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@@ -44,7 +44,7 @@
</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">1.7.1.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
</span>
</div>
@@ -174,13 +174,6 @@
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Survey
</a>
</li>
</ul>
</div>
@@ -198,7 +191,7 @@
<h1 data-toc-skip>How to conduct AMR data analysis</h1>
<h4 data-toc-skip class="author">Matthijs S. Berends</h4>
<h4 data-toc-skip class="date">17 August 2021</h4>
<h4 data-toc-skip class="date">29 August 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="hidden name"><code>AMR.Rmd</code></div>
@@ -207,7 +200,7 @@
<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/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 17 August 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/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 29 August 2021.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor" aria-hidden="true"></a>Introduction</h1>
@@ -238,21 +231,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2021-08-17</td>
<td align="center">2021-08-29</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">2021-08-17</td>
<td align="center">2021-08-29</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">2021-08-17</td>
<td align="center">2021-08-29</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@@ -349,68 +342,68 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-12-11</td>
<td align="center">B5</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-01-03</td>
<td align="center">D5</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2013-03-20</td>
<td align="center">E3</td>
<td align="center">2012-06-29</td>
<td align="center">E6</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-02-14</td>
<td align="center">L5</td>
<td align="center">Hospital B</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">M</td>
</tr>
<tr class="odd">
<td align="center">2010-04-27</td>
<td align="center">Y6</td>
<tr class="even">
<td align="center">2014-08-25</td>
<td align="center">D8</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2017-01-14</td>
<td align="center">V1</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</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>
<tr class="even">
<td align="center">2011-08-04</td>
<td align="center">O2</td>
<td align="center">2010-10-15</td>
<td align="center">X2</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">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2011-04-05</td>
<td align="center">H6</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-01-10</td>
<td align="center">Y7</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
@@ -446,16 +439,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,443</td>
<td align="right">52.22%</td>
<td align="right">10,443</td>
<td align="right">52.22%</td>
<td align="right">10,326</td>
<td align="right">51.63%</td>
<td align="right">10,326</td>
<td align="right">51.63%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,557</td>
<td align="right">47.79%</td>
<td align="right">9,674</td>
<td align="right">48.37%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@@ -510,9 +503,9 @@ 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 10,606 first weighted isolates (phenotype-based, 53.0% of total</span>
<span class="co"># =&gt; Found 10,571 first weighted isolates (phenotype-based, 52.9% of total</span>
<span class="co"># where a microbial ID was available)</span></code></pre></div>
<p>So only 53.0% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<p>So only 52.9% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">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" class="external-link">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>
@@ -520,7 +513,7 @@ 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 10,606 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,571 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" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></code></pre></div>
<table style="width:100%;" class="table">
@@ -559,27 +552,11 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2012-12-11</td>
<td align="center">B5</td>
<td align="center">Hospital D</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="left">2</td>
<td align="center">2012-01-03</td>
<td align="center">D5</td>
<td align="center">Hospital B</td>
<td align="center">2012-06-29</td>
<td align="center">E6</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_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">S</td>
@@ -589,14 +566,14 @@ Longest: 1</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2017-02-14</td>
<td align="center">L5</td>
<td align="center">Hospital B</td>
<tr class="even">
<td align="left">2</td>
<td align="center">2014-08-25</td>
<td align="center">D8</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
@@ -605,52 +582,68 @@ Longest: 1</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2012-03-07</td>
