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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>
@ -193,7 +193,7 @@
<h1 data-toc-skip>How to conduct AMR data analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">26 May 2021</h4>
<h4 class="date">03 June 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd"><code>vignettes/AMR.Rmd</code></a></small>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -202,7 +202,7 @@
<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 26 May 2021.</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 03 June 2021.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -233,21 +233,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2021-05-26</td>
<td align="center">2021-06-03</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">2021-05-26</td>
<td align="center">2021-06-03</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">2021-05-26</td>
<td align="center">2021-06-03</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -344,52 +344,52 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-04-02</td>
<td align="center">X1</td>
<td align="center">Hospital D</td>
<td align="center">2014-11-23</td>
<td align="center">A2</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-07-17</td>
<td align="center">X6</td>
<td align="center">Hospital A</td>
<td align="center">2013-08-17</td>
<td align="center">V3</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2012-09-03</td>
<td align="center">C4</td>
<td align="center">2011-02-20</td>
<td align="center">B1</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-02-11</td>
<td align="center">D2</td>
<td align="center">Hospital B</td>
<td align="center">2016-10-04</td>
<td align="center">U3</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2012-12-14</td>
<td align="center">L5</td>
<td align="center">2010-04-22</td>
<td align="center">F1</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
@ -399,12 +399,12 @@
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-01-30</td>
<td align="center">S3</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">2013-01-15</td>
<td align="center">W4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
@ -441,16 +441,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,375</td>
<td align="right">51.88%</td>
<td align="right">10,375</td>
<td align="right">51.88%</td>
<td align="right">10,416</td>
<td align="right">52.08%</td>
<td align="right">10,416</td>
<td align="right">52.08%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,625</td>
<td align="right">48.13%</td>
<td align="right">9,584</td>
<td align="right">47.92%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -505,9 +505,9 @@ Longest: 1</p>
<span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span>
<span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span>
<span class="co"># 2</span>
<span class="co"># =&gt; Found 10,550 first weighted isolates (phenotype-based, 52.8% of total</span>
<span class="co"># =&gt; Found 10,645 first weighted isolates (phenotype-based, 53.2% of total</span>
<span class="co"># where a microbial ID was available)</span></code></pre></div>
<p>So only 52.8% 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>
<p>So only 53.2% 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="cb15"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
@ -515,7 +515,7 @@ Longest: 1</p>
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
<p>So we end up with 10,550 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,645 isolates for analysis. Now our data looks like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></code></pre></div>
<table class="table">
@ -553,89 +553,25 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2013-04-02</td>
<td align="center">X1</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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="left">2</td>
<td align="center">2015-07-17</td>
<td align="center">X6</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</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>
<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="left">4</td>
<td align="center">2010-02-11</td>
<td align="center">D2</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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="left">6</td>
<td align="center">2016-01-30</td>
<td align="center">S3</td>
<td align="center">2013-08-17</td>
<td align="center">V3</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2012-10-20</td>
<td align="center">D10</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2016-03-28</td>
<td align="center">K7</td>
<td align="left">3</td>
