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(v0.9.0.9029) add uti to as.rsi()

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@ -39,7 +39,7 @@
</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">0.9.0.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9029</span>
</span>
</div>
@ -179,7 +179,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">17 February 2020</h4>
<h4 class="date">20 February 2020</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -188,7 +188,7 @@
<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 17 February 2020.</p>
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 20 February 2020.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -219,21 +219,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2020-02-17</td>
<td align="center">2020-02-20</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">2020-02-17</td>
<td align="center">2020-02-20</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">2020-02-17</td>
<td align="center">2020-02-20</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -328,52 +328,30 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-11-17</td>
<td align="center">D1</td>
<td align="center">Hospital A</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">M</td>
</tr>
<tr class="even">
<td align="center">2015-03-23</td>
<td align="center">N2</td>
<td align="center">Hospital D</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">M</td>
</tr>
<tr class="odd">
<td align="center">2010-04-13</td>
<td align="center">X4</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">2011-08-11</td>
<td align="center">M8</td>
<td align="center">2010-01-05</td>
<td align="center">F4</td>
<td align="center">Hospital A</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">2012-08-23</td>
<td align="center">J5</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</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="odd">
<td align="center">2015-01-30</td>
<td align="center">Z7</td>
<td align="center">2016-06-20</td>
<td align="center">S1</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
@ -383,14 +361,36 @@
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-12-06</td>
<td align="center">F9</td>
<td align="center">2013-05-08</td>
<td align="center">J3</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia 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>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2011-12-28</td>
<td align="center">T8</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">2016-11-05</td>
<td align="center">G9</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
</tbody>
@ -423,16 +423,16 @@ Unique: 2</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,441</td>
<td align="right">52.21%</td>
<td align="right">10,441</td>
<td align="right">52.21%</td>
<td align="right">10,402</td>
<td align="right">52.01%</td>
<td align="right">10,402</td>
<td align="right">52.01%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,559</td>
<td align="right">47.80%</td>
<td align="right">9,598</td>
<td align="right">47.99%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -452,8 +452,8 @@ Unique: 2</p>
<span id="cb13-3"><a href="#cb13-3"></a><span class="co"># Other rules by this AMR package</span></span>
<span id="cb13-4"><a href="#cb13-4"></a><span class="co"># Non-EUCAST: inherit amoxicillin results for unavailable ampicillin (no changes)</span></span>
<span id="cb13-5"><a href="#cb13-5"></a><span class="co"># Non-EUCAST: inherit ampicillin results for unavailable amoxicillin (no changes)</span></span>
<span id="cb13-6"><a href="#cb13-6"></a><span class="co"># Non-EUCAST: set amoxicillin/clav acid = S where ampicillin = S (3,072 values changed)</span></span>
<span id="cb13-7"><a href="#cb13-7"></a><span class="co"># Non-EUCAST: set ampicillin = R where amoxicillin/clav acid = R (144 values changed)</span></span>
<span id="cb13-6"><a href="#cb13-6"></a><span class="co"># Non-EUCAST: set amoxicillin/clav acid = S where ampicillin = S (2,986 values changed)</span></span>
<span id="cb13-7"><a href="#cb13-7"></a><span class="co"># Non-EUCAST: set ampicillin = R where amoxicillin/clav acid = R (157 values changed)</span></span>
<span id="cb13-8"><a href="#cb13-8"></a><span class="co"># Non-EUCAST: set piperacillin = R where piperacillin/tazobactam = R (no changes)</span></span>
<span id="cb13-9"><a href="#cb13-9"></a><span class="co"># Non-EUCAST: set piperacillin/tazobactam = S where piperacillin = S (no changes)</span></span>
<span id="cb13-10"><a href="#cb13-10"></a><span class="co"># Non-EUCAST: set trimethoprim = R where trimethoprim/sulfa = R (no changes)</span></span>
@ -479,14 +479,14 @@ Unique: 2</p>
<span id="cb13-30"><a href="#cb13-30"></a><span class="co"># Pasteurella multocida (no changes)</span></span>
<span id="cb13-31"><a href="#cb13-31"></a><span class="co"># Staphylococcus (no changes)</span></span>
<span id="cb13-32"><a href="#cb13-32"></a><span class="co"># Streptococcus groups A, B, C, G (no changes)</span></span>
