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(v0.7.0.9001) new pathovars, small fixes

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@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
</span>
</div>
@ -199,7 +199,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">03 June 2019</h4>
<h4 class="date">07 June 2019</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -208,7 +208,7 @@
<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 03 June 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 07 June 2019.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -224,21 +224,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2019-06-03</td>
<td align="center">2019-06-07</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">2019-06-03</td>
<td align="center">2019-06-07</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">2019-06-03</td>
<td align="center">2019-06-07</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -334,19 +334,52 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-12-01</td>
<td align="center">Y6</td>
<td align="center">Hospital C</td>
<td align="center">2010-01-26</td>
<td align="center">S3</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia 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">F</td>
</tr>
<tr class="even">
<td align="center">2010-08-26</td>
<td align="center">G7</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">F</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-05-04</td>
<td align="center">B8</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-05-31</td>
<td align="center">C8</td>
<td align="center">2016-11-19</td>
<td align="center">E10</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2013-07-13</td>
<td align="center">G3</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -355,45 +388,12 @@
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-04-18</td>
<td align="center">Z6</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-04-24</td>
<td align="center">W4</td>
<td align="center">2017-05-23</td>
<td align="center">V3</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2011-11-05</td>
<td align="center">A9</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia 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">M</td>
</tr>
<tr class="even">
<td align="center">2016-09-07</td>
<td align="center">Y6</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">S</td>
<td align="center">S</td>
@ -409,7 +409,7 @@
<a href="#cleaning-the-data" class="anchor"></a>Cleaning the data</h1>
<p>Use the frequency table function <code><a href="../reference/freq.html">freq()</a></code> to look specifically for unique values in any variable. For example, for the <code>gender</code> variable:</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1">data <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender) <span class="co"># this would be the same: freq(data$gender)</span></a></code></pre></div>
<pre><code># Frequency table of `gender` from a data.frame (20,000 x 9)
<pre><code># Frequency table of `gender` from `data` (20,000 x 9)
#
# Class: factor (numeric)
# Length: 20,000 (of which NA: 0 = 0.00%)
@ -418,8 +418,8 @@
#
# Item Count Percent Cum. Count Cum. Percent
# --- ----- ------- -------- ----------- -------------
# 1 M 10,407 52.0% 10,407 52.0%
# 2 F 9,593 48.0% 20,000 100.0%</code></pre>
# 1 M 10,368 51.8% 10,368 51.8%
# 2 F 9,632 48.2% 20,000 100.0%</code></pre>
<p>So, we can draw at least two conclusions immediately. From a data scientist perspective, the data looks clean: only values <code>M</code> and <code>F</code>. From a researcher perspective: there are slightly more men. Nothing we didn’t already know.</p>
<p>The data is already quite clean, but we still need to transform some variables. The <code>bacteria</code> column now consists of text, and we want to add more variables based on microbial IDs later on. So, we will transform this column to valid IDs. The <code><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" title="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span></a>
@ -449,14 +449,14 @@
<a class="sourceLine" id="cb14-18" title="18"><span class="co"># Pasteurella multocida (no new changes)</span></a>
<a class="sourceLine" id="cb14-19" title="19"><span class="co"># Staphylococcus (no new changes)</span></a>
<a class="sourceLine" id="cb14-20" title="20"><span class="co"># Streptococcus groups A, B, C, G (no new changes)</span></a>
<a class="sourceLine" id="cb14-21" title="21"><span class="co"># Streptococcus pneumoniae (1431 new changes)</span></a>
<a class="sourceLine" id="cb14-21" title="21"><span class="co"># Streptococcus pneumoniae (1,496 new changes)</span></a>
<a class="sourceLine" id="cb14-22" title="22"><span class="co"># Viridans group streptococci (no new changes)</span></a>
<a class="sourceLine" id="cb14-23" title="23"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-24" title="24"><span class="co"># EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
<a class="sourceLine" id="cb14-25" title="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1230 new changes)</span></a>
<a class="sourceLine" id="cb14-25" title="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,276 new changes)</span></a>
<a class="sourceLine" id="cb14-26" title="26"><span class="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no new changes)</span></a>
<a class="sourceLine" id="cb14-27" title="27"><span class="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no new changes)</span></a>
<a class="sourceLine" id="cb14-28" title="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2646 new changes)</span></a>