<td align="center">2011-02-20</td>
<td align="center">B1</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
@ -648,6 +584,70 @@ Longest: 1</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="center">2010-04-22</td>
<td align="center">F1</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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="left">7</td>
<td align="center">2014-07-28</td>
<td align="center">W5</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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="left">8</td>
<td align="center">2015-01-06</td>
<td align="center">V3</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</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="left">9</td>
<td align="center">2014-03-16</td>
<td align="center">H4</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</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-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -669,8 +669,8 @@ Longest: 1</p>
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,550<br>
Available: 10,550 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,645<br>
Available: 10,645 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -687,33 +687,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,566</td>
<td align="right">43.28%</td>
<td align="right">4,566</td>
<td align="right">43.28%</td>
<td align="right">4,652</td>
<td align="right">43.70%</td>
<td align="right">4,652</td>
<td align="right">43.70%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,786</td>
<td align="right">26.41%</td>
<td align="right">7,352</td>
<td align="right">69.69%</td>
<td align="right">2,744</td>
<td align="right">25.78%</td>
<td align="right">7,396</td>
<td align="right">69.48%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,025</td>
<td align="right">19.19%</td>
<td align="right">9,377</td>
<td align="right">88.88%</td>
<td align="right">2,052</td>
<td align="right">19.28%</td>
<td align="right">9,448</td>
<td align="right">88.76%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,173</td>
<td align="right">11.12%</td>
<td align="right">10,550</td>
<td align="right">1,197</td>
<td align="right">11.24%</td>
<td align="right">10,645</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -760,8 +760,8 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-03-28</td>
<td align="center">K7</td>
<td align="center">2011-02-20</td>
<td align="center">B1</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
@ -775,44 +775,14 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2010-01-30</td>
<td align="center">A1</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-12-10</td>
<td align="center">M7</td>
<td align="center">2015-01-06</td>
<td align="center">V3</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</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">2012-08-04</td>
<td align="center">Y7</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
@ -820,13 +790,28 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-08-05</td>
<td align="center">I4</td>
<td align="center">Hospital A</td>
<td align="center">2012-05-03</td>
<td align="center">B2</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-03-18</td>
<td align="center">K10</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
@ -834,14 +819,14 @@ Longest: 24</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-05-15</td>
<td align="center">H2</td>
<td align="center">Hospital A</td>
<tr class="odd">
<td align="center">2010-12-15</td>
<td align="center">H3</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -849,6 +834,21 @@ Longest: 24</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-08-10</td>
<td align="center">N2</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</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>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> function:</p>
@ -870,50 +870,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2148</td>
<td align="center">153</td>
<td align="center">2265</td>
<td align="center">4566</td>
<td align="center">2232</td>
<td align="center">119</td>
<td align="center">2301</td>
<td align="center">4652</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3344</td>
<td align="center">157</td>
<td align="center">1065</td>
<td align="center">4566</td>
<td align="center">3424</td>
<td align="center">165</td>
<td align="center">1063</td>
<td align="center">4652</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3356</td>
<td align="center">3386</td>
<td align="center">0</td>
<td align="center">1210</td>
<td align="center">4566</td>
<td align="center">1266</td>