<td align="center">I8</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="odd">
<td align="left">9</td>
<td align="center">2010-12-20</td>
<td align="center">H10</td>
<td align="left">4</td>
<td align="center">2010-10-15</td>
<td align="center">X2</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">R</td>
<td align="center">S</td>
<td align="center">M</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="even">
<td align="left">11</td>
<td align="center">2014-01-24</td>
<td align="center">M2</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="left">6</td>
<td align="center">2012-01-10</td>
<td align="center">Y7</td>
<td align="center">Hospital D</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">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">8</td>
<td align="center">2016-02-07</td>
<td align="center">V2</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">M</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">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2016-11-08</td>
<td align="center">D4</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>
</tbody>
@@ -674,8 +667,8 @@ 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" class="external-link">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: 10,606<br>
Available: 10,606 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,571<br>
Available: 10,571 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@@ -692,33 +685,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,494</td>
<td align="right">42.37%</td>
<td align="right">4,494</td>
<td align="right">42.37%</td>
<td align="right">4,507</td>
<td align="right">42.64%</td>
<td align="right">4,507</td>
<td align="right">42.64%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,785</td>
<td align="right">26.26%</td>
<td align="right">7,279</td>
<td align="right">68.63%</td>
<td align="right">2,799</td>
<td align="right">26.48%</td>
<td align="right">7,306</td>
<td align="right">69.11%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,106</td>
<td align="right">19.86%</td>
<td align="right">9,385</td>
<td align="right">88.49%</td>
<td align="right">2,087</td>
<td align="right">19.74%</td>
<td align="right">9,393</td>
<td align="right">88.86%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,221</td>
<td align="right">11.51%</td>
<td align="right">10,606</td>
<td align="right">1,178</td>
<td align="right">11.14%</td>
<td align="right">10,571</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@@ -765,8 +758,83 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-12-11</td>
<td align="center">B5</td>
<td align="center">2010-10-15</td>
<td align="center">X2</td>
<td align="center">Hospital B</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">R</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="even">
<td align="center">2012-01-10</td>
<td align="center">Y7</td>
<td align="center">Hospital D</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">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-02-02</td>
<td align="center">K7</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">R</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="center">2011-08-05</td>
<td align="center">V3</td>
<td align="center">Hospital B</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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-06-16</td>
<td align="center">Z8</td>
<td align="center">Hospital B</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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-08-23</td>
<td align="center">J10</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
@@ -779,81 +847,6 @@ Longest: 24</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-06-11</td>
<td align="center">L7</td>
<td align="center">Hospital C</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">2012-12-19</td>
<td align="center">A10</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</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">2014-12-05</td>
<td align="center">M6</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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="odd">
<td align="center">2017-05-14</td>
<td align="center">L8</td>
<td align="center">Hospital C</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">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">2010-12-14</td>
<td align="center">Q1</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">R</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>
</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>
@@ -875,50 +868,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2137</td>
<td align="center">139</td>
<td align="center">2218</td>
<td align="center">4494</td>
<td align="center">2196</td>
<td align="center">119</td>
<td align="center">2192</td>
<td align="center">4507</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3298</td>
<td align="center">157</td>
<td align="center">1039</td>
<td align="center">4494</td>
