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@ -24,7 +24,7 @@
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -162,7 +162,7 @@
<img src="../logo.svg" class="logo" alt=""><h1>How to conduct AMR data analysis</h1>
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
<h4 data-toc-skip class="date">01 September 2022</h4>
<h4 data-toc-skip class="date">05 October 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="d-none name"><code>AMR.Rmd</code></div>
@ -170,7 +170,7 @@
<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 01 September 2022.</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 05 October 2022.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -201,21 +201,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-09-01</td>
<td align="center">2022-10-05</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">2022-09-01</td>
<td align="center">2022-10-05</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">2022-09-01</td>
<td align="center">2022-10-05</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -325,69 +325,69 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-11-10</td>
<td align="center">P6</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">2014-01-04</td>
<td align="center">G6</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">F</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-10-29</td>
<td align="center">T4</td>
<td align="center">2017-04-24</td>
<td align="center">D3</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2011-07-22</td>
<td align="center">G4</td>
<td align="center">2016-11-13</td>
<td align="center">J4</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">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-04-20</td>
<td align="center">O10</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2012-08-21</td>
<td align="center">I2</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-03-26</td>
<td align="center">T2</td>
<td align="center">2017-08-20</td>
<td align="center">V6</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2012-05-20</td>
<td align="center">U5</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-12-01</td>
<td align="center">X4</td>
<td align="center">Hospital B</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">F</td>
</tr>
</tbody>
@ -422,16 +422,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,422</td>
<td align="right">52.11%</td>
<td align="right">10,422</td>
<td align="right">52.11%</td>
<td align="right">10,348</td>
<td align="right">51.74%</td>
<td align="right">10,348</td>
<td align="right">51.74%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,578</td>
<td align="right">47.89%</td>
<td align="right">9,652</td>
<td align="right">48.26%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -488,9 +488,9 @@ Longest: 1</p>
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,604 'phenotype-based' first isolates (53.0% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,738 'phenotype-based' first isolates (53.7% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></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 53.7% 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><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<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></span></code></pre></div>
@ -499,10 +499,10 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,604 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,738 isolates for analysis. Now our data looks like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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">data_1st</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<table style="width:100%;" class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -516,7 +516,7 @@ Longest: 1</p>
<col width="6%">
<col width="11%">
<col width="12%">
<col width="7%">
<col width="9%">
<col width="5%">
</colgroup>
<thead><tr class="header">
@ -537,43 +537,59 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2016-11-10</td>
<td align="center">P6</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">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">2</td>
<td align="center">2011-10-29</td>
<td align="center">T4</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2015-01-09</td>
<td align="center">J10</td>
<td align="left">3</td>
<td align="center">2016-11-13</td>
<td align="center">J4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">2017-08-20</td>
<td align="center">V6</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">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">6</td>
<td align="center">2017-12-01</td>
<td align="center">X4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2014-03-15</td>
<td align="center">H7</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>
@ -584,30 +600,14 @@ Longest: 1</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2016-05-25</td>
<td align="center">F8</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="odd">
<td align="left">10</td>
<td align="center">2010-01-21</td>
<td align="center">Z8</td>
<td align="center">Hospital A</td>
<td align="left">8</td>
<td align="center">2011-03-12</td>
<td align="center">Y2</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
@ -618,15 +618,15 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="left">11</td>
<td align="center">2012-10-12</td>