<td align="center">4652</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">3983</td>
<td align="center">4062</td>
<td align="center">0</td>
<td align="center">583</td>
<td align="center">4566</td>
<td align="center">590</td>
<td align="center">4652</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1173</td>
<td align="center">1173</td>
<td align="center">1197</td>
<td align="center">1197</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">930</td>
<td align="center">43</td>
<td align="center">200</td>
<td align="center">1173</td>
<td align="center">932</td>
<td align="center">60</td>
<td align="center">205</td>
<td align="center">1197</td>
</tr>
</tbody>
</table>
@ -936,34 +936,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">3983</td>
<td align="center">4062</td>
<td align="center">0</td>
<td align="center">583</td>
<td align="center">4566</td>
<td align="center">590</td>
<td align="center">4652</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1063</td>
<td align="center">1069</td>
<td align="center">0</td>
<td align="center">110</td>
<td align="center">1173</td>
<td align="center">128</td>
<td align="center">1197</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2490</td>
<td align="center">2444</td>
<td align="center">0</td>
<td align="center">296</td>
<td align="center">2786</td>
<td align="center">300</td>
<td align="center">2744</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">2025</td>
<td align="center">2025</td>
<td align="center">2052</td>
<td align="center">2052</td>
</tr>
</tbody>
</table>
@ -977,7 +977,7 @@ Longest: 24</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>
<span class="co"># [1] 0.5443602</span></code></pre></div>
<span class="co"># [1] 0.5431658</span></code></pre></div>
<p>Or can be used in conjunction 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="cb27"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span>
@ -991,19 +991,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5542598</td>
<td align="center">0.5461634</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5400160</td>
<td align="center">0.5394702</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5508217</td>
<td align="center">0.5609756</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5322972</td>
<td align="center">0.5316215</td>
</tr>
</tbody>
</table>
@ -1022,23 +1022,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5542598</td>
<td align="center">3087</td>
<td align="center">0.5461634</td>
<td align="center">3206</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5400160</td>
<td align="center">3761</td>
<td align="center">0.5394702</td>
<td align="center">3737</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5508217</td>
<td align="center">1643</td>
<td align="center">0.5609756</td>
<td align="center">1599</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5322972</td>
<td align="center">2059</td>
<td align="center">0.5316215</td>
<td align="center">2103</td>
</tr>
</tbody>
</table>
@ -1059,27 +1059,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7667543</td>
<td align="center">0.8723171</td>
<td align="center">0.9770039</td>
<td align="center">0.7714961</td>
<td align="center">0.8731728</td>
<td align="center">0.9776440</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8294970</td>
<td align="center">0.9062234</td>
<td align="center">0.9795396</td>
<td align="center">0.8287385</td>
<td align="center">0.8930660</td>
<td align="center">0.9824561</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7910983</td>
<td align="center">0.8937545</td>
<td align="center">0.9852836</td>
<td align="center">0.7882653</td>
<td align="center">0.8906706</td>
<td align="center">0.9839650</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5387654</td>
<td align="center">0.5414230</td>
<td align="center">0.0000000</td>
<td align="center">0.5387654</td>
<td align="center">0.5414230</td>
</tr>
</tbody>
</table>
@ -1163,16 +1163,16 @@ Longest: 24</p>
<code class="sourceCode R"><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
<span class="va">mic_values</span>
<span class="co"># Class &lt;mic&gt;</span>
<span class="co"># [1] 2 2 16 4 0.125 0.5 64 16 128 32 </span>
<span class="co"># [11] 4 32 1 0.125 128 2 8 64 64 2 </span>
<span class="co"># [21] 8 0.125 0.25 1 16 64 0.25 0.5 0.25 4 </span>
<span class="co"># [31] 16 32 0.25 1 0.5 8 64 2 0.25 0.0625</span>
<span class="co"># [41] 128 1 2 2 0.0625 0.125 64 8 8 8 </span>
<span class="co"># [51] 4 8 0.125 1 128 1 128 2 2 0.5 </span>
<span class="co"># [61] 32 64 16 32 32 16 4 1 16 2 </span>
<span class="co"># [71] 1 0.125 2 4 0.125 32 2 0.125 8 0.25 </span>
