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@ -41,7 +41,7 @@
</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">0.8.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9033</span>
</span>
</div>
@ -187,7 +187,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">18 November 2019</h4>
<h4 class="date">23 November 2019</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -196,7 +196,7 @@
<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 18 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 <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 23 November 2019.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -212,21 +212,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2019-11-18</td>
<td align="center">2019-11-23</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">2019-11-18</td>
<td align="center">2019-11-23</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">2019-11-18</td>
<td align="center">2019-11-23</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -321,71 +321,71 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-03-27</td>
<td align="center">O9</td>
<td align="center">2016-08-29</td>
<td align="center">I4</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">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-04-25</td>
<td align="center">U3</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">F</td>
</tr>
<tr class="odd">
<td align="center">2013-06-29</td>
<td align="center">W2</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</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>
</tr>
<tr class="even">
<td align="center">2011-12-21</td>
<td align="center">D5</td>
<td align="center">Hospital C</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="odd">
<td align="center">2016-10-19</td>
<td align="center">G6</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</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">2017-08-29</td>
<td align="center">Y5</td>
<td align="center">Hospital B</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">F</td>
</tr>
<tr class="even">
<td align="center">2015-09-08</td>
<td align="center">U5</td>
<td align="center">Hospital C</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">F</td>
</tr>
<tr class="odd">
<td align="center">2014-09-10</td>
<td align="center">L5</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-07-28</td>
<td align="center">D7</td>
<td align="center">Hospital A</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="odd">
<td align="center">2013-04-12</td>
<td align="center">N6</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-03-29</td>
<td align="center">F1</td>
<td align="center">Hospital A</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>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -406,8 +406,8 @@
#
# Item Count Percent Cum. Count Cum. Percent
# --- ----- ------- -------- ----------- -------------
# 1 M 10,413 52.06% 10,413 52.06%
# 2 F 9,587 47.94% 20,000 100.00%</code></pre>
# 1 M 10,451 52.26% 10,451 52.26%
# 2 F 9,549 47.75% 20,000 100.00%</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="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span></a>
@ -422,8 +422,8 @@
<a class="sourceLine" id="cb14-3" data-line-number="3"><span class="co"># Other rules by this AMR package</span></a>
<a class="sourceLine" id="cb14-4" data-line-number="4"><span class="co"># Non-EUCAST: inherit amoxicillin results for unavailable ampicillin (no changes)</span></a>
<a class="sourceLine" id="cb14-5" data-line-number="5"><span class="co"># Non-EUCAST: inherit ampicillin results for unavailable amoxicillin (no changes)</span></a>
<a class="sourceLine" id="cb14-6" data-line-number="6"><span class="co"># Non-EUCAST: set amoxicillin/clav acid = S where ampicillin = S (2,986 values changed)</span></a>
<a class="sourceLine" id="cb14-7" data-line-number="7"><span class="co"># Non-EUCAST: set ampicillin = R where amoxicillin/clav acid = R (176 values changed)</span></a>
<a class="sourceLine" id="cb14-6" data-line-number="6"><span class="co"># Non-EUCAST: set amoxicillin/clav acid = S where ampicillin = S (2,952 values changed)</span></a>
<a class="sourceLine" id="cb14-7" data-line-number="7"><span class="co"># Non-EUCAST: set ampicillin = R where amoxicillin/clav acid = R (155 values changed)</span></a>
<a class="sourceLine" id="cb14-8" data-line-number="8"><span class="co"># Non-EUCAST: set piperacillin = R where piperacillin/tazobactam = R (no changes)</span></a>
<a class="sourceLine" id="cb14-9" data-line-number="9"><span class="co"># Non-EUCAST: set piperacillin/tazobactam = S where piperacillin = S (no changes)</span></a>
<a class="sourceLine" id="cb14-10" data-line-number="10"><span class="co"># Non-EUCAST: set trimethoprim = R where trimethoprim/sulfa = R (no changes)</span></a>
@ -448,14 +448,14 @@
<a class="sourceLine" id="cb14-29" data-line-number="29"><span class="co"># Pasteurella multocida (no changes)</span></a>
<a class="sourceLine" id="cb14-30" data-line-number="30"><span class="co"># Staphylococcus (no changes)</span></a>
<a class="sourceLine" id="cb14-31" data-line-number="31"><span class="co"># Streptococcus groups A, B, C, G (no changes)</span></a>
<a class="sourceLine" id="cb14-32" data-line-number="32"><span class="co"># Streptococcus pneumoniae (1,015 values changed)</span></a>
<a class="sourceLine" id="cb14-32" data-line-number="32"><span class="co"># Streptococcus pneumoniae (984 values changed)</span></a>
<a class="sourceLine" id="cb14-33" data-line-number="33"><span class="co"># Viridans group streptococci (no changes)</span></a>
<a class="sourceLine" id="cb14-34" data-line-number="34"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-35" data-line-number="35"><span class="co"># EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
<a class="sourceLine" id="cb14-36" data-line-number="36"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,284 values changed)</span></a>