<td align="center">B5</td>
<td align="center">Hospital D</td>
<td align="center">2013-12-31</td>
<td align="center">R4</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</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>
@ -653,8 +653,8 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></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></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,604<br>
Available: 10,604 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,738<br>
Available: 10,738 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -671,33 +671,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,672</td>
<td align="right">44.06%</td>
<td align="right">4,672</td>
<td align="right">44.06%</td>
<td align="right">4,690</td>
<td align="right">43.68%</td>
<td align="right">4,690</td>
<td align="right">43.68%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,714</td>
<td align="right">25.59%</td>
<td align="right">7,386</td>
<td align="right">69.65%</td>
<td align="right">2,765</td>
<td align="right">25.75%</td>
<td align="right">7,455</td>
<td align="right">69.43%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,051</td>
<td align="right">19.34%</td>
<td align="right">9,437</td>
<td align="right">88.99%</td>
<td align="right">2,119</td>
<td align="right">19.73%</td>
<td align="right">9,574</td>
<td align="right">89.16%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,167</td>
<td align="right">11.01%</td>
<td align="right">10,604</td>
<td align="right">1,164</td>
<td align="right">10.84%</td>
<td align="right">10,738</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -716,14 +716,14 @@ Longest: 24</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="10%">
<col width="11%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@ -744,38 +744,8 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-10-12</td>
<td align="center">B5</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">R</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">2017-11-10</td>
<td align="center">A8</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="odd">
<td align="center">2010-08-21</td>
<td align="center">Y3</td>
<td align="center">2017-08-20</td>
<td align="center">V6</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
@ -789,8 +759,38 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-12-30</td>
<td align="center">B1</td>
<td align="center">2011-09-19</td>
<td align="center">V5</td>
<td align="center">Hospital C</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">2015-07-01</td>
<td align="center">C5</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="center">2010-02-13</td>
<td align="center">D1</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
@ -804,23 +804,23 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-10-15</td>
<td align="center">N2</td>
<td align="center">2010-03-01</td>
<td align="center">T3</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">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">2016-04-25</td>
<td align="center">H4</td>
<td align="center">2010-02-18</td>
<td align="center">H2</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
@ -854,50 +854,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2216</td>
<td align="center">117</td>
<td align="center">2339</td>
<td align="center">4672</td>
<td align="center">2203</td>
<td align="center">147</td>
<td align="center">2340</td>
<td align="center">4690</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3414</td>
<td align="center">156</td>
<td align="center">1102</td>
<td align="center">4672</td>
<td align="center">3438</td>
<td align="center">180</td>
<td align="center">1072</td>
<td align="center">4690</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3392</td>
<td align="center">3410</td>
<td align="center">0</td>
<td align="center">1280</td>
<td align="center">4672</td>
<td align="center">4690</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4084</td>
<td align="center">4094</td>
<td align="center">0</td>
<td align="center">588</td>
<td align="center">4672</td>
<td align="center">596</td>
<td align="center">4690</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">1167</td>
<td align="center">1167</td>
<td align="center">1164</td>
<td align="center">1164</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">912</td>
<td align="center">53</td>
<td align="center">202</td>
<td align="center">1167</td>
<td align="center">902</td>
<td align="center">39</td>
<td align="center">223</td>
<td align="center">1164</td>
</tr>
</tbody>
</table>
@ -920,34 +920,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4084</td>
<td align="center">4094</td>
<td align="center">0</td>
<td align="center">588</td>
<td align="center">4672</td>
<td align="center">596</td>
<td align="center">4690</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1054</td>
<td align="center">1060</td>
<td align="center">0</td>
<td align="center">113</td>
<td align="center">1167</td>
<td align="center">104</td>
<td align="center">1164</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2439</td>
<td align="center">2435</td>
<td align="center">0</td>
<td align="center">275</td>
<td align="center">2714</td>
<td align="center">330</td>
<td align="center">2765</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">2051</td>