<span class="co"># [81] 0.0625 4 0.5 16 128 8 128 0.125 0.0625 1 </span>
<span class="co"># [91] 1 0.25 0.0625 128 128 8 0.0625 32 128 0.25</span></code></pre></div>
<span class="co"># [1] 4 4 0.25 &gt;=512 0.0625 2 128 2 64 1 </span>
<span class="co"># [11] 64 256 32 2 2 256 0.125 128 16 32 </span>
<span class="co"># [21] 1 2 0.0625 32 16 16 0.0625 0.125 0.0625 2 </span>
<span class="co"># [31] 128 8 0.0625 0.25 4 16 1 0.0625 1 16 </span>
<span class="co"># [41] 4 0.0625 2 4 0.0625 256 16 0.5 1 1 </span>
<span class="co"># [51] 16 64 &gt;=512 64 64 1 4 0.5 16 1 </span>
<span class="co"># [61] 16 256 8 256 256 &gt;=512 8 0.5 2 2 </span>
<span class="co"># [71] &gt;=512 8 64 4 8 0.25 2 4 16 0.125 </span>
<span class="co"># [81] 0.25 4 0.125 8 0.125 0.0625 &gt;=512 0.125 64 1 </span>
<span class="co"># [91] 16 2 0.5 16 0.0625 128 2 0.0625 128 2</span></code></pre></div>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># base R:</span>
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></code></pre></div>
@ -1201,10 +1201,10 @@ Longest: 24</p>
<span class="co"># to review it.</span>
<span class="va">disk_values</span>
<span class="co"># Class &lt;disk&gt;</span>
<span class="co"># [1] 31 27 25 19 19 17 23 24 30 28 22 26 18 29 25 24 22 30 17 20 23 24 26 24 27</span>
<span class="co"># [26] 22 27 22 17 26 22 31 27 31 31 25 21 18 26 22 21 25 21 26 22 21 20 20 24 19</span>
<span class="co"># [51] 25 17 29 26 28 30 30 29 30 28 19 28 22 21 26 25 24 23 21 18 27 20 17 29 30</span>
<span class="co"># [76] 17 25 19 30 22 26 22 31 18 19 26 20 18 23 17 30 30 22 21 25 21 17 30 30 24</span></code></pre></div>
<span class="co"># [1] 27 28 23 21 23 21 28 31 26 17 23 23 24 29 20 18 27 24 26 24 27 23 30 18 26</span>
<span class="co"># [26] 31 19 26 21 27 29 29 19 19 31 25 23 19 26 21 21 20 23 29 22 18 27 28 21 27</span>
<span class="co"># [51] 21 18 19 28 26 26 29 20 31 28 30 30 21 21 25 29 28 29 30 25 27 19 23 26 24</span>
<span class="co"># [76] 20 21 25 19 26 22 19 30 28 27 18 19 18 25 31 20 19 29 31 31 29 22 20 17 31</span></code></pre></div>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># base R:</span>
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></code></pre></div>

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2
docs/articles/EUCAST.html
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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

58
docs/articles/MDR.html
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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>
@ -339,19 +339,19 @@ Unique: 2</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
<span class="co"># 1 I I I I S S</span>
<span class="co"># 2 R I S I I I</span>
<span class="co"># 3 S R R R R I</span>
<span class="co"># 4 S R S S R S</span>
<span class="co"># 5 R S I R S R</span>
<span class="co"># 6 R R R R I I</span>
<span class="co"># 1 S I R R R S</span>
<span class="co"># 2 I R R R R R</span>
<span class="co"># 3 S S S R I R</span>
<span class="co"># 4 R I R R S S</span>
<span class="co"># 5 I R S S R I</span>
<span class="co"># 6 I S S R R R</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 I</span>
<span class="co"># 2 I</span>
<span class="co"># 3 S</span>
<span class="co"># 2 R</span>
<span class="co"># 3 R</span>
<span class="co"># 4 R</span>
<span class="co"># 5 I</span>
<span class="co"># 6 I</span></code></pre></div>
<span class="co"># 5 S</span>
<span class="co"># 6 S</span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></code></pre></div>
@ -382,40 +382,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3271</td>
<td align="right">65.42%</td>
<td align="right">3271</td>
<td align="right">65.42%</td>
<td align="right">3187</td>
<td align="right">63.74%</td>
<td align="right">3187</td>
<td align="right">63.74%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">949</td>
<td align="right">18.98%</td>
<td align="right">4220</td>
<td align="right">84.40%</td>
<td align="right">1027</td>
<td align="right">20.54%</td>
<td align="right">4214</td>
<td align="right">84.28%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">449</td>
<td align="right">8.98%</td>
<td align="right">4669</td>
<td align="right">93.38%</td>
<td align="right">430</td>
<td align="right">8.60%</td>
<td align="right">4644</td>
<td align="right">92.88%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">240</td>
<td align="right">4.80%</td>
<td align="right">4909</td>
<td align="right">98.18%</td>
<td align="right">245</td>
<td align="right">4.90%</td>
<td align="right">4889</td>
<td align="right">97.78%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">91</td>
<td align="right">1.82%</td>