<a class="sourceLine" id="cb14-36" data-line-number="36"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,309 values changed)</span></a>
<a class="sourceLine" id="cb14-37" data-line-number="37"><span class="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb14-38" data-line-number="38"><span class="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb14-39" data-line-number="39"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,796 values changed)</span></a>
<a class="sourceLine" id="cb14-39" data-line-number="39"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,719 values changed)</span></a>
<a class="sourceLine" id="cb14-40" data-line-number="40"><span class="co"># Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></a>
<a class="sourceLine" id="cb14-41" data-line-number="41"><span class="co"># Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></a>
<a class="sourceLine" id="cb14-42" data-line-number="42"><span class="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)</span></a>
@ -463,15 +463,15 @@
<a class="sourceLine" id="cb14-44" data-line-number="44"><span class="co"># Table 13: Interpretive rules for quinolones (no changes)</span></a>
<a class="sourceLine" id="cb14-45" data-line-number="45"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-46" data-line-number="46"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb14-47" data-line-number="47"><span class="co"># EUCAST rules affected 6,569 out of 20,000 rows, making a total of 8,257 edits</span></a>
<a class="sourceLine" id="cb14-47" data-line-number="47"><span class="co"># EUCAST rules affected 6,464 out of 20,000 rows, making a total of 8,119 edits</span></a>
<a class="sourceLine" id="cb14-48" data-line-number="48"><span class="co"># =&gt; added 0 test results</span></a>
<a class="sourceLine" id="cb14-49" data-line-number="49"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-50" data-line-number="50"><span class="co"># =&gt; changed 8,257 test results</span></a>
<a class="sourceLine" id="cb14-51" data-line-number="51"><span class="co"># - 123 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-52" data-line-number="52"><span class="co"># - 4,779 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-53" data-line-number="53"><span class="co"># - 1,134 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-54" data-line-number="54"><span class="co"># - 369 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-55" data-line-number="55"><span class="co"># - 1,852 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-50" data-line-number="50"><span class="co"># =&gt; changed 8,119 test results</span></a>
<a class="sourceLine" id="cb14-51" data-line-number="51"><span class="co"># - 109 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-52" data-line-number="52"><span class="co"># - 4,710 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-53" data-line-number="53"><span class="co"># - 1,166 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-54" data-line-number="54"><span class="co"># - 348 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-55" data-line-number="55"><span class="co"># - 1,786 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-56" data-line-number="56"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb14-57" data-line-number="57"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-58" data-line-number="58"><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>
@ -499,8 +499,8 @@
<a class="sourceLine" id="cb16-3" 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="cb16-4" 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="cb16-5" 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="cb16-6" data-line-number="6"><span class="co"># =&gt; Found 5,699 first isolates (28.5% of total)</span></a></code></pre></div>
<p>So only 28.5% 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>
<a class="sourceLine" id="cb16-6" data-line-number="6"><span class="co"># =&gt; Found 5,669 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><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="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" 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="cb17-2" 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>
<p>For future use, the above two syntaxes can be shortened with the <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> function:</p>
@ -510,7 +510,7 @@
<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 X7, 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 T6, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -526,19 +526,19 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-03-18</td>
<td align="center">X7</td>
<td align="center">2010-02-28</td>
<td align="center">T6</td>
<td align="center">B_ESCHR_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">R</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-04-28</td>
<td align="center">X7</td>
<td align="center">2010-03-01</td>
<td align="center">T6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -548,32 +548,32 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-06-26</td>
<td align="center">X7</td>
<td align="center">2010-05-20</td>
<td align="center">T6</td>
<td align="center">B_ESCHR_COLI</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="even">
<td align="center">4</td>
<td align="center">2010-08-06</td>
<td align="center">X7</td>
<td align="center">2010-06-21</td>
<td align="center">T6</td>
<td align="center">B_ESCHR_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">R</td>
<td align="center">R</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-08-31</td>
<td align="center">X7</td>
<td align="center">2010-09-24</td>
<td align="center">T6</td>
<td align="center">B_ESCHR_COLI</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>
@ -581,19 +581,19 @@
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-10-15</td>
<td align="center">X7</td>
