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(v0.8.0.9027) adding susceptibility() and resistance()

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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">0.8.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>
@ -187,7 +187,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">09 November 2019</h4>
<h4 class="date">10 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 09 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 10 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">2019-11-09</td>
<td align="center">2019-11-10</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">2019-11-09</td>
<td align="center">2019-11-10</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">2019-11-09</td>
<td align="center">2019-11-10</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -321,68 +321,68 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-07-25</td>
<td align="center">L6</td>
<td align="center">Hospital D</td>
<td align="center">2016-01-11</td>
<td align="center">N1</td>
<td align="center">Hospital C</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">M</td>
</tr>
<tr class="even">
<td align="center">2015-11-29</td>
<td align="center">J1</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</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>
<tr class="odd">
<td align="center">2012-04-04</td>
<td align="center">C3</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">2017-10-06</td>
<td align="center">W8</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="odd">
<td align="center">2013-07-22</td>
<td align="center">Q6</td>
<td align="center">2010-12-17</td>
<td align="center">D2</td>
<td align="center">Hospital D</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">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-07-05</td>
<td align="center">L5</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">I</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">2011-06-05</td>
<td align="center">W7</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">2016-12-23</td>
<td align="center">C5</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2011-06-29</td>
<td align="center">F3</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</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>
</tr>
<tr class="even">
<td align="center">2011-07-01</td>
<td align="center">N10</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia 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">F</td>
</tr>
@ -406,8 +406,8 @@
#
# Item Count Percent Cum. Count Cum. Percent
# --- ----- ------- -------- ----------- -------------
# 1 M 10,398 51.99% 10,398 51.99%
# 2 F 9,602 48.01% 20,000 100.00%</code></pre>
# 1 M 10,264 51.32% 10,264 51.32%
# 2 F 9,736 48.68% 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>
@ -437,14 +437,14 @@
<a class="sourceLine" id="cb14-18" data-line-number="18"><span class="co"># Pasteurella multocida (no changes)</span></a>
<a class="sourceLine" id="cb14-19" data-line-number="19"><span class="co"># Staphylococcus (no changes)</span></a>
<a class="sourceLine" id="cb14-20" data-line-number="20"><span class="co"># Streptococcus groups A, B, C, G (no changes)</span></a>
<a class="sourceLine" id="cb14-21" data-line-number="21"><span class="co"># Streptococcus pneumoniae (1,452 values changed)</span></a>
<a class="sourceLine" id="cb14-21" data-line-number="21"><span class="co"># Streptococcus pneumoniae (1,477 values changed)</span></a>
<a class="sourceLine" id="cb14-22" data-line-number="22"><span class="co"># Viridans group streptococci (no changes)</span></a>
<a class="sourceLine" id="cb14-23" data-line-number="23"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-24" data-line-number="24"><span class="co"># EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
<a class="sourceLine" id="cb14-25" data-line-number="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,294 values changed)</span></a>
<a class="sourceLine" id="cb14-25" data-line-number="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,306 values changed)</span></a>
<a class="sourceLine" id="cb14-26" data-line-number="26"><span class="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb14-27" data-line-number="27"><span class="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb14-28" data-line-number="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,721 values changed)</span></a>
<a class="sourceLine" id="cb14-28" data-line-number="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,791 values changed)</span></a>
<a class="sourceLine" id="cb14-29" data-line-number="29"><span class="co"># Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></a>
<a class="sourceLine" id="cb14-30" data-line-number="30"><span class="co"># Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></a>
<a class="sourceLine" id="cb14-31" data-line-number="31"><span class="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)</span></a>
@ -452,24 +452,24 @@
<a class="sourceLine" id="cb14-33" data-line-number="33"><span class="co"># Table 13: Interpretive rules for quinolones (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"># Other rules</span></a>
<a class="sourceLine" id="cb14-36" data-line-number="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2,287 values changed)</span></a>
<a class="sourceLine" id="cb14-37" data-line-number="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (107 values changed)</span></a>
<a class="sourceLine" id="cb14-36" data-line-number="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2,203 values changed)</span></a>
