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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">0.6.1.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9035</span>
</span>
</div>
@ -76,6 +76,13 @@
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
@ -192,7 +199,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">20 May 2019</h4>
<h4 class="date">23 May 2019</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -201,7 +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 20 May 2019.</p>
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 23 May 2019.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -217,21 +224,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2019-05-20</td>
<td align="center">2019-05-23</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2019-05-20</td>
<td align="center">2019-05-23</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2019-05-20</td>
<td align="center">2019-05-23</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -327,66 +334,66 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-08-26</td>
<td align="center">Q7</td>
<td align="center">Hospital A</td>
<td align="center">2012-10-26</td>
<td align="center">T6</td>
<td align="center">Hospital D</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">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-10-04</td>
<td align="center">2011-10-13</td>
<td align="center">Y4</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2010-02-09</td>
<td align="center">O2</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2012-10-23</td>
<td align="center">C4</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</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">2011-08-17</td>
<td align="center">R4</td>
<td align="center">2010-09-18</td>
<td align="center">T5</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">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-01-18</td>
<td align="center">L2</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">2017-07-26</td>
<td align="center">J10</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="even">
<td align="center">2011-09-06</td>
<td align="center">O1</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">2015-09-19</td>
<td align="center">P5</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>
@ -411,8 +418,8 @@
#
# Item Count Percent Cum. Count Cum. Percent
# --- ----- ------- -------- ----------- -------------
# 1 M 10,378 51.9% 10,378 51.9%
# 2 F 9,622 48.1% 20,000 100.0%</code></pre>
# 1 M 10,310 51.6% 10,310 51.6%
# 2 F 9,690 48.4% 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>
@ -442,14 +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 (1443 new changes)</span></a>
<a class="sourceLine" id="cb14-21" title="21"><span class="co"># Streptococcus pneumoniae (1542 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 (1303 new changes)</span></a>
<a class="sourceLine" id="cb14-25" title="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1286 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 (2746 new changes)</span></a>
<a class="sourceLine" id="cb14-28" title="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2788 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>
@ -457,24 +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 (2313 new changes)</span></a>
<a class="sourceLine" id="cb14-37" title="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (115 new changes)</span></a>
<a class="sourceLine" id="cb14-36" title="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2231 new changes)</span></a>
<a class="sourceLine" id="cb14-37" title="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (126 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 6,579 out of 20,000 rows, making a total of 7,920 edits</span></a>
<a class="sourceLine" id="cb14-44" title="44"><span class="co"># EUCAST rules affected 6,562 out of 20,000 rows, making a total of 7,973 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 7,920 test results</span></a>
<a class="sourceLine" id="cb14-48" title="48"><span class="co"># - 123 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-49" title="49"><span class="co"># - 4,680 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-50" title="50"><span class="co"># - 1,131 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-51" title="51"><span class="co"># - 306 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-52" title="52"><span class="co"># - 1,657 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-53" title="53"><span class="co"># - 23 test results changed from R to I</span></a>
<a class="sourceLine" id="cb14-47" title="47"><span class="co"># =&gt; changed 7,973 test results</span></a>
<a class="sourceLine" id="cb14-48" title="48"><span class="co"># - 114 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-49" title="49"><span class="co"># - 4,779 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-50" title="50"><span class="co"># - 1,118 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-51" title="51"><span class="co"># - 330 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-52" title="52"><span class="co"># - 1,606 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-53" title="53"><span class="co"># - 26 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>
@ -502,8 +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 5,674 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>
