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@ -12,7 +12,7 @@
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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">1.4.0.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
</span>
</div>
@ -193,7 +193,7 @@
<h1 data-toc-skip>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">24 December 2020</h4>
<h4 class="date">26 December 2020</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 24 December 2020.</p>
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 26 December 2020.</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">2020-12-24</td>
<td align="center">2020-12-26</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2020-12-24</td>
<td align="center">2020-12-26</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2020-12-24</td>
<td align="center">2020-12-26</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -352,31 +352,9 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-10-07</td>
<td align="center">D7</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">M</td>
</tr>
<tr class="even">
<td align="center">2016-11-19</td>
<td align="center">V9</td>
<td align="center">2011-10-28</td>
<td align="center">I1</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-03-30</td>
<td align="center">D9</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
@ -385,38 +363,60 @@
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-06-28</td>
<td align="center">Z4</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-03-04</td>
<td align="center">M4</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-08-18</td>
<td align="center">D2</td>
<td align="center">Hospital B</td>
<td align="center">2011-06-05</td>
<td align="center">G5</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2014-05-12</td>
<td align="center">X7</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-02-23</td>
<td align="center">K5</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2017-09-20</td>
<td align="center">T5</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">F</td>
</tr>
<tr class="even">
<td align="center">2017-02-10</td>
<td align="center">Y6</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -449,16 +449,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,392</td>
<td align="right">51.96%</td>
<td align="right">10,392</td>
<td align="right">51.96%</td>
<td align="right">10,426</td>
<td align="right">52.13%</td>
<td align="right">10,426</td>
<td align="right">52.13%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,608</td>
<td align="right">48.04%</td>
<td align="right">9,574</td>
<td align="right">47.87%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -515,7 +515,7 @@ Longest: 1</p>
<div id="first-weighted-isolates" class="section level2">
<h2 class="hasAnchor">
<a href="#first-weighted-isolates" class="anchor"></a>First <em>weighted</em> isolates</h2>
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient M9, sorted on date:</p>
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient F3, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -531,19 +531,19 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-25</td>
<td align="center">M9</td>
<td align="center">2010-01-17</td>
<td align="center">F3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-02-01</td>
<td align="center">M9</td>
<td align="center">2010-03-13</td>
<td align="center">F3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -553,21 +553,21 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-02-22</td>
<td align="center">M9</td>
<td align="center">2010-04-21</td>
<td align="center">F3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-08-12</td>
<td align="center">M9</td>
<td align="center">2010-06-24</td>
<td align="center">F3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -575,19 +575,19 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-08-17</td>
<td align="center">M9</td>
<td align="center">2010-08-02</td>
<td align="center">F3</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">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-09-18</td>
<td align="center">M9</td>
<td align="center">2010-08-14</td>
<td align="center">F3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -597,19 +597,19 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-07-05</td>
<td align="center">M9</td>
<td align="center">2010-10-06</td>
<td align="center">F3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-07-19</td>
<td align="center">M9</td>
<td align="center">2010-10-17</td>
<td align="center">F3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
@ -619,19 +619,8 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-07-20</td>
<td align="center">M9</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-09-04</td>
<td align="center">M9</td>
<td align="center">2010-11-17</td>
<td align="center">F3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
@ -639,6 +628,17 @@ Longest: 1</p>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-02-21</td>
<td align="center">F3</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">R</td>