<a class="sourceLine" id="cb14-37" data-line-number="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (104 values changed)</span></a>
<a class="sourceLine" id="cb14-38" data-line-number="38"><span class="co"># Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no changes)</span></a>
<a class="sourceLine" id="cb14-39" data-line-number="39"><span class="co"># Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)</span></a>
<a class="sourceLine" id="cb14-40" data-line-number="40"><span class="co"># Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no changes)</span></a>
<a class="sourceLine" id="cb14-41" data-line-number="41"><span class="co"># Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)</span></a>
<a class="sourceLine" id="cb14-42" data-line-number="42"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-43" data-line-number="43"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb14-44" data-line-number="44"><span class="co"># EUCAST rules affected 6,525 out of 20,000 rows, making a total of 7,861 edits</span></a>
<a class="sourceLine" id="cb14-44" data-line-number="44"><span class="co"># EUCAST rules affected 6,529 out of 20,000 rows, making a total of 7,881 edits</span></a>
<a class="sourceLine" id="cb14-45" data-line-number="45"><span class="co"># =&gt; added 0 test results</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"># =&gt; changed 7,861 test results</span></a>
<a class="sourceLine" id="cb14-48" data-line-number="48"><span class="co"># - 100 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-49" data-line-number="49"><span class="co"># - 4,694 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-50" data-line-number="50"><span class="co"># - 1,140 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-51" data-line-number="51"><span class="co"># - 302 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-52" data-line-number="52"><span class="co"># - 1,594 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-53" data-line-number="53"><span class="co"># - 31 test results changed from R to I</span></a>
<a class="sourceLine" id="cb14-47" data-line-number="47"><span class="co"># =&gt; changed 7,881 test results</span></a>
<a class="sourceLine" id="cb14-48" data-line-number="48"><span class="co"># - 102 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-49" data-line-number="49"><span class="co"># - 4,800 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-50" data-line-number="50"><span class="co"># - 1,035 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-51" data-line-number="51"><span class="co"># - 291 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-52" data-line-number="52"><span class="co"># - 1,625 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-53" data-line-number="53"><span class="co"># - 28 test results changed from R to I</span></a>
<a class="sourceLine" id="cb14-54" data-line-number="54"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb14-55" data-line-number="55"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-56" 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="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 5,670 first isolates (28.4% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb16-6" data-line-number="6"><span class="co"># =&gt; Found 5,674 first isolates (28.4% of total)</span></a></code></pre></div>
<p>So only 28.4% 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>
@ -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 Y8, 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 S8, 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">2010-04-05</td>
<td align="center">Y8</td>
<td align="center">2010-01-27</td>
<td align="center">S8</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>
@ -535,10 +535,10 @@
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-04-09</td>
<td align="center">Y8</td>
<td align="center">2010-06-01</td>
<td align="center">S8</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>
@ -546,32 +546,32 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-04-14</td>
<td align="center">Y8</td>
<td align="center">2010-09-13</td>
<td align="center">S8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</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">2010-05-23</td>
<td align="center">Y8</td>
<td align="center">2010-09-27</td>
<td align="center">S8</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">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-07-05</td>
<td align="center">Y8</td>
<td align="center">2010-10-15</td>
<td align="center">S8</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>
@ -579,8 +579,8 @@
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-07-05</td>
<td align="center">Y8</td>
<td align="center">2010-12-25</td>
<td align="center">S8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
@ -590,32 +590,32 @@
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-07-10</td>
<td align="center">Y8</td>
<td align="center">2011-02-06</td>
<td align="center">S8</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">FALSE</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">2010-08-07</td>
<td align="center">Y8</td>
<td align="center">2011-03-27</td>
<td align="center">S8</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>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-09-24</td>
<td align="center">Y8</td>
<td align="center">2011-05-14</td>
<td align="center">S8</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>
@ -623,18 +623,18 @@
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-02-13</td>