<span id="cb13-33"><a href="#cb13-33"></a><span class="co"># Streptococcus pneumoniae (1,007 values changed)</span></span>
<span id="cb13-33"><a href="#cb13-33"></a><span class="co"># Streptococcus pneumoniae (1,017 values changed)</span></span>
<span id="cb13-34"><a href="#cb13-34"></a><span class="co"># Viridans group streptococci (no changes)</span></span>
<span id="cb13-35"><a href="#cb13-35"></a><span class="co"># </span></span>
<span id="cb13-36"><a href="#cb13-36"></a><span class="co"># EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></span>
<span id="cb13-37"><a href="#cb13-37"></a><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,261 values changed)</span></span>
<span id="cb13-37"><a href="#cb13-37"></a><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,297 values changed)</span></span>
<span id="cb13-38"><a href="#cb13-38"></a><span class="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></span>
<span id="cb13-39"><a href="#cb13-39"></a><span class="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></span>
<span id="cb13-40"><a href="#cb13-40"></a><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,767 values changed)</span></span>
<span id="cb13-40"><a href="#cb13-40"></a><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,752 values changed)</span></span>
<span id="cb13-41"><a href="#cb13-41"></a><span class="co"># Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></span>
<span id="cb13-42"><a href="#cb13-42"></a><span class="co"># Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></span>
<span id="cb13-43"><a href="#cb13-43"></a><span class="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)</span></span>
@ -494,15 +494,15 @@ Unique: 2</p>
<span id="cb13-45"><a href="#cb13-45"></a><span class="co"># Table 13: Interpretive rules for quinolones (no changes)</span></span>
<span id="cb13-46"><a href="#cb13-46"></a><span class="co"># </span></span>
<span id="cb13-47"><a href="#cb13-47"></a><span class="co"># -------------------------------------------------------------------------------</span></span>
<span id="cb13-48"><a href="#cb13-48"></a><span class="co"># EUCAST rules affected 6,578 out of 20,000 rows, making a total of 8,251 edits</span></span>
<span id="cb13-48"><a href="#cb13-48"></a><span class="co"># EUCAST rules affected 6,502 out of 20,000 rows, making a total of 8,209 edits</span></span>
<span id="cb13-49"><a href="#cb13-49"></a><span class="co"># =&gt; added 0 test results</span></span>
<span id="cb13-50"><a href="#cb13-50"></a><span class="co"># </span></span>
<span id="cb13-51"><a href="#cb13-51"></a><span class="co"># =&gt; changed 8,251 test results</span></span>
<span id="cb13-52"><a href="#cb13-52"></a><span class="co"># - 122 test results changed from S to I</span></span>
<span id="cb13-53"><a href="#cb13-53"></a><span class="co"># - 4,709 test results changed from S to R</span></span>
<span id="cb13-51"><a href="#cb13-51"></a><span class="co"># =&gt; changed 8,209 test results</span></span>
<span id="cb13-52"><a href="#cb13-52"></a><span class="co"># - 124 test results changed from S to I</span></span>
<span id="cb13-53"><a href="#cb13-53"></a><span class="co"># - 4,743 test results changed from S to R</span></span>
<span id="cb13-54"><a href="#cb13-54"></a><span class="co"># - 1,209 test results changed from I to S</span></span>
<span id="cb13-55"><a href="#cb13-55"></a><span class="co"># - 348 test results changed from I to R</span></span>
<span id="cb13-56"><a href="#cb13-56"></a><span class="co"># - 1,863 test results changed from R to S</span></span>
<span id="cb13-55"><a href="#cb13-55"></a><span class="co"># - 356 test results changed from I to R</span></span>
<span id="cb13-56"><a href="#cb13-56"></a><span class="co"># - 1,777 test results changed from R to S</span></span>
<span id="cb13-57"><a href="#cb13-57"></a><span class="co"># -------------------------------------------------------------------------------</span></span>
<span id="cb13-58"><a href="#cb13-58"></a><span class="co"># </span></span>
<span id="cb13-59"><a href="#cb13-59"></a><span class="co"># Use eucast_rules(..., verbose = TRUE) (on your original data) to get a data.frame with all specified edits instead.</span></span></code></pre></div>
@ -530,8 +530,8 @@ Unique: 2</p>
<span id="cb15-3"><a href="#cb15-3"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `bacteria` as input for `col_mo`.</span></span>
<span id="cb15-4"><a href="#cb15-4"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></span>
<span id="cb15-5"><a href="#cb15-5"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></span>
<span id="cb15-6"><a href="#cb15-6"></a><span class="co"># =&gt; Found 5,663 first isolates (28.3% of total)</span></span></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>
<span id="cb15-6"><a href="#cb15-6"></a><span class="co"># =&gt; Found 5,695 first isolates (28.5% of total)</span></span></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>