<td align="center">3378</td>
<td align="center">151</td>
<td align="center">978</td>
<td align="center">4507</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3230</td>
<td align="center">3282</td>
<td align="center">0</td>
<td align="center">1264</td>
<td align="center">4494</td>
<td align="center">1225</td>
<td align="center">4507</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">3946</td>
<td align="center">3929</td>
<td align="center">0</td>
<td align="center">548</td>
<td align="center">4494</td>
<td align="center">578</td>
<td align="center">4507</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">1221</td>
<td align="center">1221</td>
<td align="center">1178</td>
<td align="center">1178</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">967</td>
<td align="center">44</td>
<td align="center">210</td>
<td align="center">1221</td>
<td align="center">930</td>
<td align="center">45</td>
<td align="center">203</td>
<td align="center">1178</td>
</tr>
</tbody>
</table>
@@ -941,34 +934,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">3946</td>
<td align="center">3929</td>
<td align="center">0</td>
<td align="center">548</td>
<td align="center">4494</td>
<td align="center">578</td>
<td align="center">4507</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1088</td>
<td align="center">1052</td>
<td align="center">0</td>
<td align="center">133</td>
<td align="center">1221</td>
<td align="center">126</td>
<td align="center">1178</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2490</td>
<td align="center">2473</td>
<td align="center">0</td>
<td align="center">295</td>
<td align="center">2785</td>
<td align="center">326</td>
<td align="center">2799</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">2106</td>
<td align="center">2106</td>
<td align="center">2087</td>
<td align="center">2087</td>
</tr>
</tbody>
</table>
@@ -982,7 +975,7 @@ 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] 0.5427117</span></code></pre></div>
<span class="co"># [1] 0.5403462</span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">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>
@@ -996,19 +989,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5356582</td>
<td align="center">0.5487147</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5408108</td>
<td align="center">0.5436519</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5371153</td>
<td align="center">0.5257549</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5614714</td>
<td align="center">0.5338095</td>
</tr>
</tbody>
</table>
@@ -1027,23 +1020,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5356582</td>
<td align="center">3183</td>
<td align="center">0.5487147</td>
<td align="center">3151</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5408108</td>
<td align="center">3700</td>
<td align="center">0.5436519</td>
<td align="center">3631</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5371153</td>
<td align="center">1657</td>
<td align="center">0.5257549</td>
<td align="center">1689</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5614714</td>
<td align="center">2066</td>
<td align="center">0.5338095</td>
<td align="center">2100</td>
</tr>
</tbody>
</table>
@@ -1064,27 +1057,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7688028</td>
<td align="center">0.8780596</td>
<td align="center">0.9815309</td>
<td align="center">0.7830042</td>
<td align="center">0.8717550</td>
<td align="center">0.9764810</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8280098</td>
<td align="center">0.8910729</td>
<td align="center">0.9754300</td>
<td align="center">0.8276740</td>
<td align="center">0.8930390</td>
<td align="center">0.9787776</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7921005</td>
<td align="center">0.8940754</td>
<td align="center">0.9795332</td>
<td align="center">0.7874241</td>
<td align="center">0.8835298</td>
<td align="center">0.9828510</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5351377</td>
<td align="center">0.5318639</td>
<td align="center">0.0000000</td>
<td align="center">0.5351377</td>
<td align="center">0.5318639</td>
</tr>
</tbody>
</table>
@@ -1109,23 +1102,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">53.6%</td>
<td align="right">26.4%</td>
<td align="right">54.9%</td>
<td align="right">25.8%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.1%</td>
<td align="right">24.6%</td>
<td align="right">54.4%</td>
<td align="right">27.8%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">53.7%</td>
<td align="right">27.5%</td>
<td align="right">52.6%</td>
<td align="right">25.0%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">56.1%</td>
<td align="right">29.0%</td>
<td align="right">53.4%</td>
<td align="right">24.3%</td>
</tr>
</tbody>
</table>
@@ -1209,16 +1202,16 @@ 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] 0.25 16 0.0625 32 0.025 1 256 64 0.002 0.005 </span>
<span class="co"># [11] 0.01 0.005 8 0.01 0.025 128 0.01 8 0.005 256 </span>