<a class="sourceLine" id="cb14-28" title="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,809 new changes)</span></a>
<a class="sourceLine" id="cb14-29" title="29"><span class="co"># Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no new changes)</span></a>
<a class="sourceLine" id="cb14-30" title="30"><span class="co"># Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no new changes)</span></a>
<a class="sourceLine" id="cb14-31" title="31"><span class="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no new changes)</span></a>
@ -464,24 +464,24 @@
<a class="sourceLine" id="cb14-33" title="33"><span class="co"># Table 13: Interpretive rules for quinolones (no new changes)</span></a>
<a class="sourceLine" id="cb14-34" title="34"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-35" title="35"><span class="co"># Other rules</span></a>
<a class="sourceLine" id="cb14-36" title="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2197 new changes)</span></a>
<a class="sourceLine" id="cb14-37" title="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (99 new changes)</span></a>
<a class="sourceLine" id="cb14-36" title="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2,244 new changes)</span></a>
<a class="sourceLine" id="cb14-37" title="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (111 new changes)</span></a>
<a class="sourceLine" id="cb14-38" title="38"><span class="co"># Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no new changes)</span></a>
<a class="sourceLine" id="cb14-39" title="39"><span class="co"># Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no new changes)</span></a>
<a class="sourceLine" id="cb14-40" title="40"><span class="co"># Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no new changes)</span></a>
<a class="sourceLine" id="cb14-41" title="41"><span class="co"># Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no new changes)</span></a>
<a class="sourceLine" id="cb14-42" title="42"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-43" title="43"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb14-44" title="44"><span class="co"># EUCAST rules affected 6,284 out of 20,000 rows, making a total of 7,603 edits</span></a>
<a class="sourceLine" id="cb14-44" title="44"><span class="co"># EUCAST rules affected 6,565 out of 20,000 rows, making a total of 7,936 edits</span></a>
<a class="sourceLine" id="cb14-45" title="45"><span class="co"># =&gt; added 0 test results</span></a>
<a class="sourceLine" id="cb14-46" title="46"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-47" title="47"><span class="co"># =&gt; changed 7,603 test results</span></a>
<a class="sourceLine" id="cb14-48" title="48"><span class="co"># - 111 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-49" title="49"><span class="co"># - 4,561 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-50" title="50"><span class="co"># - 1,028 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-51" title="51"><span class="co"># - 292 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-52" title="52"><span class="co"># - 1,595 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-53" title="53"><span class="co"># - 16 test results changed from R to I</span></a>
<a class="sourceLine" id="cb14-47" title="47"><span class="co"># =&gt; changed 7,936 test results</span></a>
<a class="sourceLine" id="cb14-48" title="48"><span class="co"># - 116 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-49" title="49"><span class="co"># - 4,801 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-50" title="50"><span class="co"># - 1,059 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-51" title="51"><span class="co"># - 347 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-52" title="52"><span class="co"># - 1,596 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-53" title="53"><span class="co"># - 17 test results changed from R to I</span></a>
<a class="sourceLine" id="cb14-54" title="54"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb14-55" title="55"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-56" title="56"><span class="co"># Use verbose = TRUE to get a data.frame with all specified edits instead.</span></a></code></pre></div>
@ -509,8 +509,8 @@
<a class="sourceLine" id="cb16-3" title="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" title="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" title="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" title="6"><span class="co"># =&gt; Found 5,652 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>
<a class="sourceLine" id="cb16-6" title="6"><span class="co"># =&gt; Found 5,692 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>
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="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" title="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>
@ -536,8 +536,8 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-03-08</td>
<td align="center">C7</td>
<td align="center">2010-01-16</td>
<td align="center">V9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -547,10 +547,10 @@
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-04-14</td>
<td align="center">C7</td>
<td align="center">2010-02-23</td>
<td align="center">V9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -558,8 +558,8 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-04-18</td>
<td align="center">C7</td>
<td align="center">2010-04-05</td>
<td align="center">V9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -569,19 +569,19 @@
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-04-22</td>
<td align="center">C7</td>
<td align="center">2010-04-28</td>