<td align="center">2051</td>
<td align="center">2119</td>
<td align="center">2119</td>
</tr>
</tbody>
</table>
@ -961,7 +961,7 @@ 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><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></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>
<span><span class="co"># [1] 0.5453602</span></span></code></pre></div>
<span><span class="co"># [1] 0.5406035</span></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><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@ -975,19 +975,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5524672</td>
<td align="center">0.5406669</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5320304</td>
<td align="center">0.5451918</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5509434</td>
<td align="center">0.5203562</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5535714</td>
<td align="center">0.5471874</td>
</tr>
</tbody>
</table>
@ -1008,23 +1008,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5524672</td>
<td align="center">3202</td>
<td align="center">0.5406669</td>
<td align="center">3209</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5320304</td>
<td align="center">3684</td>
<td align="center">0.5451918</td>
<td align="center">3806</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5509434</td>
<td align="center">1590</td>
<td align="center">0.5203562</td>
<td align="center">1572</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5535714</td>
<td align="center">2128</td>
<td align="center">0.5471874</td>
<td align="center">2151</td>
</tr>
</tbody>
</table>
@ -1047,27 +1047,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7641267</td>
<td align="center">0.8741438</td>
<td align="center">0.9762414</td>
<td align="center">0.7714286</td>
<td align="center">0.8729211</td>
<td align="center">0.9754797</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8269066</td>
<td align="center">0.9031705</td>
<td align="center">0.9837189</td>
<td align="center">0.8084192</td>
<td align="center">0.9106529</td>
<td align="center">0.9862543</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7940310</td>
<td align="center">0.8986735</td>
<td align="center">0.9812085</td>
<td align="center">0.7895118</td>
<td align="center">0.8806510</td>
<td align="center">0.9793852</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5324232</td>
<td align="center">0.5394054</td>
<td align="center">0.0000000</td>
<td align="center">0.5324232</td>
<td align="center">0.5394054</td>
</tr>
</tbody>
</table>
@ -1092,23 +1092,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">55.2%</td>
<td align="right">26.6%</td>
<td align="right">54.1%</td>
<td align="right">25.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">53.2%</td>
<td align="right">26.1%</td>
<td align="right">54.5%</td>
<td align="right">27.3%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">55.1%</td>
<td align="right">27.3%</td>
<td align="right">52.0%</td>
<td align="right">27.1%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">55.4%</td>
<td align="right">27.0%</td>
<td align="right">54.7%</td>
<td align="right">26.5%</td>
</tr>
</tbody>
</table>
@ -1206,18 +1206,18 @@ Longest: 24</p>
<code class="sourceCode R"><span><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>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class &lt;mic&gt;</span></span>
<span><span class="co"># [1] 0.0625 128 32 32 0.125 2 0.0625 8 0.002 </span></span>
<span><span class="co"># [10] 2 0.0625 64 2 128 0.025 0.125 0.002 64 </span></span>
<span><span class="co"># [19] 0.025 4 0.002 &lt;=0.001 0.0625 0.125 8 16 0.0625 </span></span>
<span><span class="co"># [28] 128 128 256 8 8 16 0.0625 &lt;=0.001 &lt;=0.001</span></span>
<span><span class="co"># [37] 8 256 0.025 &lt;=0.001 32 0.125 128 0.125 1 </span></span>
<span><span class="co"># [46] 0.01 64 0.125 4 2 0.005 128 0.25 32 </span></span>
<span><span class="co"># [55] 1 0.01 0.25 0.0625 0.01 0.25 0.25 8 0.125 </span></span>
<span><span class="co"># [64] 0.25 0.025 &lt;=0.001 8 1 4 1 32 64 </span></span>
<span><span class="co"># [73] 0.5 32 2 2 0.125 0.01 32 64 &lt;=0.001</span></span>
<span><span class="co"># [82] 4 0.5 0.5 4 0.25 4 &lt;=0.001 256 1 </span></span>
<span><span class="co"># [91] 4 4 0.002 0.125 0.125 2 0.002 8 16 </span></span>
<span><span class="co"># [100] 1</span></span></code></pre></div>
<span><span class="co"># [1] 128 128 1 &lt;=0.001 &gt;=256 0.002 0.5 0.25 0.125 </span></span>
<span><span class="co"># [10] &lt;=0.001 128 &lt;=0.001 1 &lt;=0.001 2 0.25 &gt;=256 &gt;=256 </span></span>
<span><span class="co"># [19] 0.0625 0.002 128 0.01 0.025 0.01 0.01 8 0.0625 </span></span>
<span><span class="co"># [28] &lt;=0.001 &lt;=0.001 4 0.125 4 0.01 0.125 &lt;=0.001 4 </span></span>
<span><span class="co"># [37] 0.005 0.0625 0.0625 &gt;=256 4 0.025 8 16 0.005 </span></span>
<span><span class="co"># [46] 0.0625 0.005 0.002 1 0.025 32 64 8 2 </span></span>
<span><span class="co"># [55] 1 0.25 0.0625 &lt;=0.001 4 16 0.002 0.0625 2 </span></span>
<span><span class="co"># [64] 0.5 4 64 0.005 &gt;=256 0.025 0.25 0.25 8 </span></span>
<span><span class="co"># [73] 0.25 0.0625 0.125 &lt;=0.001 1 1 64 0.25 0.0625 </span></span>
<span><span class="co"># [82] 0.0625 0.025 32 64 0.025 0.025 16 64 0.25 </span></span>