<td align="center">2010-11-18</td>
<td align="center">T6</td>
<td align="center">B_ESCHR_COLI</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">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-11-19</td>
<td align="center">X7</td>
<td align="center">2011-02-07</td>
<td align="center">T6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
@ -603,30 +603,30 @@
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-01-20</td>
<td align="center">X7</td>
<td align="center">2011-03-09</td>
<td align="center">T6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-03-23</td>
<td align="center">T6</td>
<td align="center">B_ESCHR_COLI</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">9</td>
<td align="center">2011-04-10</td>
<td align="center">X7</td>
<td align="center">B_ESCHR_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">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-04-12</td>
<td align="center">X7</td>
<td align="center">2011-04-01</td>
<td align="center">T6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -647,7 +647,7 @@
<a class="sourceLine" id="cb19-7" 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="cb19-8" 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="cb19-9" data-line-number="9"><span class="co"># [Criterion] Inclusion based on key antibiotics, ignoring I</span></a>
<a class="sourceLine" id="cb19-10" data-line-number="10"><span class="co"># =&gt; Found 15,085 first weighted isolates (75.4% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb19-10" data-line-number="10"><span class="co"># =&gt; Found 15,096 first weighted isolates (75.5% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -664,68 +664,56 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-03-18</td>
<td align="center">X7</td>
<td align="center">2010-02-28</td>
<td align="center">T6</td>
<td align="center">B_ESCHR_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">R</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-04-28</td>
<td align="center">X7</td>
<td align="center">2010-03-01</td>
<td align="center">T6</td>
<td align="center">B_ESCHR_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">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-06-26</td>
<td align="center">X7</td>
<td align="center">2010-05-20</td>
<td align="center">T6</td>
<td align="center">B_ESCHR_COLI</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">TRUE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-08-06</td>
<td align="center">X7</td>
<td align="center">2010-06-21</td>
<td align="center">T6</td>
<td align="center">B_ESCHR_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">R</td>
<td align="center">R</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-08-31</td>
<td align="center">X7</td>
<td align="center">B_ESCHR_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">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-10-15</td>
<td align="center">X7</td>
<td align="center">2010-09-24</td>
<td align="center">T6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
@ -734,61 +722,73 @@
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-11-18</td>
<td align="center">T6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-11-19</td>
<td align="center">X7</td>
<td align="center">2011-02-07</td>
<td align="center">T6</td>
<td align="center">B_ESCHR_COLI</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="even">
<td align="center">8</td>
<td align="center">2011-01-20</td>
<td align="center">X7</td>
<td align="center">2011-03-09</td>
<td align="center">T6</td>
<td align="center">B_ESCHR_COLI</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">FALSE</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-04-10</td>
<td align="center">X7</td>
<td align="center">2011-03-23</td>
<td align="center">T6</td>
<td align="center">B_ESCHR_COLI</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">TRUE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-04-12</td>
<td align="center">X7</td>
<td align="center">2011-04-01</td>
<td align="center">T6</td>
<td align="center">B_ESCHR_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">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Instead of 2, now 6 isolates are flagged. In total, 75.4% of all isolates are marked ‘first weighted’ - 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 2, now 10 isolates are flagged. In total, 75.5% of all isolates are marked ‘first weighted’ - 47.1% 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>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="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" 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="cb20-2" 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 15,085 isolates for analysis.</p>
<p>So we end up with 15,096 isolates for analysis.</p>
<p>We can remove unneeded columns:</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_1st <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="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(first, keyab))</a></code></pre></div>
@ -814,44 +814,12 @@
<tbody>
<tr class="odd">
<td>1</td>
<td align="center">2011-03-27</td>
<td align="center">O9</td>
<td align="center">2016-08-29</td>
<td align="center">I4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_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">F</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>4</td>
<td align="center">2011-07-28</td>
<td align="center">D7</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_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>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>8</td>
<td align="center">2015-08-23</td>
<td align="center">M1</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</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">R</td>
<td align="center">M</td>
@ -861,31 +829,31 @@
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>9</td>
<td align="center">2017-03-08</td>