<td align="center">V9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-05-30</td>
<td align="center">C7</td>
<td align="center">2010-05-20</td>
<td align="center">V9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -591,19 +591,19 @@
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-10-09</td>
<td align="center">C7</td>
<td align="center">2010-07-07</td>
<td align="center">V9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-01-26</td>
<td align="center">C7</td>
<td align="center">2010-09-11</td>
<td align="center">V9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -613,8 +613,8 @@
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-02-19</td>
<td align="center">C7</td>
<td align="center">2010-09-19</td>
<td align="center">V9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -624,29 +624,29 @@
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-03-25</td>
<td align="center">C7</td>
<td align="center">2010-10-07</td>
<td align="center">V9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-04-17</td>
<td align="center">C7</td>
<td align="center">2011-01-14</td>
<td align="center">V9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
</tbody>
</table>
<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>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>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" title="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb19-2" title="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>
@ -657,7 +657,7 @@
<a class="sourceLine" id="cb19-7" title="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" title="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" title="9"><span class="co"># [Criterion] Inclusion based on key antibiotics, ignoring I.</span></a>
<a class="sourceLine" id="cb19-10" title="10"><span class="co"># =&gt; Found 15,076 first weighted isolates (75.4% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb19-10" title="10"><span class="co"># =&gt; Found 15,072 first weighted isolates (75.4% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -674,8 +674,8 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-03-08</td>
<td align="center">C7</td>
<td align="center">2010-01-16</td>
<td align="center">V9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -686,68 +686,68 @@
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-04-14</td>
<td align="center">C7</td>
<td align="center">2010-02-23</td>
<td align="center">V9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-04-18</td>
<td align="center">C7</td>
<td align="center">2010-04-05</td>
<td align="center">V9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-04-22</td>
<td align="center">C7</td>
<td align="center">2010-04-28</td>
<td align="center">V9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-05-30</td>
<td align="center">C7</td>
<td align="center">2010-05-20</td>
<td align="center">V9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-10-09</td>
<td align="center">C7</td>
<td align="center">2010-07-07</td>
<td align="center">V9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-01-26</td>
<td align="center">C7</td>
<td align="center">2010-09-11</td>
<td align="center">V9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -758,8 +758,8 @@
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-02-19</td>
<td align="center">C7</td>
<td align="center">2010-09-19</td>
<td align="center">V9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -770,35 +770,35 @@
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-03-25</td>
<td align="center">C7</td>
<td align="center">2010-10-07</td>
<td align="center">V9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-04-17</td>
<td align="center">C7</td>
<td align="center">2011-01-14</td>
<td align="center">V9</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Instead of 2, now 9 isolates are flagged. In total, 75.4% 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>Instead of 1, now 4 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>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" title="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" title="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 15,076 isolates for analysis.</p>
<p>So we end up with 15,072 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" title="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" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(first, keyab))</a></code></pre></div>
@ -806,6 +806,7 @@
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(data_1st)</a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th></th>
<th align="center">date</th>
<th align="center">patient_id</th>
<th align="center">hospital</th>
@ -822,13 +823,14 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-12-01</td>
<td align="center">Y6</td>
<td align="center">Hospital C</td>
<td>1</td>
<td align="center">2010-01-26</td>
<td align="center">S3</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram negative</td>
@ -837,8 +839,41 @@
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-05-31</td>
<td align="center">C8</td>
<td>2</td>
<td align="center">2010-08-26</td>
<td align="center">G7</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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>3</td>
<td align="center">2016-05-04</td>
<td align="center">B8</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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>5</td>
<td align="center">2013-07-13</td>
<td align="center">G3</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
@ -852,63 +887,35 @@
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-04-18</td>