<td align="center">TRUE</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>
@ -665,20 +665,20 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-25</td>
<td align="center">M9</td>
<td align="center">2010-01-17</td>
<td align="center">F3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-02-01</td>
<td align="center">M9</td>
<td align="center">2010-03-13</td>
<td align="center">F3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -689,68 +689,68 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-02-22</td>
<td align="center">M9</td>
<td align="center">2010-04-21</td>
<td align="center">F3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-08-12</td>
<td align="center">M9</td>
<td align="center">2010-06-24</td>
<td align="center">F3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-08-17</td>
<td align="center">M9</td>
<td align="center">2010-08-02</td>
<td align="center">F3</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">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-09-18</td>
<td align="center">M9</td>
<td align="center">2010-08-14</td>
<td align="center">F3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-07-05</td>
<td align="center">M9</td>
<td align="center">2010-10-06</td>
<td align="center">F3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</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">8</td>
<td align="center">2011-07-19</td>
<td align="center">M9</td>
<td align="center">2010-10-17</td>
<td align="center">F3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
@ -761,36 +761,36 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-07-20</td>
<td align="center">M9</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-09-04</td>
<td align="center">M9</td>
<td align="center">2010-11-17</td>
<td align="center">F3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-02-21</td>
<td align="center">F3</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">R</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Instead of 2, now 8 isolates are flagged. In total, 78.4% of all isolates are marked ‘first weighted’ - 50.0% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>Instead of 2, now 6 isolates are flagged. In total, 78.5% of all isolates are marked ‘first weighted’ - 50.1% 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="cb19"><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_weighted_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
<p>So we end up with 15,683 isolates for analysis.</p>
<p>So we end up with 15,695 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data_1st</span> <span class="op">%&gt;%</span>
@ -834,13 +834,29 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2012-10-07</td>
<td align="center">D7</td>
<td align="center">Hospital B</td>
<td align="center">2011-10-28</td>
<td align="center">I1</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2011-06-05</td>
<td align="center">G5</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
@ -848,63 +864,15 @@ Longest: 1</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2016-11-19</td>
<td align="center">V9</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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">3</td>
<td align="center">2015-03-30</td>
<td align="center">D9</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">2014-03-04</td>
<td align="center">M4</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2011-02-08</td>
<td align="center">S3</td>
<td align="center">2014-05-12</td>
<td align="center">X7</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@ -913,16 +881,48 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2015-12-31</td>
<td align="center">I5</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="left">4</td>
<td align="center">2011-02-23</td>
<td align="center">K5</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="center">2017-09-20</td>
<td align="center">T5</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2017-12-17</td>
<td align="center">Z3</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
@ -949,8 +949,8 @@ 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: 15,683<br>
Available: 15,683 (100%, NA: 0 = 0%)<br>
Length: 15,695<br>
Available: 15,695 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -967,33 +967,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,815</td>
<td align="right">49.83%</td>
<td align="right">7,815</td>
<td align="right">49.83%</td>
<td align="right">7,828</td>
<td align="right">49.88%</td>
<td align="right">7,828</td>
<td align="right">49.88%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">4,001</td>
<td align="right">25.51%</td>
<td align="right">11,816</td>
<td align="right">75.34%</td>
<td align="right">3,977</td>
<td align="right">25.34%</td>
<td align="right">11,805</td>
<td align="right">75.22%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,330</td>
<td align="right">14.86%</td>
<td align="right">14,146</td>
<td align="right">90.20%</td>
<td align="right">2,320</td>
<td align="right">14.78%</td>
<td align="right">14,125</td>