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb16-1"><a href="#cb16-1"></a>data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></span>
<span id="cb16-2"><a href="#cb16-2"></a><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>)</span></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>
@ -541,7 +541,7 @@ Unique: 2</p>
<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 I4, 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 N2, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -557,30 +557,30 @@ Unique: 2</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-04-12</td>
<td align="center">I4</td>
<td align="center">2010-02-09</td>
<td align="center">N2</td>
<td align="center">B_ESCHR_COLI</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">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-05-10</td>
<td align="center">I4</td>
<td align="center">2010-03-02</td>
<td align="center">N2</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">FALSE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-07-25</td>
<td align="center">I4</td>
<td align="center">2010-04-05</td>
<td align="center">N2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -590,19 +590,19 @@ Unique: 2</p>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-09-13</td>
<td align="center">I4</td>
<td align="center">2010-05-19</td>
<td align="center">N2</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">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-09-29</td>
<td align="center">I4</td>
<td align="center">2010-07-08</td>
<td align="center">N2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
@ -612,8 +612,8 @@ Unique: 2</p>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-11-25</td>
<td align="center">I4</td>
<td align="center">2010-08-09</td>
<td align="center">N2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -623,51 +623,51 @@ Unique: 2</p>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-11-25</td>
<td align="center">I4</td>
<td align="center">2011-05-26</td>
<td align="center">N2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</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">8</td>
<td align="center">2010-11-28</td>
<td align="center">I4</td>
<td align="center">2011-05-26</td>
<td align="center">N2</td>
<td align="center">B_ESCHR_COLI</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="odd">
<td align="center">9</td>
<td align="center">2010-12-27</td>
<td align="center">I4</td>
<td align="center">2011-06-19</td>
<td align="center">N2</td>
<td align="center">B_ESCHR_COLI</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">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-01-01</td>
<td align="center">I4</td>
<td align="center">2011-07-29</td>
<td align="center">N2</td>
<td align="center">B_ESCHR_COLI</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">FALSE</td>
</tr>
</tbody>
</table>
<p>Only 1 isolates are marked as ‘first’ 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><a href="../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 2 isolates are marked as ‘first’ 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><a href="../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 ‘key(…)ab’ the <code><a href="../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>
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb18-1"><a href="#cb18-1"></a>data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></span>
<span id="cb18-2"><a href="#cb18-2"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">keyab =</span> <span class="kw"><a href="../reference/key_antibiotics.html">key_antibiotics</a></span>(.)) <span class="op">%&gt;%</span><span class="st"> </span></span>
@ -678,7 +678,7 @@ Unique: 2</p>
<span id="cb18-7"><a href="#cb18-7"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></span>
<span id="cb18-8"><a href="#cb18-8"></a><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></span>
<span id="cb18-9"><a href="#cb18-9"></a><span class="co"># [Criterion] Inclusion based on key antibiotics, ignoring I</span></span>
<span id="cb18-10"><a href="#cb18-10"></a><span class="co"># =&gt; Found 14,979 first weighted isolates (74.9% of total)</span></span></code></pre></div>
<span id="cb18-10"><a href="#cb18-10"></a><span class="co"># =&gt; Found 15,096 first weighted isolates (75.5% of total)</span></span></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -695,20 +695,32 @@ Unique: 2</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-04-12</td>
<td align="center">I4</td>
<td align="center">2010-02-09</td>
<td align="center">N2</td>
<td align="center">B_ESCHR_COLI</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">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-05-10</td>
<td align="center">I4</td>
<td align="center">2010-03-02</td>
<td align="center">N2</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">R</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-04-05</td>