<td align="center">Y8</td>
<td align="center">2011-09-12</td>
<td align="center">S8</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>
</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="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" data-line-number="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb19-2" data-line-number="2"><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></a>
@ -645,7 +645,7 @@
<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 15,079 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 15,253 first weighted isolates (76.3% 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">2010-04-05</td>
<td align="center">Y8</td>
<td align="center">2010-01-27</td>
<td align="center">S8</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>
@ -674,10 +674,10 @@
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-04-09</td>
<td align="center">Y8</td>
<td align="center">2010-06-01</td>
<td align="center">S8</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>
@ -686,34 +686,34 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-04-14</td>
<td align="center">Y8</td>
<td align="center">2010-09-13</td>
<td align="center">S8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</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">4</td>
<td align="center">2010-09-27</td>
<td align="center">S8</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">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-05-23</td>
<td align="center">Y8</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">2010-07-05</td>
<td align="center">Y8</td>
<td align="center">2010-10-15</td>
<td align="center">S8</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>
@ -722,46 +722,46 @@
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-07-05</td>
<td align="center">Y8</td>
<td align="center">2010-12-25</td>
<td align="center">S8</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="odd">
<td align="center">7</td>
<td align="center">2010-07-10</td>
<td align="center">Y8</td>
<td align="center">2011-02-06</td>
<td align="center">S8</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">FALSE</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">2010-08-07</td>
<td align="center">Y8</td>
<td align="center">2011-03-27</td>
<td align="center">S8</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">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-09-24</td>
<td align="center">Y8</td>
<td align="center">2011-05-14</td>
<td align="center">S8</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>
@ -770,23 +770,23 @@
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-02-13</td>
<td align="center">Y8</td>
<td align="center">2011-09-12</td>
<td align="center">S8</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">FALSE</td>
</tr>
</tbody>
</table>
<p>Instead of 1, now 7 isolates are flagged. In total, 75.4% 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>Instead of 2, now 6 isolates are flagged. In total, 76.3% of all isolates are marked ‘first weighted’ - 47.9% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>As with <code><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 15,079 isolates for analysis.</p>
<p>So we end up with 15,253 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>
@ -811,29 +811,29 @@
</tr></thead>
<tbody>
<tr class="odd">
<td>1</td>
<td align="center">2011-07-25</td>
<td align="center">L6</td>
<td>2</td>
<td align="center">2010-12-17</td>
<td align="center">D2</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</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">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">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>3</td>
<td align="center">2012-04-04</td>
<td align="center">C3</td>
<td align="center">2016-07-05</td>
<td align="center">L5</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">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
@ -844,31 +844,31 @@
</tr>
<tr class="odd">
<td>4</td>
<td align="center">2017-10-06</td>
<td align="center">W8</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">2016-12-23</td>
<td align="center">C5</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNMN</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">S</td>
<td align="center">F</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">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>5</td>
<td align="center">2013-07-22</td>
<td align="center">Q6</td>
<td align="center">Hospital D</td>
<td align="center">2011-06-29</td>
<td align="center">F3</td>
<td align="center">Hospital A</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">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-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
@ -876,13 +876,13 @@
</tr>
<tr class="odd">
<td>6</td>
<td align="center">2011-06-05</td>
<td align="center">W7</td>
<td align="center">Hospital B</td>
<td align="center">2011-07-01</td>
<td align="center">N10</td>
<td align="center">Hospital A</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
@ -891,19 +891,19 @@
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>9</td>
<td align="center">2013-04-24</td>
<td align="center">D1</td>
<td>8</td>
<td align="center">2010-01-02</td>
<td align="center">X9</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</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-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</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>
</tbody>
@ -925,7 +925,7 @@
<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: 15,079 (of which NA: 0 = 0%)<br>