<span class="co"># [21] 0.005 8 0.0625 0.125 0.005 16 8 2 0.5 4 </span>
<span class="co"># [31] 2 32 0.25 0.25 8 0.025 0.25 8 64 1 </span>
<span class="co"># [41] 0.005 0.01 0.005 256 0.025 0.5 2 0.025 0.5 0.005 </span>
<span class="co"># [51] 0.0625 128 4 1 0.0625 0.002 16 0.002 8 0.005 </span>
<span class="co"># [61] 1 1 8 32 0.002 32 0.25 8 4 0.001 </span>
<span class="co"># [71] 2 16 16 0.025 0.005 0.0625 2 128 0.001 2 </span>
<span class="co"># [81] 64 0.025 16 64 2 128 8 0.5 4 256 </span>
<span class="co"># [91] 0.5 32 0.001 0.01 2 64 4 32 4 0.0625</span></code></pre></div>
<span class="co"># [1] 1 128 0.01 0.25 0.01 16 0.001 0.125 0.25 0.01 </span>
<span class="co"># [11] 0.005 16 0.0625 64 &gt;=256 0.5 0.01 16 0.5 0.0625</span>
<span class="co"># [21] 0.001 0.5 0.0625 4 2 8 0.5 0.0625 0.125 128 </span>
<span class="co"># [31] 0.002 0.25 2 8 0.125 0.0625 0.125 16 128 0.002 </span>
<span class="co"># [41] 1 0.005 2 32 0.01 0.0625 &gt;=256 64 16 0.005 </span>
<span class="co"># [51] 2 0.001 &gt;=256 32 64 &gt;=256 128 0.01 0.005 0.001 </span>
<span class="co"># [61] 0.01 0.125 2 0.125 &gt;=256 32 64 0.01 2 0.25 </span>
<span class="co"># [71] 0.01 64 0.5 128 0.001 64 128 0.002 &gt;=256 64 </span>
<span class="co"># [81] 0.01 8 0.5 4 16 0.025 0.025 0.001 0.125 0.025 </span>
<span class="co"># [91] 2 64 64 128 32 128 0.001 32 2 0.005</span></code></pre></div>
<div class="sourceCode" id="cb37"><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>
@@ -1247,10 +1240,10 @@ 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] 26 25 28 21 24 22 21 27 22 21 31 25 26 17 28 29 18 31 21 30 23 28 22 18 28</span>
<span class="co"># [26] 21 25 26 18 30 22 28 25 28 25 21 29 26 19 21 19 26 31 17 25 22 21 27 24 26</span>
<span class="co"># [51] 20 17 18 27 31 31 20 31 26 22 25 22 19 22 27 19 25 27 30 17 24 27 22 28 18</span>
<span class="co"># [76] 26 30 29 25 23 26 29 19 25 25 24 25 30 29 25 29 17 26 21 20 29 26 23 29 31</span></code></pre></div>
<span class="co"># [1] 30 29 25 23 27 18 23 21 31 26 17 30 18 31 30 25 22 19 18 26 31 19 21 25 29</span>
<span class="co"># [26] 22 26 30 20 20 18 19 18 29 22 17 27 21 24 18 17 23 27 18 19 31 18 29 30 25</span>
<span class="co"># [51] 27 23 21 20 31 19 19 25 25 23 23 19 17 25 21 30 20 31 26 23 29 27 30 29 24</span>
<span class="co"># [76] 20 23 23 27 20 24 19 28 24 31 29 26 23 20 29 23 18 17 27 21 28 28 17 23 17</span></code></pre></div>
<div class="sourceCode" id="cb43"><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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9
docs/articles/EUCAST.html
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@@ -44,7 +44,7 @@
</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">1.7.1.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
</span>
</div>
@@ -174,13 +174,6 @@
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Survey
</a>
</li>
</ul>
</div>

55
docs/articles/MDR.html
View File

@@ -44,7 +44,7 @@
</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">1.7.1.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
</span>
</div>
@@ -174,13 +174,6 @@
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Survey
</a>
</li>
</ul>
</div>
@@ -364,19 +357,19 @@ 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" class="external-link">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 S R R</span>
<span class="co"># 2 I R R R I R</span>
<span class="co"># 3 S I R S I I</span>
<span class="co"># 4 S S S S I R</span>
<span class="co"># 5 R S R I I S</span>
<span class="co"># 6 I R S R R I</span>
<span class="co"># 1 S I I R I I</span>
<span class="co"># 2 S S I I R R</span>
<span class="co"># 3 I S S I I R</span>
<span class="co"># 4 S R S R S R</span>
<span class="co"># 5 R S R S R R</span>
<span class="co"># 6 I S S R I S</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 I</span>
<span class="co"># 2 R</span>
<span class="co"># 3 I</span>
<span class="co"># 4 R</span>
<span class="co"># 5 R</span>
<span class="co"># 6 S</span></code></pre></div>
<span class="co"># 6 I</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>
@@ -419,40 +412,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3227</td>
<td align="right">64.54%</td>
<td align="right">3227</td>
<td align="right">64.54%</td>
<td align="right">3144</td>
<td align="right">62.88%</td>
<td align="right">3144</td>
<td align="right">62.88%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">990</td>
<td align="right">19.80%</td>
<td align="right">4217</td>
<td align="right">84.34%</td>
<td align="right">1027</td>
<td align="right">20.54%</td>
<td align="right">4171</td>
<td align="right">83.42%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">464</td>
<td align="right">9.28%</td>
<td align="right">4681</td>
<td align="right">93.62%</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">223</td>
<td align="right">4.46%</td>
<td align="right">4904</td>
<td align="right">98.08%</td>
<td align="right">257</td>