<td align="center">N2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -717,34 +729,10 @@ Unique: 2</p>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-07-25</td>
<td align="center">I4</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">4</td>
<td align="center">2010-09-13</td>
<td align="center">I4</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="odd">
<td align="center">5</td>
<td align="center">2010-09-29</td>
<td align="center">I4</td>
<td align="center">2010-05-19</td>
<td align="center">N2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
@ -753,10 +741,22 @@ Unique: 2</p>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-07-08</td>
<td align="center">N2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</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">2010-11-25</td>
<td align="center">I4</td>
<td align="center">2010-08-09</td>
<td align="center">N2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -767,23 +767,23 @@ Unique: 2</p>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-11-25</td>
<td align="center">I4</td>
<td align="center">2011-05-26</td>
<td align="center">N2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-11-28</td>
<td align="center">I4</td>
<td align="center">2011-05-26</td>
<td align="center">N2</td>
<td align="center">B_ESCHR_COLI</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>
@ -791,35 +791,35 @@ Unique: 2</p>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-12-27</td>
<td align="center">I4</td>
<td align="center">2011-06-19</td>
<td align="center">N2</td>
<td align="center">B_ESCHR_COLI</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">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-01-01</td>
<td align="center">I4</td>
<td align="center">2011-07-29</td>
<td align="center">N2</td>
<td align="center">B_ESCHR_COLI</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">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Instead of 1, now 7 isolates are flagged. In total, 74.9% of all isolates are marked ‘first weighted’ - 46.6% 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, 75.5% of all isolates are marked ‘first weighted’ - 47.0% 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="cb19"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb19-1"><a href="#cb19-1"></a>data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></span>
<span id="cb19-2"><a href="#cb19-2"></a><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</span></code></pre></div>
<p>So we end up with 14,979 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="cb20"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb20-1"><a href="#cb20-1"></a>data_1st &lt;-<span class="st"> </span>data_1st <span class="op">%&gt;%</span><span class="st"> </span></span>
<span id="cb20-2"><a href="#cb20-2"></a><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))</span></code></pre></div>
@ -845,56 +845,8 @@ Unique: 2</p>
<tbody>
<tr class="odd">
<td>1</td>
<td align="center">2017-11-17</td>
<td align="center">D1</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</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-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>2</td>
<td align="center">2015-03-23</td>
<td align="center">N2</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</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-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>3</td>
<td align="center">2010-04-13</td>
<td align="center">X4</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">2011-08-11</td>
<td align="center">M8</td>
<td align="center">2010-01-05</td>
<td align="center">F4</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
@ -907,11 +859,27 @@ Unique: 2</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<tr class="even">
<td>6</td>
<td align="center">2014-12-06</td>
<td align="center">F9</td>
<td align="center">Hospital A</td>
<td align="center">2016-11-05</td>
<td align="center">G9</td>
<td align="center">Hospital C</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">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>7</td>
<td align="center">2016-05-20</td>
<td align="center">A10</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -924,21 +892,53 @@ Unique: 2</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>7</td>
<td align="center">2016-02-10</td>
<td align="center">A4</td>
<td align="center">Hospital B</td>
<td>9</td>
<td align="center">2015-10-02</td>
<td align="center">R3</td>
<td align="center">Hospital C</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">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="odd">
<td>10</td>
<td align="center">2016-03-04</td>
<td align="center">B10</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</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="even">
<td>11</td>
<td align="center">2013-09-10</td>