Length: 15,253 (of which NA: 0 = 0%)<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">7,442</td>
<td align="right">49.35%</td>
<td align="right">7,442</td>
<td align="right">49.35%</td>
<td align="right">7,529</td>
<td align="right">49.36%</td>
<td align="right">7,529</td>
<td align="right">49.36%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,732</td>
<td align="right">24.75%</td>
<td align="right">11,174</td>
<td align="right">74.10%</td>
<td align="right">3,765</td>
<td align="right">24.68%</td>
<td align="right">11,294</td>
<td align="right">74.04%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,323</td>
<td align="right">2,350</td>
<td align="right">15.41%</td>
<td align="right">13,497</td>
<td align="right">89.51%</td>
<td align="right">13,644</td>
<td align="right">89.45%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,582</td>
<td align="right">10.49%</td>
<td align="right">15,079</td>
<td align="right">1,609</td>
<td align="right">10.55%</td>
<td align="right">15,253</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -977,13 +977,14 @@ Longest: 24</p>
<div id="resistance-percentages" class="section level2">
<h2 class="hasAnchor">
<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="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/portion.html">portion_R</a></span>(AMX)</a>
<a class="sourceLine" id="cb25-2" data-line-number="2"><span class="co"># [1] 0.4668081</span></a></code></pre></div>
<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] 0.4715794</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>
<a class="sourceLine" id="cb26-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(<span class="dt">amoxicillin =</span> <span class="kw"><a href="../reference/portion.html">portion_R</a></span>(AMX))</a></code></pre></div>
<a class="sourceLine" id="cb26-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(<span class="dt">amoxicillin =</span> <span class="kw"><a href="../reference/proportion.html">resistance</a></span>(AMX))</a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">hospital</th>
@ -992,26 +993,26 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4627198</td>
<td align="center">0.4697103</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4745283</td>
<td align="center">0.4727821</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4721269</td>
<td align="center">0.4739112</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4549763</td>
<td align="center">0.4705116</td>
</tr>
</tbody>
</table>
<p>Of course it would be very convenient to know the number of isolates responsible for the percentages. For that purpose the <code><a href="../reference/count.html">n_rsi()</a></code> can be used, which works exactly like <code><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct()</a></code> from the <code>dplyr</code> package. It counts all isolates available for every group (i.e. values S, I or R):</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>
<a class="sourceLine" id="cb27-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(<span class="dt">amoxicillin =</span> <span class="kw"><a href="../reference/portion.html">portion_R</a></span>(AMX),</a>
<a class="sourceLine" id="cb27-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(<span class="dt">amoxicillin =</span> <span class="kw"><a href="../reference/proportion.html">resistance</a></span>(AMX),</a>
<a class="sourceLine" id="cb27-4" data-line-number="4"> <span class="dt">available =</span> <span class="kw"><a href="../reference/count.html">n_rsi</a></span>(AMX))</a></code></pre></div>
<table class="table">
<thead><tr class="header">
@ -1022,32 +1023,32 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4627198</td>
<td align="center">4493</td>
<td align="center">0.4697103</td>
<td align="center">4556</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4745283</td>
<td align="center">5300</td>
<td align="center">0.4727821</td>
<td align="center">5309</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4721269</td>
<td align="center">2332</td>
<td align="center">0.4739112</td>
<td align="center">2319</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4549763</td>
<td align="center">2954</td>
<td align="center">0.4705116</td>
<td align="center">3069</td>
</tr>
</tbody>
</table>
<p>These functions can also be used to get the portion of multiple antibiotics, to calculate empiric susceptibility of combination therapies very easily:</p>
<p>These functions can also be used to get the proportion of multiple antibiotics, to calculate empiric susceptibility of combination therapies very easily:</p>
<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb28-2" 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>(genus) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb28-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(<span class="dt">amoxiclav =</span> <span class="kw"><a href="../reference/portion.html">portion_SI</a></span>(AMC),</a>
<a class="sourceLine" id="cb28-4" data-line-number="4"> <span class="dt">gentamicin =</span> <span class="kw"><a href="../reference/portion.html">portion_SI</a></span>(GEN),</a>
<a class="sourceLine" id="cb28-5" data-line-number="5"> <span class="dt">amoxiclav_genta =</span> <span class="kw"><a href="../reference/portion.html">portion_SI</a></span>(AMC, GEN))</a></code></pre></div>
<a class="sourceLine" id="cb28-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(<span class="dt">amoxiclav =</span> <span class="kw"><a href="../reference/proportion.html">susceptibility</a></span>(AMC),</a>