<td align="center">G2</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td>2</td>
<td align="center">2016-04-25</td>
<td align="center">U3</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">F</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>10</td>
<td align="center">2013-11-09</td>
<td align="center">Q8</td>
<td align="center">Hospital A</td>
<td>3</td>
<td align="center">2013-06-29</td>
<td align="center">W2</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
@ -893,21 +861,53 @@
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>16</td>
<td align="center">2010-06-08</td>
<td align="center">O4</td>
<td align="center">Hospital A</td>
<td>5</td>
<td align="center">2016-10-19</td>
<td align="center">G6</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</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">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>6</td>
<td align="center">2017-08-29</td>
<td align="center">Y5</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</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-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>10</td>
<td align="center">2016-02-16</td>
<td align="center">L3</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</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>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -927,7 +927,7 @@
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(genus, species)</a></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 15,085 (of which NA: 0 = 0%)<br>
Length: 15,096 (of which NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -944,33 +944,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,426</td>
<td align="right">49.23%</td>
<td align="right">7,426</td>
<td align="right">49.23%</td>
<td align="right">7,646</td>
<td align="right">50.65%</td>
<td align="right">7,646</td>
<td align="right">50.65%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,769</td>
<td align="right">24.99%</td>
<td align="right">11,195</td>
<td align="right">74.21%</td>
<td align="right">3,610</td>
<td align="right">23.91%</td>
<td align="right">11,256</td>
<td align="right">74.56%</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">15.51%</td>
<td align="right">13,535</td>
<td align="right">89.72%</td>
<td align="right">2,315</td>
<td align="right">15.34%</td>
<td align="right">13,571</td>
<td align="right">89.90%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,550</td>
<td align="right">10.28%</td>
<td align="right">15,085</td>
<td align="right">1,525</td>
<td align="right">10.10%</td>
<td align="right">15,096</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -982,7 +982,7 @@ Longest: 24</p>
<p>The functions <code><a href="../reference/proportion.html">resistance()</a></code> and <code><a href="../reference/proportion.html">susceptibility()</a></code> can be used to calculate antimicrobial resistance or susceptibility. For more specific analyses, the functions <code><a href="../reference/proportion.html">proportion_S()</a></code>, <code><a href="../reference/proportion.html">proportion_SI()</a></code>, <code><a href="../reference/proportion.html">proportion_I()</a></code>, <code><a href="../reference/proportion.html">proportion_IR()</a></code> and <code><a href="../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><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<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="../reference/proportion.html">resistance</a></span>(AMX)</a>
<a class="sourceLine" id="cb25-2" data-line-number="2"><span class="co"># [1] 0.4684123</span></a></code></pre></div>
<a class="sourceLine" id="cb25-2" data-line-number="2"><span class="co"># [1] 0.4690647</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="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></a>
<a class="sourceLine" id="cb26-2" 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>
@ -995,19 +995,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4666964</td>
<td align="center">0.4740061</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4711845</td>
<td align="center">0.4707669</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4627451</td>
<td align="center">0.4640934</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4704102</td>
<td align="center">0.4622766</td>
</tr>
</tbody>
</table>
@ -1025,23 +1025,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4666964</td>
<td align="center">4489</td>
<td align="center">0.4740061</td>
<td align="center">4578</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4711845</td>
<td align="center">5327</td>
<td align="center">0.4707669</td>
<td align="center">5268</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4627451</td>
<td align="center">2295</td>
<td align="center">0.4640934</td>
<td align="center">2228</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4704102</td>
<td align="center">2974</td>
<td align="center">0.4622766</td>
<td align="center">3022</td>
</tr>
</tbody>
</table>
@ -1061,27 +1061,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.9243200</td>
<td align="center">0.8955023</td>
<td align="center">0.9934016</td>
<td align="center">0.9193042</td>
<td align="center">0.8966780</td>
<td align="center">0.9935914</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.9174194</td>
<td align="center">0.9019355</td>
<td align="center">0.9967742</td>
<td align="center">0.9285246</td>
<td align="center">0.8878689</td>
<td align="center">0.9940984</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.9193420</td>
<td align="center">0.9211993</td>
<td align="center">0.9936323</td>
<td align="center">0.9166205</td>
<td align="center">0.9171745</td>
<td align="center">0.9919668</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.6128205</td>
<td align="center">0.6241901</td>
<td align="center">0.0000000</td>
<td align="center">0.6128205</td>
<td align="center">0.6241901</td>
</tr>
</tbody>
</table>