<a class="sourceLine" id="cb16-6" title="6"><span class="co"># =&gt; Found 5,699 first isolates (28.5% of total)</span></a></code></pre></div>
<p>So only 28.5% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<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>
@ -529,8 +536,8 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-03-19</td>
<td align="center">N8</td>
<td align="center">2010-04-13</td>
<td align="center">S1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -540,10 +547,10 @@
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-05-06</td>
<td align="center">N8</td>
<td align="center">2010-06-02</td>
<td align="center">S1</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>
@ -551,43 +558,43 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-05-20</td>
<td align="center">N8</td>
<td align="center">2010-07-21</td>
<td align="center">S1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-07-20</td>
<td align="center">N8</td>
<td align="center">2010-09-19</td>
<td align="center">S1</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">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-09-04</td>
<td align="center">N8</td>
<td align="center">2010-09-19</td>
<td align="center">S1</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">R</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-09-13</td>
<td align="center">N8</td>
<td align="center">2010-10-14</td>
<td align="center">S1</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>
@ -595,19 +602,19 @@
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-04-01</td>
<td align="center">N8</td>
<td align="center">2010-10-28</td>
<td align="center">S1</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">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-10-15</td>
<td align="center">N8</td>
<td align="center">2010-12-09</td>
<td align="center">S1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
@ -617,8 +624,8 @@
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-11-14</td>
<td align="center">N8</td>
<td align="center">2010-12-15</td>
<td align="center">S1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -628,18 +635,18 @@
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2012-02-11</td>
<td align="center">N8</td>
<td align="center">2011-01-07</td>
<td align="center">S1</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">I</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>
@ -650,7 +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 14,968 first weighted isolates (74.8% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb19-10" title="10"><span class="co"># =&gt; Found 15,125 first weighted isolates (75.6% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -667,8 +674,8 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-03-19</td>
<td align="center">N8</td>
<td align="center">2010-04-13</td>
<td align="center">S1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -679,58 +686,58 @@
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-05-06</td>
<td align="center">N8</td>
<td align="center">2010-06-02</td>
<td align="center">S1</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">2010-05-20</td>
<td align="center">N8</td>
<td align="center">2010-07-21</td>
<td align="center">S1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-07-20</td>
<td align="center">N8</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>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-09-04</td>
<td align="center">N8</td>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-09-19</td>
<td align="center">S1</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">R</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">2010-09-19</td>
<td align="center">S1</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">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-09-13</td>
<td align="center">N8</td>
<td align="center">2010-10-14</td>
<td align="center">S1</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>
@ -739,20 +746,20 @@
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-04-01</td>
<td align="center">N8</td>
<td align="center">2010-10-28</td>
<td align="center">S1</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">TRUE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-10-15</td>
<td align="center">N8</td>
<td align="center">2010-12-09</td>
<td align="center">S1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
@ -763,8 +770,8 @@
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-11-14</td>
<td align="center">N8</td>
<td align="center">2010-12-15</td>
<td align="center">S1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -775,23 +782,23 @@
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2012-02-11</td>
<td align="center">N8</td>
<td align="center">2011-01-07</td>
<td align="center">S1</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">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Instead of 2, now 7 isolates are flagged. In total, 74.8% of all isolates are marked ‘first weighted’ - 46.5% 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 7 isolates are flagged. In total, 75.6% of all isolates are marked ‘first weighted’ - 47.1% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>As with <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" 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 14,968 isolates for analysis.</p>