<td align="right">5.14%</td>
<td align="right">4892</td>
<td align="right">97.84%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">96</td>
<td align="right">1.92%</td>
<td align="right">108</td>
<td align="right">2.16%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

9
docs/articles/PCA.html
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@@ -44,7 +44,7 @@
</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">1.7.1.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
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</a>
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<a href="../survey.html">
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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">1.7.1.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
</span>
</div>
@@ -174,13 +174,6 @@
Source Code
</a>
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<span class="fa fa-clipboard-list"></span>
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@@ -198,7 +191,7 @@
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
<h4 data-toc-skip class="author">Matthijs S. Berends</h4>
<h4 data-toc-skip class="date">17 August 2021</h4>
<h4 data-toc-skip class="date">29 August 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="hidden name"><code>SPSS.Rmd</code></div>
@@ -233,7 +226,7 @@
</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" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">414,789 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" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">415,751 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>

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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">1.7.1.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
</span>
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@@ -174,13 +174,6 @@
Source Code
</a>
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<a href="../survey.html">
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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">1.7.1.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
</span>
</div>
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@@ -231,32 +224,19 @@
times <span class="op">=</span> <span class="fl">25</span><span class="op">)</span>
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">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") 12.0 13.0 14 13.0 13.0 45.0</span>
<span class="co"># as.mo("stau") 55.0 58.0 72 60.0 92.0 100.0</span>
<span class="co"># as.mo("STAU") 54.0 59.0 85 91.0 94.0 200.0</span>
<span class="co"># as.mo("staaur") 11.0 12.0 19 13.0 15.0 58.0</span>
<span class="co"># as.mo("STAAUR") 12.0 13.0 21 14.0 16.0 63.0</span>
<span class="co"># as.mo("S. aureus") 24.0 28.0 41 30.0 62.0 73.0</span>
<span class="co"># as.mo("S aureus") 26.0 28.0 37 30.0 33.0 75.0</span>
<span class="co"># as.mo("Staphylococcus aureus") 3.1 3.8 4 3.9 4.2 4.7</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 250.0 260.0 270 260.0 290.0 300.0</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 160.0 200.0 200 200.0 200.0 240.0</span>
<span class="co"># as.mo("MRSA") 11.0 13.0 20 13.0 15.0 55.0</span>
<span class="co"># as.mo("VISA") 21.0 22.0 31 23.0 27.0 69.0</span>
<span class="co"># neval</span>
<span class="co"># 25</span>
<span class="co"># 25</span>
<span class="co"># 25</span>
<span class="co"># 25</span>
<span class="co"># 25</span>
<span class="co"># 25</span>
<span class="co"># 25</span>
<span class="co"># 25</span>
<span class="co"># 25</span>
<span class="co"># 25</span>
<span class="co"># 25</span>
<span class="co"># 25</span></code></pre></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 12.0 13.0 15.0 14.0 15.0 48 25</span>
<span class="co"># as.mo("stau") 54.0 57.0 73.0 62.0 92.0 99 25</span>
<span class="co"># as.mo("STAU") 54.0 58.0 73.0 63.0 91.0 98 25</span>
<span class="co"># as.mo("staaur") 13.0 13.0 20.0 14.0 15.0 52 25</span>
<span class="co"># as.mo("STAAUR") 11.0 13.0 18.0 14.0 16.0 47 25</span>
<span class="co"># as.mo("S. aureus") 27.0 30.0 38.0 31.0 36.0 63 25</span>
<span class="co"># as.mo("S aureus") 27.0 29.0 42.0 33.0 60.0 66 25</span>
<span class="co"># as.mo("Staphylococcus aureus") 3.8 4.1 6.8 4.2 4.6 36 25</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 240.0 250.0 280.0 270.0 300.0 320 25</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 160.0 190.0 200.0 200.0 210.0 340 25</span>
<span class="co"># as.mo("MRSA") 13.0 13.0 17.0 14.0 15.0 46 25</span>
<span class="co"># as.mo("VISA") 20.0 23.0 34.0 25.0 52.0 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>
@@ -278,7 +258,7 @@
<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" class="external-link">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_AURS B_STPHY_CONS B_ESCHR_COLI B_STRPT_PYGN B_STPHY_CONS</span>
<span class="co"># [1] B_STRPT_PNMN B_KLBSL_PNMN B_ESCHR_COLI B_SERRT_MRCS B_STPHY_CONS</span>
