2010-09-27</td>
<td align="center">W2</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -568,32 +568,32 @@
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-11-13</td>
<td align="center">M4</td>
<td align="center">2010-10-28</td>
<td align="center">W2</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-11-16</td>
<td align="center">M4</td>
<td align="center">2010-12-01</td>
<td align="center">W2</td>
<td align="center">B_ESCHR_COL</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">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-01-03</td>
<td align="center">M4</td>
<td align="center">2011-01-20</td>
<td align="center">W2</td>
<td align="center">B_ESCHR_COL</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>
@ -601,30 +601,30 @@
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-03-16</td>
<td align="center">M4</td>
<td align="center">2011-02-09</td>
<td align="center">W2</td>
<td align="center">B_ESCHR_COL</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">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-04-21</td>
<td align="center">M4</td>
<td align="center">2011-03-08</td>
<td align="center">W2</td>
<td align="center">B_ESCHR_COL</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">R</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-04-24</td>
<td align="center">M4</td>
<td align="center">2011-04-14</td>
<td align="center">W2</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -645,7 +645,7 @@
<a class="sourceLine" id="cb20-7" data-line-number="7"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<a class="sourceLine" id="cb20-8" data-line-number="8"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.</span></a>
<a class="sourceLine" id="cb20-9" data-line-number="9"><span class="co"># [Criterion] Inclusion based on key antibiotics, ignoring I.</span></a>
<a class="sourceLine" id="cb20-10" data-line-number="10"><span class="co"># =&gt; Found 14,973 first weighted isolates (74.9% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb20-10" data-line-number="10"><span class="co"># =&gt; Found 15,032 first weighted isolates (75.2% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -662,10 +662,10 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-04-02</td>
<td align="center">M4</td>
<td align="center">2010-02-15</td>
<td align="center">W2</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
@ -674,8 +674,8 @@
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-05-26</td>
<td align="center">M4</td>
<td align="center">2010-05-10</td>
<td align="center">W2</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -686,35 +686,35 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-07-15</td>
<td align="center">M4</td>
<td align="center">2010-08-30</td>
<td align="center">W2</td>
<td align="center">B_ESCHR_COL</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">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-09-11</td>
<td align="center">M4</td>
<td align="center">2010-09-27</td>
<td align="center">W2</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-11-13</td>
<td align="center">M4</td>
<td align="center">2010-10-28</td>
<td align="center">W2</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
@ -722,71 +722,71 @@
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-11-16</td>
<td align="center">M4</td>
<td align="center">2010-12-01</td>
<td align="center">W2</td>
<td align="center">B_ESCHR_COL</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">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-01-03</td>
<td align="center">M4</td>
<td align="center">2011-01-20</td>
<td align="center">W2</td>
<td align="center">B_ESCHR_COL</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">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-03-16</td>
<td align="center">M4</td>
<td align="center">2011-02-09</td>
<td align="center">W2</td>
<td align="center">B_ESCHR_COL</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">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-04-21</td>
<td align="center">M4</td>
<td align="center">2011-03-08</td>
<td align="center">W2</td>
<td align="center">B_ESCHR_COL</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">R</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-04-24</td>
<td align="center">M4</td>
<td align="center">2011-04-14</td>
<td align="center">W2</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Instead of 2, now 7 isolates are flagged. In total, of all isolates are marked ‘first weighted’ - 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, of all isolates are marked ‘first weighted’ - 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><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb21-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</a></code></pre></div>
<p>So we end up with 14,973 isolates for analysis.</p>
<p>So we end up with 15,032 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb22-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(first, keyab))</a></code></pre></div>
@ -812,59 +812,43 @@
<tbody>
<tr class="odd">
<td>3</td>
<td align="center">2015-08-15</td>
<td align="center">R1</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">2011-12-06</td>
<td align="center">I5</td>
<td align="center">Hospital C</td>
<td align="center">B_KLBSL_PNE</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">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">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>4</td>
<td align="center">2012-01-09</td>
<td align="center">X9</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</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>5</td>
<td align="center">2014-06-18</td>
<td align="center">Z7</td>
<td align="center">2011-03-10</td>
<td align="center">B9</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNE</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">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>6</td>