<td align="right">90.00%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,537</td>
<td align="right">9.80%</td>
<td align="right">15,683</td>
<td align="right">1,570</td>
<td align="right">10.00%</td>
<td align="right">15,695</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -1020,50 +1020,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">3744</td>
<td align="center">257</td>
<td align="center">3814</td>
<td align="center">7815</td>
<td align="center">3731</td>
<td align="center">275</td>
<td align="center">3822</td>
<td align="center">7828</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">6185</td>
<td align="center">294</td>
<td align="center">1336</td>
<td align="center">7815</td>
<td align="center">6146</td>
<td align="center">297</td>
<td align="center">1385</td>
<td align="center">7828</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">5934</td>
<td align="center">5918</td>
<td align="center">0</td>
<td align="center">1881</td>
<td align="center">7815</td>
<td align="center">1910</td>
<td align="center">7828</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">7005</td>
<td align="center">7087</td>
<td align="center">0</td>
<td align="center">810</td>
<td align="center">7815</td>
<td align="center">741</td>
<td align="center">7828</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">1537</td>
<td align="center">1537</td>
<td align="center">1570</td>
<td align="center">1570</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">1225</td>
<td align="center">45</td>
<td align="center">267</td>
<td align="center">1537</td>
<td align="center">1231</td>
<td align="center">57</td>
<td align="center">282</td>
<td align="center">1570</td>
</tr>
</tbody>
</table>
@ -1086,34 +1086,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">5934</td>
<td align="center">5918</td>
<td align="center">0</td>
<td align="center">1881</td>
<td align="center">7815</td>
<td align="center">1910</td>
<td align="center">7828</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">CIP</td>
<td align="center">1189</td>
<td align="center">1191</td>
<td align="center">0</td>
<td align="center">348</td>
<td align="center">1537</td>
<td align="center">379</td>
<td align="center">1570</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">CIP</td>
<td align="center">3064</td>
<td align="center">3045</td>
<td align="center">0</td>
<td align="center">937</td>
<td align="center">4001</td>
<td align="center">932</td>
<td align="center">3977</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">CIP</td>
<td align="center">1780</td>
<td align="center">1785</td>
<td align="center">0</td>
<td align="center">550</td>
<td align="center">2330</td>
<td align="center">535</td>
<td align="center">2320</td>
</tr>
</tbody>
</table>
@ -1126,7 +1126,7 @@ 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="cb27"><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] 0.5342728</span></code></pre></div>
<span class="co"># [1] 0.536604</span></code></pre></div>
<p>Or can be used in conjuction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span>
@ -1141,19 +1141,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5253802</td>
<td align="center">0.5429950</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5367779</td>
<td align="center">0.5429998</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5470814</td>
<td align="center">0.5283993</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5334627</td>
<td align="center">0.5222153</td>
</tr>
</tbody>
</table>
@ -1173,23 +1173,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5253802</td>
<td align="center">4669</td>
<td align="center">0.5429950</td>
<td align="center">4768</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5367779</td>
<td align="center">5574</td>
<td align="center">0.5429998</td>
<td align="center">5407</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5470814</td>
<td align="center">2347</td>
<td align="center">0.5283993</td>
<td align="center">2324</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5334627</td>
<td align="center">3093</td>
<td align="center">0.5222153</td>
<td align="center">3196</td>
</tr>
</tbody>
</table>
@ -1211,27 +1211,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.8290467</td>
<td align="center">0.8963532</td>
<td align="center">0.9843890</td>
<td align="center">0.8230710</td>
<td align="center">0.9053398</td>
<td align="center">0.9872253</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8262850</td>
<td align="center">0.9095641</td>
<td align="center">0.9837345</td>
<td align="center">0.8203822</td>
<td align="center">0.9076433</td>
<td align="center">0.9847134</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8307923</td>
<td align="center">0.9122719</td>
<td align="center">0.9872532</td>
<td align="center">0.8287654</td>
<td align="center">0.9192859</td>
<td align="center">0.9894393</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5351931</td>
<td align="center">0.5379310</td>
<td align="center">0.0000000</td>
<td align="center">0.5351931</td>
<td align="center">0.5379310</td>