<span class="co"># [6] B_ESCHR_COLI</span>
<span class="co"># as the example_isolates data set has 2,000 rows, we should have 2 million items</span>
@@ -295,7 +275,7 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">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) 163 204 267 233 346 398 10</span></code></pre></div>
<span class="co"># mo_name(x) 188 202 260 233 335 408 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.233 seconds. That is 116 nanoseconds on average. You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
@@ -310,10 +290,10 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">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 7.93 8.08 14.50 8.35 8.46 70.00 10</span>
<span class="co"># B 22.40 22.80 24.30 24.30 24.60 27.20 10</span>
<span class="co"># C 1.89 2.00 2.19 2.15 2.30 2.76 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>
<span class="co"># A 8.09 8.18 8.94 8.69 9.47 10.50 10</span>
<span class="co"># B 23.40 24.90 31.90 27.90 28.20 80.70 10</span>
<span class="co"># C 2.03 2.20 2.35 2.35 2.48 2.66 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 0.0023 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" class="external-link">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>,
@@ -327,14 +307,14 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">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 1.73 1.78 1.83 1.81 1.90 1.90 10</span>
<span class="co"># B 1.73 1.83 1.90 1.89 1.98 2.04 10</span>
<span class="co"># C 1.72 1.79 1.88 1.85 1.95 2.08 10</span>
<span class="co"># D 1.75 1.75 1.85 1.88 1.91 1.93 10</span>
<span class="co"># E 1.70 1.78 1.82 1.80 1.83 2.02 10</span>
<span class="co"># F 1.68 1.78 1.79 1.79 1.81 1.91 10</span>
<span class="co"># G 1.69 1.75 1.79 1.79 1.81 1.89 10</span>
<span class="co"># H 1.68 1.71 1.85 1.76 1.85 2.65 10</span></code></pre></div>
<span class="co"># A 1.68 1.72 1.88 1.88 1.97 2.32 10</span>
<span class="co"># B 1.64 1.80 1.90 1.95 1.98 2.14 10</span>
<span class="co"># C 1.71 1.74 1.88 1.80 2.08 2.21 10</span>
<span class="co"># D 1.70 1.79 1.86 1.87 1.96 1.99 10</span>
<span class="co"># E 1.73 1.85 1.94 1.91 2.03 2.20 10</span>
<span class="co"># F 1.71 1.78 1.91 1.89 2.00 2.25 10</span>
<span class="co"># G 1.66 1.78 1.87 1.88 1.98 2.04 10</span>
<span class="co"># H 1.73 1.82 2.06 1.98 2.07 2.80 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">
@@ -362,13 +342,13 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">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 19.47 20.23 24.54 20.72 21.85 89.57 100</span>
<span class="co"># de 30.58 31.52 41.31 32.78 34.76 86.03 100</span>
<span class="co"># nl 34.81 35.58 45.89 36.76 39.41 94.01 100</span>
<span class="co"># es 34.41 35.12 40.08 36.22 37.33 94.71 100</span>
<span class="co"># it 23.93 24.65 27.31 25.15 25.84 81.01 100</span>
<span class="co"># fr 23.59 24.40 31.40 25.01 25.62 200.30 100</span>
<span class="co"># pt 23.69 24.73 30.23 25.57 26.32 82.19 100</span></code></pre></div>
<span class="co"># en 19.64 20.10 28.32 20.72 22.65 104.80 100</span>
<span class="co"># de 30.76 31.59 37.06 32.27 33.87 95.10 100</span>
<span class="co"># nl 34.88 35.58 43.87 36.41 38.73 94.00 100</span>
<span class="co"># es 34.62 35.22 44.72 36.04 37.88 97.92 100</span>
<span class="co"># it 24.03 24.59 28.09 25.19 26.12 79.32 100</span>
<span class="co"># fr 23.79 24.37 30.37 24.89 26.29 194.10 100</span>
<span class="co"># pt 23.85 24.42 28.21 24.90 26.22 83.14 100</span></code></pre></div>
<p>Currently supported non-English languages are German, Dutch, Spanish, Italian, French and Portuguese.</p>
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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">1.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
</span>
</div>
@@ -190,7 +190,7 @@
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">21 August 2021</h4>
<h4 data-toc-skip class="date">29 August 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
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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">1.7.1.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
</span>
</div>
@@ -222,13 +222,6 @@
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</a>
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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">1.7.1.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
</span>
</div>
@@ -174,13 +174,6 @@
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</a>
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@@ -44,7 +44,7 @@
</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">1.7.1.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
</span>
</div>
@@ -174,13 +174,6 @@
Source Code
</a>
</li>
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<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Survey
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</ul>
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