<p>So we end up with 15,125 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>
@ -799,6 +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>
@ -815,12 +823,13 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-08-26</td>
<td align="center">Q7</td>
<td align="center">Hospital A</td>
<td>1</td>
<td align="center">2012-10-26</td>
<td align="center">T6</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
@ -830,9 +839,58 @@
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-10-04</td>
<td>2</td>
<td align="center">2011-10-13</td>
<td align="center">Y4</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>3</td>
<td align="center">2010-02-09</td>
<td align="center">O2</td>
<td align="center">Hospital A</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>6</td>
<td align="center">2015-09-19</td>
<td align="center">P5</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>7</td>
<td align="center">2011-05-13</td>
<td align="center">X5</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
@ -844,60 +902,16 @@
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-10-23</td>
<td align="center">C4</td>
<tr class="even">
<td>8</td>
<td align="center">2015-03-07</td>
<td align="center">Z7</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">2011-08-17</td>
<td align="center">R4</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">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="odd">
<td align="center">2016-01-18</td>
<td align="center">L2</td>
<td align="center">Hospital B</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">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">2011-09-06</td>
<td align="center">O1</td>
<td align="center">Hospital A</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">F</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
@ -921,9 +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> (14,968 x 13)</strong></p>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (15,125 x 13)</strong></p>
<p>Columns: 2<br>
Length: 14,968 (of which NA: 0 = 0.00%)<br>
Length: 15,125 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -940,33 +954,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,394</td>
<td align="right">49.4%</td>
<td align="right">7,394</td>
<td align="right">49.4%</td>
<td align="right">7,486</td>
<td align="right">49.5%</td>
<td align="right">7,486</td>
<td align="right">49.5%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,716</td>
<td align="right">24.8%</td>
<td align="right">11,110</td>
<td align="right">3,731</td>
<td align="right">24.7%</td>
<td align="right">11,217</td>
<td align="right">74.2%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,291</td>
<td align="right">15.3%</td>
<td align="right">13,401</td>
<td align="right">89.5%</td>
<td align="right">2,360</td>
<td align="right">15.6%</td>
<td align="right">13,577</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">1,567</td>
<td align="right">10.5%</td>
<td align="right">14,968</td>
<td align="right">1,548</td>
<td align="right">10.2%</td>
<td align="right">15,125</td>
<td align="right">100.0%</td>
</tr>
</tbody>
@ -977,7 +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] 0.4659941</span></a></code></pre></div>
<a class="sourceLine" id="cb25-2" title="2"><span class="co"># [1] 0.4628099</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>
@ -990,19 +1004,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4708540</td>
<td align="center">0.4556355</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4617585</td>
<td align="center">0.4661553</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4622030</td>
<td align="center">0.4759657</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4691689</td>
<td align="center">0.4577347</td>
</tr>
</tbody>
</table>
@ -1020,23 +1034,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4708540</td>
<td align="center">4426</td>
<td align="center">0.4556355</td>
<td align="center">4587</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4617585</td>
<td align="center">5243</td>
<td align="center">0.4661553</td>
<td align="center">5215</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4622030</td>
<td align="center">2315</td>
<td align="center">0.4759657</td>
<td align="center">2330</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4691689</td>
<td align="center">2984</td>
<td align="center">0.4577347</td>
<td align="center">2993</td>
</tr>
</tbody>
</table>
@ -1056,27 +1070,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.9249391</td>
<td align="center">0.8991074</td>
<td align="center">0.9935082</td>
<td align="center">0.9226556</td>
<td align="center">0.8966070</td>
<td align="center">0.9941224</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8162093</td>
<td align="center">0.9119336</td>
<td align="center">0.9910657</td>
<td align="center">0.8113695</td>
<td align="center">0.9102067</td>
<td align="center">0.9909561</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.9179225</td>
<td align="center">0.9198062</td>
<td align="center">0.9916577</td>
<td align="center">0.9187885</td>
<td align="center">0.9193246</td>
<td align="center">0.9949075</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.6294195</td>
<td align="center">0.6152542</td>
<td align="center">0.0000000</td>
<td align="center">0.6294195</td>
<td align="center">0.6152542</td>
</tr>
</tbody>
</table>