<td align="center">P4</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</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-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -958,8 +958,8 @@ Unique: 2</p>
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb23-1"><a href="#cb23-1"></a>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)</span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 14,979<br>
Available: 14,979 (100%, NA: 0 = 0%)<br>
Length: 15,096<br>
Available: 15,096 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -976,33 +976,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,462</td>
<td align="right">49.82%</td>
<td align="right">7,462</td>
<td align="right">49.82%</td>
<td align="right">7,491</td>
<td align="right">49.62%</td>
<td align="right">7,491</td>
<td align="right">49.62%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,695</td>
<td align="right">24.67%</td>
<td align="right">11,157</td>
<td align="right">74.48%</td>
<td align="right">3,729</td>
<td align="right">24.70%</td>
<td align="right">11,220</td>
<td align="right">74.32%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,321</td>
<td align="right">2,340</td>
<td align="right">15.50%</td>
<td align="right">13,478</td>
<td align="right">89.98%</td>
<td align="right">13,560</td>
<td align="right">89.83%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,501</td>
<td align="right">10.02%</td>
<td align="right">14,979</td>
<td align="right">1,536</td>
<td align="right">10.17%</td>
<td align="right">15,096</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -1014,7 +1014,7 @@ 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="cb24"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb24-1"><a href="#cb24-1"></a>data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/proportion.html">resistance</a></span>(AMX)</span>
<span id="cb24-2"><a href="#cb24-2"></a><span class="co"># [1] 0.4633153</span></span></code></pre></div>
<span id="cb24-2"><a href="#cb24-2"></a><span class="co"># [1] 0.4681373</span></span></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="cb25"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb25-1"><a href="#cb25-1"></a>data_1st <span class="op">%&gt;%</span><span class="st"> </span></span>
<span id="cb25-2"><a href="#cb25-2"></a><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></span>
@ -1027,19 +1027,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4589178</td>
<td align="center">0.4648446</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4609652</td>
<td align="center">0.4689223</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4542615</td>
<td align="center">0.4656180</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4815972</td>
<td align="center">0.4734787</td>
</tr>
</tbody>
</table>
@ -1057,23 +1057,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4589178</td>
<td align="center">4491</td>
<td align="center">0.4648446</td>
<td align="center">4537</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4609652</td>
<td align="center">5367</td>
<td align="center">0.4689223</td>
<td align="center">5261</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4542615</td>
<td align="center">2241</td>
<td align="center">0.4656180</td>
<td align="center">2225</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4815972</td>
<td align="center">2880</td>
<td align="center">0.4734787</td>
<td align="center">3073</td>
</tr>
</tbody>
</table>
@ -1093,27 +1093,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.9234790</td>
<td align="center">0.8998928</td>
<td align="center">0.9963817</td>
<td align="center">0.9255106</td>
<td align="center">0.8972100</td>
<td align="center">0.9937258</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.9347102</td>
<td align="center">0.8974017</td>
<td align="center">0.9940040</td>
<td align="center">0.9199219</td>
<td align="center">0.8932292</td>
<td align="center">0.9934896</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.9271989</td>
<td align="center">0.9188092</td>
<td align="center">0.9929635</td>
<td align="center">0.9187450</td>
<td align="center">0.9133816</td>
<td align="center">0.9924913</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.6066351</td>
<td align="center">0.6128205</td>
<td align="center">0.0000000</td>
<td align="center">0.6066351</td>
<td align="center">0.6128205</td>
</tr>
</tbody>
</table>

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@ -39,7 +39,7 @@
</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">0.9.0.9025</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9029</span>
</span>
</div>
@ -179,7 +179,7 @@
<h1>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">17 February 2020</h4>
<h4 class="date">20 February 2020</h4>
<div class="hidden name"><code>EUCAST.Rmd</code></div>

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<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">0.9.0.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9000</span>
</span>
</div>