<span><span class="co"># [91] &gt;=256 0.025 16 128 0.01 0.5 0.002 0.5 0.0625 </span></span>
<span><span class="co"># [100] 0.125</span></span></code></pre></div>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<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></span></code></pre></div>
@ -1242,14 +1242,12 @@ Longest: 24</p>
<p>For disk diffusion values, there is not much of a difference in plotting:</p>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</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></span>
<span><span class="co"># ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span></span>
<span><span class="co"># coli). Run `mo_uncertainties()` to review this.</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class &lt;disk&gt;</span></span>
<span><span class="co"># [1] 28 26 29 24 22 28 18 17 22 24 17 18 20 25 23 22 30 21 24 30 26 18 23 28 19</span></span>
<span><span class="co"># [26] 25 24 25 17 25 21 25 20 30 20 29 20 22 25 19 17 29 21 28 28 18 24 26 25 28</span></span>
<span><span class="co"># [51] 20 26 24 19 24 27 19 22 18 28 29 30 31 30 30 30 17 18 20 26 27 27 28 24 23</span></span>
<span><span class="co"># [76] 25 30 29 20 20 20 20 30 24 28 20 30 31 17 17 23 25 27 26 18 23 21 18 22 21</span></span></code></pre></div>
<span><span class="co"># [1] 28 24 28 24 21 20 19 24 27 24 27 26 23 27 19 31 28 20 25 29 23 18 22 18 23</span></span>
<span><span class="co"># [26] 20 19 30 31 22 22 19 18 25 30 30 28 27 20 23 31 20 22 29 31 25 29 19 27 31</span></span>
<span><span class="co"># [51] 18 21 27 31 20 19 30 30 30 22 22 23 18 26 30 17 25 29 19 19 24 26 22 18 20</span></span>
<span><span class="co"># [76] 28 29 20 28 21 18 19 28 26 28 22 30 27 24 21 28 26 25 23 28 26 21 20 26 18</span></span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<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></span></code></pre></div>
@ -1321,7 +1319,7 @@ Longest: 24</p>
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@ -38,7 +38,7 @@
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@ -38,7 +38,7 @@
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@ -314,19 +314,19 @@ Unique: 2</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 R R I S S R</span></span>
<span><span class="co"># 2 S I R S S S</span></span>
<span><span class="co"># 3 S R R S S I</span></span>
<span><span class="co"># 4 R I R R I I</span></span>
<span><span class="co"># 5 S R I R R I</span></span>
<span><span class="co"># 6 R I R R R S</span></span>
<span><span class="co"># 1 I I I I I S</span></span>
<span><span class="co"># 2 R R S R R S</span></span>
<span><span class="co"># 3 I S I S R I</span></span>
<span><span class="co"># 4 S I S I S R</span></span>
<span><span class="co"># 5 R S R S S R</span></span>
<span><span class="co"># 6 I I R R R S</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 2 I</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 I</span></span></code></pre></div>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 R</span></span>
<span><span class="co"># 6 R</span></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><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></span></code></pre></div>
@ -357,40 +357,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3202</td>
<td align="right">64.04%</td>
<td align="right">3202</td>
<td align="right">64.04%</td>
<td align="right">3139</td>
<td align="right">62.78%</td>
<td align="right">3139</td>
<td align="right">62.78%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">970</td>
<td align="right">19.40%</td>
<td align="right">4172</td>
<td align="right">83.44%</td>
<td align="right">1034</td>
<td align="right">20.68%</td>
<td align="right">4173</td>
<td align="right">83.46%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">472</td>
<td align="right">9.44%</td>
<td align="right">4644</td>
<td align="right">92.88%</td>
<td align="right">469</td>
<td align="right">9.38%</td>
<td align="right">4642</td>
<td align="right">92.84%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">257</td>
<td align="right">5.14%</td>
<td align="right">4901</td>
<td align="right">98.02%</td>
<td align="right">250</td>
<td align="right">5.00%</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">99</td>
<td align="right">1.98%</td>
<td align="right">108</td>
<td align="right">2.16%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>
@ -410,7 +410,7 @@ Unique: 5</p>
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
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@ -162,7 +162,7 @@
<img src="../logo.svg" class="logo" alt=""><h1>How to import data from SPSS / SAS / Stata</h1>
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
<h4 data-toc-skip class="date">01 September 2022</h4>
<h4 data-toc-skip class="date">05 October 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="d-none name"><code>SPSS.Rmd</code></div>
@ -196,7 +196,7 @@
</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">461,064 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">465,095 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>
@ -380,7 +380,7 @@
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -379,7 +379,7 @@ Drug group: Beta-lactams/penicillins<br>
<div class="pkgdown-footer-right">
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@ -161,7 +161,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">01 September 2022</h4>