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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">0.6.1.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9035</span>
</span>
</div>
@ -76,6 +76,13 @@
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
@ -192,7 +199,7 @@
<h1>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">20 May 2019</h4>
<h4 class="date">23 May 2019</h4>
<div class="hidden name"><code>EUCAST.Rmd</code></div>

11
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@ -40,7 +40,7 @@
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<h1>How to use the <em>G</em>-test</h1>
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<h1>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">23 May 2019</h4>
<div class="hidden name"><code>MDR.Rmd</code></div>
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<p>With the function <code><a href="../reference/mdro.html">mdro()</a></code>, you can determine multi-drug resistant organisms (MDRO). It currently support these guidelines:</p>
<ul>
<li>“Intrinsic Resistance and Exceptional Phenotypes Tables”, by EUCAST (European Committee on Antimicrobial Susceptibility Testing)</li>
<li>“Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis”, by WHO (World Health Organization)</li>
<li>“WIP-Richtlijn Bijzonder Resistente Micro-organismen (BRMO)”, by RIVM (Rijksinstituut voor de Volksgezondheid, the Netherlands National Institute for Public Health and the Environment)</li>
</ul>
<p>As an example, I will make a data set to determine multi-drug resistant TB:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="co"># a helper function to get a random vector with values S, I and R</span></a>
<a class="sourceLine" id="cb1-2" title="2"><span class="co"># with the probabilities 50%-10%-40%</span></a>
<a class="sourceLine" id="cb1-3" title="3">sample_rsi &lt;-<span class="st"> </span><span class="cf">function</span>() {</a>
<a class="sourceLine" id="cb1-4" title="4"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/sample">sample</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>),</a>
<a class="sourceLine" id="cb1-5" title="5"> <span class="dt">size =</span> <span class="dv">5000</span>,</a>
<a class="sourceLine" id="cb1-6" title="6"> <span class="dt">prob =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.1</span>, <span class="fl">0.4</span>),</a>
<a class="sourceLine" id="cb1-7" title="7"> <span class="dt">replace =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb1-8" title="8">}</a>
<a class="sourceLine" id="cb1-9" title="9"></a>
<a class="sourceLine" id="cb1-10" title="10">my_TB_data &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(<span class="dt">rifampicin =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-11" title="11"> <span class="dt">isoniazid =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-12" title="12"> <span class="dt">gatifloxacin =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-13" title="13"> <span class="dt">ethambutol =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-14" title="14"> <span class="dt">pyrazinamide =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-15" title="15"> <span class="dt">moxifloxacin =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-16" title="16"> <span class="dt">kanamycin =</span> <span class="kw">sample_rsi</span>())</a></code></pre></div>
<p>Because all column names are automatically verified for valid drug names or codes, this would have worked exactly the same:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1">my_TB_data &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(<span class="dt">RIF =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb2-2" title="2"> <span class="dt">INH =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb2-3" title="3"> <span class="dt">GAT =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb2-4" title="4"> <span class="dt">ETH =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb2-5" title="5"> <span class="dt">PZA =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb2-6" title="6"> <span class="dt">MFX =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb2-7" title="7"> <span class="dt">KAN =</span> <span class="kw">sample_rsi</span>())</a></code></pre></div>
<p>The data set looks like this now:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb3-2" title="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># 1 R R R R R S</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># 2 S R R S R S</span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="co"># 3 R S S I S S</span></a>
<a class="sourceLine" id="cb3-6" title="6"><span class="co"># 4 R S S R S S</span></a>
<a class="sourceLine" id="cb3-7" title="7"><span class="co"># 5 R R S I I R</span></a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># 6 R S S S S S</span></a>
<a class="sourceLine" id="cb3-9" title="9"><span class="co"># kanamycin</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co"># 1 S</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># 2 R</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># 3 S</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># 4 R</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># 5 S</span></a>