<td align="center">Z6</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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 align="center">2011-04-24</td>
<td align="center">W4</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-11-05</td>
<td align="center">A9</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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 align="center">2016-09-07</td>
<td>8</td>
<td align="center">2016-11-20</td>
<td align="center">Y6</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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">2015-11-03</td>
<td align="center">W8</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -928,9 +935,9 @@
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1"><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste</a></span>(data_1st<span class="op">$</span>genus, data_1st<span class="op">$</span>species))</a></code></pre></div>
<p>Or can be used like the <code>dplyr</code> way, which is easier readable:</p>
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus, species)</a></code></pre></div>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (15,076 x 13)</strong></p>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from <code>data_1st</code> (15,072 x 13)</strong></p>
<p>Columns: 2<br>
Length: 15,076 (of which NA: 0 = 0.00%)<br>
Length: 15,072 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -947,33 +954,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,402</td>
<td align="right">49.1%</td>
<td align="right">7,402</td>
<td align="right">49.1%</td>
<td align="right">7,451</td>
<td align="right">49.4%</td>
<td align="right">7,451</td>
<td align="right">49.4%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,887</td>
<td align="right">25.8%</td>
<td align="right">11,289</td>
<td align="right">74.9%</td>
<td align="right">3,713</td>
<td align="right">24.6%</td>
<td align="right">11,164</td>
<td align="right">74.1%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,244</td>
<td align="right">14.9%</td>
<td align="right">13,533</td>
<td align="right">2,367</td>
<td align="right">15.7%</td>
<td align="right">13,531</td>
<td align="right">89.8%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,543</td>
<td align="right">1,541</td>
<td align="right">10.2%</td>
<td align="right">15,076</td>
<td align="right">15,072</td>
<td align="right">100.0%</td>
</tr>
</tbody>
@ -984,7 +991,7 @@ Longest: 24</p>
<a href="#resistance-percentages" class="anchor"></a>Resistance percentages</h2>
<p>The functions <code><a href="../reference/portion.html">portion_S()</a></code>, <code><a href="../reference/portion.html">portion_SI()</a></code>, <code><a href="../reference/portion.html">portion_I()</a></code>, <code><a href="../reference/portion.html">portion_IR()</a></code> and <code><a href="../reference/portion.html">portion_R()</a></code> can be used to determine the portion of a specific antimicrobial outcome. As per the EUCAST guideline of 2019, we calculate resistance as the portion of R (<code><a href="../reference/portion.html">portion_R()</a></code>) and susceptibility as the portion of S and I (<code><a href="../reference/portion.html">portion_SI()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" title="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" title="2"><span class="co"># [1] 0.4678297</span></a></code></pre></div>
<a class="sourceLine" id="cb25-2" title="2"><span class="co"># [1] 0.4620488</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" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb26-2" title="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>
@ -997,19 +1004,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4700949</td>
<td align="center">0.4472198</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4625218</td>
<td align="center">0.4684564</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4715272</td>
<td align="center">0.4662494</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4706266</td>
<td align="center">0.4704907</td>
</tr>
</tbody>
</table>
@ -1027,23 +1034,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4700949</td>
<td align="center">4531</td>
<td align="center">0.4472198</td>
<td align="center">4604</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4625218</td>
<td align="center">5163</td>
<td align="center">0.4684564</td>
<td align="center">5215</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4715272</td>
<td align="center">2318</td>
<td align="center">0.4662494</td>
<td align="center">2237</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4706266</td>
<td align="center">3064</td>
<td align="center">0.4704907</td>
<td align="center">3016</td>
</tr>
</tbody>
</table>
@ -1063,27 +1070,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.9297487</td>
<td align="center">0.8940827</td>
<td align="center">0.9944610</td>
<td align="center">0.9256476</td>
<td align="center">0.8916924</td>
<td align="center">0.9938263</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8243681</td>
<td align="center">0.9047310</td>
<td align="center">0.9831497</td>
<td align="center">0.8208955</td>
<td align="center">0.8974692</td>
<td align="center">0.9883193</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.9248778</td>
<td align="center">0.9253923</td>
<td align="center">0.9935683</td>
<td align="center">0.9237813</td>
<td align="center">0.9165096</td>
<td align="center">0.9929976</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.6114082</td>
<td align="center">0.6138572</td>
<td align="center">0.0000000</td>
<td align="center">0.6114082</td>
<td align="center">0.6138572</td>
</tr>
</tbody>
</table>