<td align="right">111</td>
<td align="right">2.22%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
docs/articles/PCA.html
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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

6
docs/articles/SPSS.html
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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>
@ -193,7 +193,7 @@
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">26 May 2021</h4>
<h4 class="date">03 June 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="hidden name"><code>SPSS.Rmd</code></div>
@ -228,7 +228,7 @@
</li>
<li>
<p><strong>R has a huge community.</strong></p>
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes">403,383 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes">404,559 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
</li>
<li>
<p><strong>R understands any data type, including SPSS/SAS/Stata.</strong></p>

2
docs/articles/WHONET.html
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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

78
docs/articles/benchmarks.html
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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>
@ -227,18 +227,18 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 10.0 11.0 16.0 11.0 13.0 50 25</span>
<span class="co"># as.mo("stau") 54.0 58.0 72.0 61.0 89.0 99 25</span>
<span class="co"># as.mo("STAU") 53.0 55.0 67.0 56.0 91.0 95 25</span>
<span class="co"># as.mo("staaur") 10.0 11.0 16.0 11.0 13.0 47 25</span>
<span class="co"># as.mo("STAAUR") 10.0 11.0 17.0 12.0 13.0 58 25</span>
<span class="co"># as.mo("S. aureus") 26.0 27.0 36.0 31.0 33.0 70 25</span>
<span class="co"># as.mo("S aureus") 26.0 27.0 40.0 29.0 61.0 68 25</span>
<span class="co"># as.mo("Staphylococcus aureus") 2.6 3.2 6.5 3.5 3.8 42 25</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 240.0 250.0 260.0 260.0 270.0 290 25</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 190.0 190.0 200.0 200.0 210.0 300 25</span>
<span class="co"># as.mo("MRSA") 10.0 11.0 13.0 12.0 13.0 40 25</span>
<span class="co"># as.mo("VISA") 18.0 19.0 32.0 20.0 24.0 130 25</span></code></pre></div>
<span class="co"># as.mo("sau") 13.0 13.0 16.0 15.0 16.0 44 25</span>
<span class="co"># as.mo("stau") 55.0 58.0 75.0 62.0 94.0 110 25</span>
<span class="co"># as.mo("STAU") 55.0 59.0 77.0 89.0 94.0 100 25</span>
<span class="co"># as.mo("staaur") 11.0 13.0 20.0 14.0 16.0 48 25</span>
<span class="co"># as.mo("STAAUR") 11.0 13.0 17.0 15.0 16.0 49 25</span>
<span class="co"># as.mo("S. aureus") 26.0 30.0 41.0 32.0 60.0 68 25</span>
<span class="co"># as.mo("S aureus") 27.0 29.0 44.0 32.0 58.0 160 25</span>
<span class="co"># as.mo("Staphylococcus aureus") 3.3 3.9 5.5 4.2 4.7 37 25</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 250.0 260.0 280.0 280.0 290.0 320 25</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 170.0 200.0 210.0 200.0 220.0 250 25</span>
<span class="co"># as.mo("MRSA") 12.0 14.0 21.0 15.0 17.0 56 25</span>
<span class="co"># as.mo("VISA") 20.0 23.0 33.0 25.0 51.0 59 25</span></code></pre></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="750"></p>
<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 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 200 times slower to determine.</p>
<p>To improve performance, we implemented two important algorithms to save unnecessary calculations: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
@ -260,8 +260,8 @@
<span class="co"># what do these values look like? They are of class &lt;mo&gt;:</span>
<span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
<span class="co"># Class &lt;mo&gt;</span>
<span class="co"># [1] B_STPHY_EPDR B_STRPT_GRPA B_STPHY_AURS B_BCTRD_FRGL B_STPHY_HMNS</span>
<span class="co"># [6] B_STPHY_CONS</span>
<span class="co"># [1] B_STPHY_CONS B_ESCHR_COLI B_STPHY_AURS B_STRPT_PYGN B_ESCHR_COLI</span>
<span class="co"># [6] B_HMPHL_INFL</span>
<span class="co"># as the example_isolates data set has 2,000 rows, we should have 2 million items</span>
<span class="fu"><a href="https://rdrr.io/r/base/length.html">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
@ -277,8 +277,8 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># mo_name(x) 187 223 233 226 229 318 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.226 seconds. That is 113 nanoseconds on average. You only lose time on your unique input values.</p>
<span class="co"># mo_name(x) 165 238 258 246 253 369 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.246 seconds. That is 123 nanoseconds on average. You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -291,11 +291,11 @@