<a class="sourceLine" id="cb3-15" title="15"><span class="co"># 6 I</span></a></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">my_TB_data<span class="op">$</span>mdr &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mdro.html">mdr_tb</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb4-2" title="2"><span class="co"># </span><span class="al">NOTE</span><span class="co">: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span></a>
<a class="sourceLine" id="cb4-3" title="3"><span class="co"># Determining multidrug-resistant organisms (MDRO), according to:</span></a>
<a class="sourceLine" id="cb4-4" title="4"><span class="co"># Guideline: Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis</span></a>
<a class="sourceLine" id="cb4-5" title="5"><span class="co"># Version: WHO/HTM/TB/2014.11</span></a>
<a class="sourceLine" id="cb4-6" title="6"><span class="co"># Author: WHO (World Health Organization)</span></a>
<a class="sourceLine" id="cb4-7" title="7"><span class="co"># Source: https://www.who.int/tb/publications/pmdt_companionhandbook/en/</span></a>
<a class="sourceLine" id="cb4-8" title="8"><span class="co"># Warning: Reliability might be improved if these antimicrobial results</span></a>
<a class="sourceLine" id="cb4-9" title="9"><span class="co"># would be available too: `CAP` (capreomycin), `RIB` (rifabutin), `RFP`</span></a>
<a class="sourceLine" id="cb4-10" title="10"><span class="co"># (rifapentine)</span></a></code></pre></div>
<p>And review the result with a frequency table:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_TB_data<span class="op">$</span>mdr)</a>
<a class="sourceLine" id="cb5-2" title="2"><span class="co"># </span></a>
<a class="sourceLine" id="cb5-3" title="3"><span class="co"># </span></a>
<a class="sourceLine" id="cb5-4" title="4"><span class="co"># **Frequency table of `mdr` from `my_TB_data` (5,000 x 8)** </span></a>
<a class="sourceLine" id="cb5-5" title="5"><span class="co"># </span></a>
<a class="sourceLine" id="cb5-6" title="6"><span class="co"># Class: `factor` &gt; `ordered` (`numeric`) </span></a>
<a class="sourceLine" id="cb5-7" title="7"><span class="co"># Length: 5,000 (of which NA: 0 = 0.00%) </span></a>
<a class="sourceLine" id="cb5-8" title="8"><span class="co"># Levels: 5: `Negative` &lt; `Mono-resistance` &lt; `Poly-resistance` &lt; `Multidrug res...` </span></a>
<a class="sourceLine" id="cb5-9" title="9"><span class="co"># Unique: 5</span></a>
<a class="sourceLine" id="cb5-10" title="10"><span class="co"># </span></a>
<a class="sourceLine" id="cb5-11" title="11"><span class="co"># </span></a>
<a class="sourceLine" id="cb5-12" title="12"><span class="co"># | |Item | Count| Percent| Cum. Count| Cum. Percent|</span></a>
<a class="sourceLine" id="cb5-13" title="13"><span class="co"># |:--|:-------------------------|-----:|-------:|----------:|------------:|</span></a>
<a class="sourceLine" id="cb5-14" title="14"><span class="co"># |1 |Mono-resistance | 3,297| 65.9%| 3,297| 65.9%|</span></a>
<a class="sourceLine" id="cb5-15" title="15"><span class="co"># |2 |Negative | 627| 12.5%| 3,924| 78.5%|</span></a>
<a class="sourceLine" id="cb5-16" title="16"><span class="co"># |3 |Multidrug resistance | 612| 12.2%| 4,536| 90.7%|</span></a>
<a class="sourceLine" id="cb5-17" title="17"><span class="co"># |4 |Poly-resistance | 263| 5.3%| 4,799| 96.0%|</span></a>
<a class="sourceLine" id="cb5-18" title="18"><span class="co"># |5 |Extensive drug resistance | 201| 4.0%| 5,000| 100.0%|</span></a></code></pre></div>
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</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">0.6.1.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9035</span>
</span>
</div>
@ -76,6 +76,13 @@
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
@ -192,7 +199,7 @@
<h1>How to get properties of an antibiotic</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">20 May 2019</h4>
<h4 class="date">23 May 2019</h4>
<div class="hidden name"><code>ab_property.Rmd</code></div>

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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">0.6.1.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9035</span>
</span>
</div>
@ -76,6 +76,13 @@
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
@ -192,7 +199,7 @@
<h1>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">20 May 2019</h4>
<h4 class="date">23 May 2019</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -217,14 +224,14 @@
<a class="sourceLine" id="cb2-8" title="8"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb2-9" title="9"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb2-10" title="10"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb2-11" title="11"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb2-12" title="12"><span class="co"># as.mo("sau") 18 18 22.0 18 18.0 62.0 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co"># as.mo("stau") 47 47 57.0 48 50.0 92.0 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co"># as.mo("staaur") 17 18 23.0 18 19.0 62.0 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co"># as.mo("STAAUR") 17 17 18.0 17 18.0 23.0 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co"># as.mo("S. aureus") 28 28 38.0 29 29.0 78.0 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co"># as.mo("S. aureus") 28 28 48.0 29 73.0 130.0 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co"># as.mo("Staphylococcus aureus") 8 8 8.1 8 8.1 8.2 10</span></a></code></pre></div>