</tr>
</tbody>
</table>

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@ -12,7 +12,7 @@
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
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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">1.4.0.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
</span>
</div>

58
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@ -12,7 +12,7 @@
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
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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">1.4.0.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
</span>
</div>
@ -311,17 +311,17 @@ Unique: 2</p>
<div class="sourceCode" id="cb5"><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 S S R I R S</span>
<span class="co"># 2 I S R I I R</span>
<span class="co"># 3 R R R S I R</span>
<span class="co"># 4 I I R R S S</span>
<span class="co"># 5 I R I S S R</span>
<span class="co"># 6 I R I I S I</span>
<span class="co"># 1 R I R S I S</span>
<span class="co"># 2 I S I S S R</span>
<span class="co"># 3 I I I R I R</span>
<span class="co"># 4 S S I S R I</span>
<span class="co"># 5 I R S R S R</span>
<span class="co"># 6 I I I R S I</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 R</span>
<span class="co"># 2 S</span>
<span class="co"># 1 S</span>
<span class="co"># 2 I</span>
<span class="co"># 3 I</span>
<span class="co"># 4 I</span>
<span class="co"># 4 S</span>
<span class="co"># 5 I</span>
<span class="co"># 6 R</span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
@ -354,40 +354,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3214</td>
<td align="right">64.28%</td>
<td align="right">3214</td>
<td align="right">64.28%</td>
<td align="right">3219</td>
<td align="right">64.38%</td>
<td align="right">3219</td>
<td align="right">64.38%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">997</td>
<td align="right">19.94%</td>
<td align="right">4211</td>
<td align="right">84.22%</td>
<td align="right">982</td>
<td align="right">19.64%</td>
<td align="right">4201</td>
<td align="right">84.02%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">442</td>
<td align="right">8.84%</td>
<td align="right">4653</td>
<td align="right">93.06%</td>
<td align="right">434</td>
<td align="right">8.68%</td>
<td align="right">4635</td>
<td align="right">92.70%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">239</td>
<td align="right">4.78%</td>
<td align="right">4892</td>
<td align="right">97.84%</td>
<td align="right">251</td>
<td align="right">5.02%</td>
<td align="right">4886</td>
<td align="right">97.72%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">108</td>
<td align="right">2.16%</td>
<td align="right">114</td>
<td align="right">2.28%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

4
docs/articles/PCA.html
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@ -12,7 +12,7 @@
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@ -39,7 +39,7 @@
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
</span>
</div>

6
docs/articles/SPSS.html
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@ -12,7 +12,7 @@
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<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
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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">1.4.0.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</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">24 December 2020</h4>
<h4 class="date">26 December 2020</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>

4
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@ -12,7 +12,7 @@
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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">1.4.0.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
</span>
</div>

90
docs/articles/benchmarks.html
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@ -12,7 +12,7 @@
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<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
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@ -39,7 +39,7 @@
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
</span>
</div>
@ -227,34 +227,20 @@
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">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</span>
<span class="co"># as.mo("sau") 9.9 12.0 15.0 13.0 13.0 42.0</span>
<span class="co"># as.mo("stau") 100.0 100.0 130.0 120.0 140.0 190.0</span>
<span class="co"># as.mo("STAU") 110.0 110.0 130.0 130.0 140.0 150.0</span>
<span class="co"># as.mo("staaur") 9.8 12.0 26.0 13.0 41.0 60.0</span>
<span class="co"># as.mo("STAAUR") 11.0 11.0 15.0 13.0 13.0 41.0</span>
<span class="co"># as.mo("S. aureus") 26.0 28.0 50.0 58.0 63.0 75.0</span>
<span class="co"># as.mo("S aureus") 26.0 27.0 46.0 51.0 60.0 67.0</span>
<span class="co"># as.mo("Staphylococcus aureus") 1.9 2.2 2.5 2.5 2.8 3.1</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 870.0 880.0 1100.0 910.0 1000.0 2400.0</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 360.0 370.0 400.0 380.0 420.0 540.0</span>