<a class="sourceLine" id="cb28-4" data-line-number="4"> <span class="dt">gentamicin =</span> <span class="kw"><a href="../reference/proportion.html">susceptibility</a></span>(GEN),</a>
<a class="sourceLine" id="cb28-5" data-line-number="5"> <span class="dt">amoxiclav_genta =</span> <span class="kw"><a href="../reference/proportion.html">susceptibility</a></span>(AMC, GEN))</a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">genus</th>
@ -1058,36 +1059,36 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.9250202</td>
<td align="center">0.8972051</td>
<td align="center">0.9965063</td>
<td align="center">0.9246912</td>
<td align="center">0.8918847</td>
<td align="center">0.9929606</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8160556</td>
<td align="center">0.8982301</td>
<td align="center">0.9841972</td>
<td align="center">0.8309509</td>
<td align="center">0.9030454</td>
<td align="center">0.9869484</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.9217578</td>
<td align="center">0.9161308</td>
<td align="center">0.9930332</td>
<td align="center">0.9301461</td>
<td align="center">0.9189907</td>
<td align="center">0.9933599</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.6147223</td>
<td align="center">0.6251064</td>
<td align="center">0.0000000</td>
<td align="center">0.6147223</td>
<td align="center">0.6251064</td>
</tr>
</tbody>
</table>
<p>To make a transition to the next part, let’s see how this difference could be plotted:</p>
<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb29-2" 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>(genus) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb29-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(<span class="st">"1. Amoxi/clav"</span> =<span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_SI</a></span>(AMC),</a>
<a class="sourceLine" id="cb29-4" data-line-number="4"> <span class="st">"2. Gentamicin"</span> =<span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_SI</a></span>(GEN),</a>
<a class="sourceLine" id="cb29-5" data-line-number="5"> <span class="st">"3. Amoxi/clav + genta"</span> =<span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_SI</a></span>(AMC, GEN)) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb29-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(<span class="st">"1. Amoxi/clav"</span> =<span class="st"> </span><span class="kw"><a href="../reference/proportion.html">susceptibility</a></span>(AMC),</a>
<a class="sourceLine" id="cb29-4" data-line-number="4"> <span class="st">"2. Gentamicin"</span> =<span class="st"> </span><span class="kw"><a href="../reference/proportion.html">susceptibility</a></span>(GEN),</a>
<a class="sourceLine" id="cb29-5" data-line-number="5"> <span class="st">"3. Amoxi/clav + genta"</span> =<span class="st"> </span><span class="kw"><a href="../reference/proportion.html">susceptibility</a></span>(AMC, GEN)) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb29-6" data-line-number="6"><span class="st"> </span>tidyr<span class="op">::</span><span class="kw"><a href="https://tidyr.tidyverse.org/reference/gather.html">gather</a></span>(<span class="st">"antibiotic"</span>, <span class="st">"S"</span>, <span class="op">-</span>genus) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb29-7" data-line-number="7"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span>(<span class="kw"><a href="https://ggplot2.tidyverse.org/reference/aes.html">aes</a></span>(<span class="dt">x =</span> genus,</a>
<a class="sourceLine" id="cb29-8" data-line-number="8"> <span class="dt">y =</span> S,</a>
@ -1111,7 +1112,7 @@ Longest: 24</p>
<a class="sourceLine" id="cb30-10" data-line-number="10"><span class="co"># or as short as:</span></a>
<a class="sourceLine" id="cb30-11" data-line-number="11"><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span>(a_data_set) <span class="op">+</span></a>
<a class="sourceLine" id="cb30-12" data-line-number="12"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html">geom_bar</a></span>(<span class="kw"><a href="https://ggplot2.tidyverse.org/reference/aes.html">aes</a></span>(year))</a></code></pre></div>
<p>The <code>AMR</code> package contains functions to extend this <code>ggplot2</code> package, for example <code><a href="../reference/ggplot_rsi.html">geom_rsi()</a></code>. It automatically transforms data with <code><a href="../reference/count.html">count_df()</a></code> or <code><a href="../reference/portion.html">portion_df()</a></code> and show results in stacked bars. Its simplest and shortest example:</p>
<p>The <code>AMR</code> package contains functions to extend this <code>ggplot2</code> package, for example <code><a href="../reference/ggplot_rsi.html">geom_rsi()</a></code>. It automatically transforms data with <code><a href="../reference/count.html">count_df()</a></code> or <code><a href="../reference/proportion.html">proportion_df()</a></code> and show results in stacked bars. Its simplest and shortest example:</p>
<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" data-line-number="1"><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span>(data_1st) <span class="op">+</span></a>
<a class="sourceLine" id="cb31-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/ggplot_rsi.html">geom_rsi</a></span>(<span class="dt">translate_ab =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<p><img src="AMR_files/figure-html/plot%203-1.png" width="720"></p>

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@ -84,7 +84,7 @@
</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">0.8.0.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>