<a class="sourceLine" id="cb2-11" title="11"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb2-12" title="12"><span class="co"># as.mo("sau") 17.0 18 32.0 18 62.0 68.0 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co"># as.mo("stau") 48.0 48 64.0 53 92.0 96.0 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co"># as.mo("staaur") 17.0 18 18.0 18 18.0 19.0 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co"># as.mo("STAAUR") 17.0 17 18.0 18 18.0 20.0 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co"># as.mo("S. aureus") 28.0 28 33.0 29 29.0 73.0 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co"># as.mo("S. aureus") 28.0 28 44.0 28 29.0 140.0 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co"># as.mo("Staphylococcus aureus") 7.9 8 8.1 8 8.2 8.2 10</span></a></code></pre></div>
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.</p>
<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Thermus islandicus</em> (<code>B_THERMS_ISL</code>), a bug probably never found before in humans:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">T.islandicus &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"theisl"</span>),</a>
@ -236,12 +243,12 @@
<a class="sourceLine" id="cb3-7" title="7"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(T.islandicus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb3-9" title="9"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co"># as.mo("theisl") 470 480 510 520 530 530 10</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># as.mo("THEISL") 470 470 500 490 520 530 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># as.mo("T. islandicus") 74 75 85 76 81 120 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># as.mo("T. islandicus") 74 75 92 76 120 140 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># as.mo("Thermus islandicus") 73 73 74 74 74 75 10</span></a></code></pre></div>
<p>That takes 8.2 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
<a class="sourceLine" id="cb3-10" title="10"><span class="co"># as.mo("theisl") 470 470 500 500 520 520 10</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># as.mo("THEISL") 470 470 510 520 520 530 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># as.mo("T. islandicus") 73 74 79 74 74 120 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># as.mo("T. islandicus") 73 74 84 74 75 130 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># as.mo("Thermus islandicus") 74 74 94 75 120 140 10</span></a></code></pre></div>
<p>That takes 8.1 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
<p>In the figure below, we compare <em>Escherichia coli</em> (which is very common) with <em>Prevotella brevis</em> (which is moderately common) and with <em>Thermus islandicus</em> (which is very uncommon):</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/par">par</a></span>(<span class="dt">mar =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">5</span>, <span class="dv">16</span>, <span class="dv">4</span>, <span class="dv">2</span>)) <span class="co"># set more space for left margin text (16)</span></a>
<a class="sourceLine" id="cb4-2" title="2"></a>
@ -287,8 +294,8 @@
<a class="sourceLine" id="cb5-24" title="24"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb5-25" title="25"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb5-26" title="26"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb5-27" title="27"><span class="co"># mo_fullname(x) 677 770 812 790 884 988 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.79 seconds (789 ms). You only lose time on your unique input values.</p>
<a class="sourceLine" id="cb5-27" title="27"><span class="co"># mo_fullname(x) 633 675 747 722 763 933 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.72 seconds (721 ms). You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -300,10 +307,10 @@
<a class="sourceLine" id="cb6-4" title="4"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb6-5" title="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb6-6" title="6"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb6-7" title="7"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb6-8" title="8"><span class="co"># A 12.9 13.20 13.30 13.40 13.50 13.50 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co"># B 25.3 25.80 30.40 25.80 26.20 71.60 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co"># C 1.3 1.37 1.56 1.67 1.73 1.74 10</span></a></code></pre></div>
<a class="sourceLine" id="cb6-7" title="7"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb6-8" title="8"><span class="co"># A 12.90 13.1 18.0 13.20 14.10 59.1 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co"># B 25.20 25.3 26.2 26.10 27.00 27.4 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co"># C 1.25 1.4 1.6 1.68 1.69 1.9 10</span></a></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0017 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
<a class="sourceLine" id="cb7-2" title="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
@ -317,14 +324,14 @@