<td align="center">2015-02-18</td>
<td align="center">F4</td>
<td align="center">Hospital A</td>
<tr class="odd">
<td>5</td>
<td align="center">2010-06-27</td>
<td align="center">A2</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COL</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>
@ -874,31 +858,47 @@
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>6</td>
<td align="center">2017-12-11</td>
<td align="center">F8</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNE</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>7</td>
<td align="center">2010-11-14</td>
<td align="center">W5</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">S</td>
<td align="center">S</td>
<td>8</td>
<td align="center">2014-06-01</td>
<td align="center">W7</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COL</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-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</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>8</td>
<td align="center">2010-12-25</td>
<td align="center">F4</td>
<td align="center">Hospital B</td>
<td>9</td>
<td align="center">2017-12-09</td>
<td align="center">A1</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COL</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">M</td>
<td align="center">Gram-negative</td>
@ -925,7 +925,7 @@
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(genus, species)</a></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 14,973 (of which NA: 0 = 0.00%)<br>
Length: 15,032 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -942,33 +942,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,385</td>
<td align="right">49.3%</td>
<td align="right">7,385</td>
<td align="right">49.3%</td>
<td align="right">7,421</td>
<td align="right">49.4%</td>
<td align="right">7,421</td>
<td align="right">49.4%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,709</td>
<td align="right">24.8%</td>
<td align="right">11,094</td>
<td align="right">74.1%</td>
<td align="right">3,771</td>
<td align="right">25.1%</td>
<td align="right">11,192</td>
<td align="right">74.5%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,340</td>
<td align="right">15.6%</td>
<td align="right">13,434</td>
<td align="right">89.7%</td>
<td align="right">2,303</td>
<td align="right">15.3%</td>
<td align="right">13,495</td>
<td align="right">89.8%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,539</td>
<td align="right">10.3%</td>
<td align="right">14,973</td>
<td align="right">1,537</td>
<td align="right">10.2%</td>
<td align="right">15,032</td>
<td align="right">100.0%</td>
</tr>
</tbody>
@ -979,7 +979,7 @@ Longest: 24</p>
<a href="#resistance-percentages" class="anchor"></a>Resistance percentages</h2>
<p>The functions <code><a href="../reference/portion.html">portion_S()</a></code>, <code><a href="../reference/portion.html">portion_SI()</a></code>, <code><a href="../reference/portion.html">portion_I()</a></code>, <code><a href="../reference/portion.html">portion_IR()</a></code> and <code><a href="../reference/portion.html">portion_R()</a></code> can be used to determine the portion of a specific antimicrobial outcome. As per the EUCAST guideline of 2019, we calculate resistance as the portion of R (<code><a href="../reference/portion.html">portion_R()</a></code>) and susceptibility as the portion of S and I (<code><a href="../reference/portion.html">portion_SI()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_R</a></span>(AMX)</a>
<a class="sourceLine" id="cb26-2" data-line-number="2"><span class="co"># [1] 0.4646363</span></a></code></pre></div>
<a class="sourceLine" id="cb26-2" data-line-number="2"><span class="co"># [1] 0.4640766</span></a></code></pre></div>
<p>Or can be used in conjuction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb27-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital) <span class="op">%&gt;%</span><span class="st"> </span></a>
@ -992,19 +992,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4721851</td>
<td align="center">0.4620994</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4554570</td>
<td align="center">0.4646182</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4683715</td>
<td align="center">0.4689655</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4663838</td>
<td align="center">0.4625253</td>
</tr>
</tbody>
</table>
@ -1022,23 +1022,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4721851</td>
<td align="center">4494</td>
<td align="center">0.4620994</td>
<td align="center">4525</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4554570</td>
<td align="center">5186</td>
<td align="center">0.4646182</td>
<td align="center">5370</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4683715</td>
<td align="center">2229</td>
<td align="center">0.4689655</td>
<td align="center">2175</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4663838</td>
<td align="center">3064</td>
<td align="center">0.4625253</td>
<td align="center">2962</td>
</tr>
</tbody>
</table>
@ -1058,27 +1058,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.9243060</td>
<td align="center">0.8958700</td>
<td align="center">0.9932295</td>
<td align="center">0.9217087</td>
<td align="center">0.8948929</td>
<td align="center">0.9932624</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8401559</td>
<td align="center">0.8992853</td>
<td align="center">0.9837557</td>
<td align="center">0.8217306</td>
<td align="center">0.9050098</td>
<td align="center">0.9915420</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.9280129</td>
<td align="center">0.9263953</td>
<td align="center">0.9967646</td>
<td align="center">0.9254840</td>
<td align="center">0.9252188</td>
<td align="center">0.9952267</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.6303419</td>
<td align="center">0.6139818</td>
<td align="center">0.0000000</td>
<td align="center">0.6303419</td>
<td align="center">0.6139818</td>
</tr>
</tbody>
</table>