<span class="co"># as.mo("MRSA") 9.7 11.0 17.0 12.0 13.0 66.0</span>
<span class="co"># as.mo("VISA") 19.0 19.0 36.0 35.0 53.0 56.0</span>
<span class="co"># as.mo("VRSA") 17.0 20.0 20.0 21.0 21.0 23.0</span>
<span class="co"># neval</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span></code></pre></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 9.9 11 19.0 12.0 13.0 47.0 10</span>
<span class="co"># as.mo("stau") 100.0 110 130.0 130.0 140.0 150.0 10</span>
<span class="co"># as.mo("STAU") 110.0 110 130.0 140.0 140.0 150.0 10</span>
<span class="co"># as.mo("staaur") 11.0 11 15.0 12.0 13.0 40.0 10</span>
<span class="co"># as.mo("STAAUR") 12.0 12 21.0 13.0 40.0 46.0 10</span>
<span class="co"># as.mo("S. aureus") 26.0 31 45.0 34.0 60.0 86.0 10</span>
<span class="co"># as.mo("S aureus") 26.0 29 36.0 31.0 33.0 58.0 10</span>
<span class="co"># as.mo("Staphylococcus aureus") 1.6 2 2.3 2.3 2.7 2.8 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 880.0 900 910.0 910.0 920.0 950.0 10</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 370.0 370 380.0 380.0 380.0 400.0 10</span>
<span class="co"># as.mo("MRSA") 9.9 11 18.0 13.0 14.0 47.0 10</span>
<span class="co"># as.mo("VISA") 17.0 19 29.0 21.0 48.0 50.0 10</span>
<span class="co"># as.mo("VRSA") 16.0 19 29.0 20.0 47.0 55.0 10</span></code></pre></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="562.5"></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 100 milliseconds, this is only 10 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations can take up to 500-1000 times as much time.</p>
<p>To improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
@ -284,8 +270,8 @@
<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) 134 167 201 179 207 310 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.179 seconds. You only lose time on your unique input values.</p>
<span class="co"># mo_name(x) 136 169 210 198 247 317 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.198 seconds. You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -299,10 +285,10 @@
<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 7.59 7.93 8.24 8.09 8.66 9.06 10</span>
<span class="co"># B 23.60 23.70 29.20 24.30 27.10 66.10 10</span>
<span class="co"># C 1.84 2.13 2.22 2.19 2.35 2.62 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>
<span class="co"># A 7.21 7.32 7.92 7.69 8.49 9.43 10</span>
<span class="co"># B 22.60 23.50 28.90 24.70 26.10 69.20 10</span>
<span class="co"># C 1.87 1.92 2.10 2.08 2.27 2.34 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 0.0021 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">microbenchmark</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>,
@ -316,14 +302,14 @@
<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 1.69 1.77 1.82 1.83 1.86 1.92 10</span>
<span class="co"># B 1.78 1.79 1.89 1.91 1.95 2.06 10</span>
<span class="co"># C 1.74 1.79 1.88 1.87 1.94 2.06 10</span>
<span class="co"># D 1.75 1.77 1.94 1.95 1.99 2.41 10</span>
<span class="co"># E 1.70 1.75 1.84 1.81 1.87 2.08 10</span>
<span class="co"># F 1.66 1.70 1.76 1.74 1.80 1.89 10</span>
<span class="co"># G 1.68 1.70 1.82 1.75 1.93 2.09 10</span>
<span class="co"># H 1.66 1.69 1.75 1.74 1.80 1.92 10</span></code></pre></div>
<span class="co"># A 1.34 1.59 1.66 1.65 1.74 2.18 10</span>
<span class="co"># B 1.34 1.63 1.73 1.72 1.85 2.31 10</span>
<span class="co"># C 1.41 1.61 1.65 1.65 1.72 1.83 10</span>
<span class="co"># D 1.59 1.63 1.77 1.77 1.89 2.03 10</span>
<span class="co"># E 1.33 1.60 1.68 1.65 1.73 2.08 10</span>
<span class="co"># F 1.31 1.34 1.56 1.52 1.71 2.11 10</span>
<span class="co"># G 1.34 1.60 1.75 1.64 1.76 2.74 10</span>
<span class="co"># H 1.32 1.38 1.57 1.63 1.71 1.78 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 ‘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">
@ -350,14 +336,14 @@
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 15.91 16.98 21.87 17.54 18.34 168.50 100</span>
<span class="co"># de 18.98 20.14 26.30 20.74 22.64 66.68 100</span>
<span class="co"># nl 31.02 32.71 37.56 33.84 35.81 82.77 100</span>
<span class="co"># es 19.13 20.06 22.96 20.54 21.42 65.26 100</span>
<span class="co"># it 18.90 19.84 24.26 20.59 22.80 60.30 100</span>
<span class="co"># fr 18.89 19.92 23.46 20.49 21.72 62.85 100</span>
<span class="co"># pt 18.90 19.99 23.80 20.70 22.17 61.42 100</span></code></pre></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 15.73 16.35 20.85 16.74 17.71 56.56 100</span>
<span class="co"># de 18.96 19.62 22.32 19.86 20.46 59.58 100</span>
<span class="co"># nl 31.06 31.91 37.31 32.78 34.57 75.58 100</span>
<span class="co"># es 18.92 19.59 23.43 19.92 20.42 62.72 100</span>
<span class="co"># it 18.80 19.36 22.59 19.74 20.54 62.72 100</span>
<span class="co"># fr 18.88 19.53 23.89 19.85 20.91 61.56 100</span>
<span class="co"># pt 18.89 19.51 21.46 19.87 20.29 59.12 100</span></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
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