<a class="sourceLine" id="cb7-10" title="10"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb7-11" title="11"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb7-12" title="12"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb7-13" title="13"><span class="co"># A 0.442 0.477 0.583 0.572 0.673 0.806 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co"># B 0.442 0.502 0.626 0.611 0.761 0.826 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co"># C 1.360 1.620 1.820 1.810 2.060 2.150 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co"># D 0.449 0.514 0.622 0.639 0.725 0.798 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co"># E 0.401 0.440 0.530 0.508 0.568 0.799 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co"># F 0.353 0.391 0.502 0.494 0.635 0.695 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co"># G 0.451 0.559 0.595 0.609 0.646 0.747 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co"># H 0.191 0.278 0.395 0.376 0.528 0.653 10</span></a></code></pre></div>
<a class="sourceLine" id="cb7-13" title="13"><span class="co"># A 0.357 0.374 0.447 0.435 0.514 0.567 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co"># B 0.404 0.507 0.541 0.533 0.575 0.755 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co"># C 1.350 1.400 1.700 1.720 1.890 2.150 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co"># D 0.416 0.550 0.589 0.603 0.632 0.750 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co"># E 0.400 0.480 0.559 0.541 0.667 0.737 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co"># F 0.346 0.384 0.493 0.498 0.628 0.643 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co"># G 0.393 0.421 0.486 0.430 0.570 0.620 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co"># H 0.258 0.280 0.332 0.290 0.377 0.508 10</span></a></code></pre></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> too, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
</div>
<div id="results-in-other-languages" class="section level3">
@ -351,13 +358,13 @@
<a class="sourceLine" id="cb8-18" title="18"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
<a class="sourceLine" id="cb8-19" title="19"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb8-20" title="20"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb8-21" title="21"><span class="co"># en 18.16 18.23 22.82 18.29 18.57 63.28 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co"># de 23.00 23.09 23.35 23.21 23.59 23.96 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co"># nl 36.60 36.74 37.00 36.97 37.32 37.41 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co"># es 23.10 23.15 23.40 23.29 23.63 23.97 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co"># it 23.04 23.14 23.28 23.27 23.43 23.58 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co"># fr 23.13 23.21 33.12 23.90 28.96 68.96 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co"># pt 22.98 23.16 23.37 23.44 23.51 23.65 10</span></a></code></pre></div>
<a class="sourceLine" id="cb8-21" title="21"><span class="co"># en 18.10 18.20 18.30 18.25 18.38 18.57 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co"># de 23.06 23.14 32.22 23.21 23.48 68.37 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co"># nl 36.30 36.40 41.09 36.59 36.85 81.13 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co"># es 22.85 23.07 23.24 23.20 23.46 23.72 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co"># it 22.92 22.99 27.72 23.17 23.61 68.07 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co"># fr 23.02 23.14 27.79 23.23 23.58 68.27 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co"># pt 23.00 23.09 23.24 23.19 23.45 23.52 10</span></a></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
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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">0.6.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9035</span>
</span>
</div>
@ -76,6 +76,13 @@
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
@ -192,7 +199,7 @@
<h1>How to create frequency tables</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">17 May 2019</h4>
<h4 class="date">23 May 2019</h4>
<div class="hidden name"><code>freq.Rmd</code></div>
@ -714,7 +721,7 @@ Median: 31 July 2009 (47.39%)</p>
<div id="assigning-a-frequency-table-to-an-object" class="section level2">
<h2 class="hasAnchor">
<a href="#assigning-a-frequency-table-to-an-object" class="anchor"></a>Assigning a frequency table to an object</h2>
<p>A frequency table is actaually a regular <code>data.frame</code>, with the exception that it contains an additional class.</p>
<p>A frequency table is actually a regular <code>data.frame</code>, with the exception that it contains an additional class.</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1">my_df &lt;-<span class="st"> </span>septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age)</a>
<a class="sourceLine" id="cb11-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/class">class</a></span>(my_df)</a></code></pre></div>
<p>[1] “frequency_tbl” “data.frame”</p>
@ -729,7 +736,7 @@ Median: 31 July 2009 (47.39%)</p>
<h3 class="hasAnchor">
<a href="#parameter-na-rm" class="anchor"></a>Parameter <code>na.rm</code>
</h3>
<p>With the <code>na.rm</code> parameter (defaults to <code>TRUE</code>, but they will always be shown into the header), you can include <code>NA</code> values in the frequency table:</p>
<p>With the <code>na.rm</code> parameter you can remove <code>NA</code> values from the frequency table (defaults to <code>TRUE</code>, but the number of <code>NA</code> values will always be shown into the header):</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb13-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(AMX, <span class="dt">na.rm =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<p><strong>Frequency table of <code>AMX</code> from a <code>data.frame</code> (2,000 x 49)</strong></p>