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 7.28 7.59 8.01 8.03 8.45 8.66 10</span>
<span class="co"># B 23.00 24.10 30.30 25.50 27.30 75.30 10</span>
<span class="co"># C 1.55 1.74 7.31 1.95 2.01 56.10 10</span></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0019 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>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 8.20 8.33 13.30 8.53 9.71 53.2 10</span>
<span class="co"># B 22.80 23.50 29.20 24.60 26.80 69.3 10</span>
<span class="co"># C 1.82 2.04 2.25 2.16 2.38 2.9 10</span></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0022 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="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"Staphylococcus"</span><span class="op">)</span>,
@ -308,15 +308,15 @@
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 1.42 1.45 1.56 1.50 1.57 2.00 10</span>
<span class="co"># B 1.43 1.46 1.49 1.47 1.55 1.59 10</span>
<span class="co"># C 1.41 1.43 1.58 1.49 1.57 2.19 10</span>
<span class="co"># D 1.41 1.48 1.61 1.54 1.63 2.33 10</span>
<span class="co"># E 1.41 1.45 1.64 1.51 1.56 2.68 10</span>
<span class="co"># F 1.42 1.52 1.63 1.57 1.71 1.99 10</span>
<span class="co"># G 1.41 1.46 1.65 1.56 1.90 1.98 10</span>
<span class="co"># H 1.42 1.46 1.59 1.55 1.70 1.88 10</span></code></pre></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 1.66 1.70 1.86 1.77 1.90 2.41 10</span>
<span class="co"># B 1.61 1.71 1.99 1.84 2.37 2.56 10</span>
<span class="co"># C 1.64 1.72 1.79 1.74 1.77 2.14 10</span>
<span class="co"># D 1.68 1.71 2.06 2.06 2.23 2.77 10</span>
<span class="co"># E 1.63 1.71 1.85 1.75 1.92 2.43 10</span>
<span class="co"># F 1.61 1.67 1.80 1.75 1.86 2.22 10</span>
<span class="co"># G 1.63 1.67 4.37 1.96 2.58 25.70 10</span>
<span class="co"># H 1.67 1.73 1.88 1.83 2.01 2.28 10</span></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> anyway, there is no point in calculating the result. And because this package contains all phyla of all known bacteria, it can just return the initial value immediately.</p>
</div>
<div id="results-in-other-languages" class="section level3">
@ -343,14 +343,14 @@
times <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 17.81 18.24 21.93 18.78 19.44 60.56 100</span>
<span class="co"># de 28.82 29.53 37.92 30.33 32.62 81.75 100</span>
<span class="co"># nl 32.65 33.61 44.22 34.43 37.44 193.90 100</span>
<span class="co"># es 32.51 32.95 41.88 33.70 36.39 80.63 100</span>
<span class="co"># it 22.00 22.57 27.98 23.15 25.14 67.04 100</span>
<span class="co"># fr 21.71 22.22 27.20 22.83 24.41 66.08 100</span>
<span class="co"># pt 21.71 22.54 26.97 23.06 23.94 67.41 100</span></code></pre></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 19.99 20.43 25.64 21.15 22.38 82.52 100</span>
<span class="co"># de 31.03 31.96 38.34 32.88 35.27 82.31 100</span>
<span class="co"># nl 35.25 36.19 43.25 37.63 39.66 85.19 100</span>
<span class="co"># es 35.01 35.85 40.89 36.91 38.58 83.68 100</span>
<span class="co"># it 24.35 24.90 30.43 25.81 28.03 78.90 100</span>
<span class="co"># fr 23.87 25.02 31.72 26.03 27.46 83.88 100</span>
<span class="co"># pt 24.00 24.99 31.16 26.05 28.06 80.74 100</span></code></pre></div>
<p>Currently supported non-English languages are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>
@ -192,7 +192,7 @@
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 class="date">01 June 2021</h4>
<h4 class="date">03 June 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
<div class="hidden name"><code>datasets.Rmd</code></div>
@ -1007,7 +1007,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<a href="#interpretation-from-mic-values-disk-diameters-to-rsi" class="anchor"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
<p>A data set with 21,996 rows and 10 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 1 June 2021 14:31:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p>It was last updated on 1 June 2021 14:47:11 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds">R file</a> (37 kB)<br>

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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="Latest development version">1.7.0.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
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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="Latest development version">1.7.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</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="Latest development version">1.7.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>