@ -784,14 +791,68 @@ Group: Beta-lactams/penicillins<br>
</tr>
</tbody>
</table>
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb14-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(AMX, <span class="dt">na.rm =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<p><strong>Frequency table of <code>AMX</code> from a <code>data.frame</code> (2,000 x 49)</strong></p>
<p>Class: <code>factor</code> &gt; <code>ordered</code> &gt; <code>rsi</code> (<code>numeric</code>)<br>
Length: 2,000 (of which NA: 771 = 38.55%)<br>
Levels: 3: <code>S</code> &lt; <code>I</code> &lt; <code>R</code><br>
Unique: 4</p>
<p>Drug: Amoxicillin (AMX, J01CA04)<br>
Group: Beta-lactams/penicillins<br>
%SI: 44.43%</p>
<table class="table">
<thead><tr class="header">
<th align="left"></th>
<th align="left">Item</th>
<th align="right">Count</th>
<th align="right">Percent</th>
<th align="right">Cum. Count</th>
<th align="right">Cum. Percent</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="left">(NA)</td>
<td align="right">771</td>
<td align="right">38.6%</td>
<td align="right">771</td>
<td align="right">38.6%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">R</td>
<td align="right">683</td>
<td align="right">34.2%</td>
<td align="right">1,454</td>
<td align="right">72.7%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">S</td>
<td align="right">543</td>
<td align="right">27.2%</td>
<td align="right">1,997</td>
<td align="right">99.8%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">I</td>
<td align="right">3</td>
<td align="right">0.2%</td>
<td align="right">2,000</td>
<td align="right">100.0%</td>
</tr>
</tbody>
</table>
</div>
<div id="parameter-row-names" class="section level3">
<h3 class="hasAnchor">
<a href="#parameter-row-names" class="anchor"></a>Parameter <code>row.names</code>
</h3>
<p>The default frequency tables shows row indices. To remove them, use <code>row.names = FALSE</code>:</p>
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb14-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id, <span class="dt">row.names =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<p>A frequency table shows row indices. To remove them, use <code>row.names = FALSE</code>:</p>
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb15-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id, <span class="dt">row.names =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<p><strong>Frequency table of <code>hospital_id</code> from a <code>data.frame</code> (2,000 x 49)</strong></p>
<p>Class: <code>factor</code> (<code>numeric</code>)<br>
Length: 2,000 (of which NA: 0 = 0.00%)<br>
@ -842,8 +903,8 @@ Unique: 4</p>
<a href="#parameter-markdown" class="anchor"></a>Parameter <code>markdown</code>
</h3>
<p>The <code>markdown</code> parameter is <code>TRUE</code> at default in non-interactive sessions, like in reports created with R Markdown. This will always print all rows, unless <code>nmax</code> is set.</p>
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb15-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id, <span class="dt">markdown =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb16-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id, <span class="dt">markdown =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
<p><strong>Frequency table of <code>hospital_id</code> from a <code>data.frame</code> (2,000 x 49)</strong></p>
<p>Class: <code>factor</code> (<code>numeric</code>)<br>
Length: 2,000 (of which NA: 0 = 0.00%)<br>

10
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@ -78,7 +78,7 @@
</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">0.6.1.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9035</span>
</span>
</div>
@ -114,6 +114,13 @@
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
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@ -239,6 +246,7 @@
<li><a href="AMR.html">How to conduct AMR analysis</a></li>
<li><a href="EUCAST.html">How to apply EUCAST rules</a></li>
<li><a href="G_test.html">How to use the *G*-test</a></li>
<li><a href="MDR.html">How to determine multi-drug resistance (MDR)</a></li>
<li><a href="SPSS.html">How to import data from SPSS / SAS / Stata</a></li>
<li><a href="WHONET.html">How to work with WHONET data</a></li>
<li><a href="ab_property.html">How to get properties of an antibiotic</a></li>

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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">0.6.1.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9035</span>
</span>
</div>
@ -76,6 +76,13 @@
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
@ -192,7 +199,7 @@
<h1>How to get properties of a microorganism</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">20 May 2019</h4>
<h4 class="date">23 May 2019</h4>
<div class="hidden name"><code>mo_property.Rmd</code></div>

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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">0.6.1.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9035</span>
</span>
</div>
@ -76,6 +76,13 @@
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
@ -192,7 +199,7 @@
<h1>How to predict antimicrobial resistance</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">20 May 2019</h4>
<h4 class="date">23 May 2019</h4>
<div class="hidden name"><code>resistance_predict.Rmd</code></div>