<h4 data-toc-skip class="date">05 October 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
@ -172,41 +172,40 @@
<p>All reference data (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are reliable, up-to-date and freely available. We continually export our data sets to formats for use in R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated text files that are machine-readable and suitable for input in any software program, such as laboratory information systems.</p>
<p>On this page, we explain how to download them and how the structure of the data sets look like.</p>
<div class="section level2">
<h2 id="microorganisms-microbial-taxonomy-currently-accepted-names">
<code>microorganisms</code>: Microbial Taxonomy (currently accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-microbial-taxonomy-currently-accepted-names"></a>
<h2 id="microorganisms-full-microbial-taxonomy">
<code>microorganisms</code>: Full Microbial Taxonomy<a class="anchor" aria-label="anchor" href="#microorganisms-full-microbial-taxonomy"></a>
</h2>
<p>A data set with 70,764 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
<p>A data set with 48,787 rows and 22 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>source</em>, <em>lpsn</em>, <em>lpsn_parent</em>, <em>lpsn_renamed_to</em>, <em>gbif</em>, <em>gbif_parent</em>, <em>gbif_renamed_to</em>, <em>prevalence</em> and <em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 1 September 2022 13:33:21 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p>It was last updated on 5 October 2022 10:27:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">original R Data Structure (RDS) file</a> (1.3 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">original R Data Structure (RDS) file</a> (1.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">tab-separated text file</a> (13.1 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">tab-separated text file</a> (0.4 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Microsoft Excel workbook</a> (5.1 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Microsoft Excel workbook</a> (4.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.feather" class="external-link">Apache Feather file</a> (5.6 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.feather" class="external-link">Apache Feather file</a> (5.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.parquet" class="external-link">Apache Parquet file</a> (2.7 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.parquet" class="external-link">Apache Parquet file</a> (2.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS data file</a> (69.1 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS data file</a> (47.7 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">IBM SPSS Statistics data file</a> (20.8 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">IBM SPSS Statistics data file</a> (15.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata DTA file</a> (62.2 MB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata DTA file</a> (44.4 MB)</li>
</ul>
<p><strong>NOTE: The exported files for Excel, SAS, SPSS and Stata contain only the first 50 SNOMED codes per record, as their file size would otherwise exceed 100 MB; the file size limit of GitHub.</strong> Advice? Use R instead.</p>
<div class="section level3">
<h3 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a>
</h3>
<p>Our full taxonomy of microorganisms is based on the authoritative and comprehensive:</p>
<p>This data set contains the full microbial taxonomy of five kingdoms from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF):</p>
<ul>
<li>
<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (included version: 2019)</li>
<li>
<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
<li>US Edition of SNOMED CT from 1 September 2020, retrieved from the <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)</a>, OID 2.16.840.1.114222.4.11.1009, version 12</li>
<li>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong> International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; . Accessed from <a href="https://lpsn.dsmz.de" class="external-link uri">https://lpsn.dsmz.de</a> on 12 September, 2022.</li>
<li>GBIF Secretariat (November 26, 2021). GBIF Backbone Taxonomy. Checklist dataset . Accessed from <a href="https://www.gbif.org" class="external-link uri">https://www.gbif.org</a> on 12 September, 2022.</li>
<li>Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link uri">https://phinvads.cdc.gov</a>
</li>
</ul>
</div>
<div class="section level3">
@ -221,53 +220,60 @@
<tbody>
<tr class="odd">
<td align="center">(unknown kingdom)</td>
<td align="center">5</td>
<td align="center">3</td>
</tr>
<tr class="even">
<td align="center">Animalia</td>
<td align="center">2,153</td>
<td align="center">1,523</td>
</tr>
<tr class="odd">
<td align="center">Archaea</td>
<td align="center">694</td>
<td align="center">1,237</td>
</tr>
<tr class="even">
<td align="center">Bacteria</td>
<td align="center">22,852</td>
<td align="center">33,713</td>
</tr>
<tr class="odd">
<td align="center">Chromista</td>
<td align="center">32,167</td>
<td align="center">Fungi</td>
<td align="center">7,365</td>
</tr>
<tr class="even">
<td align="center">Fungi</td>
<td align="center">9,582</td>
<td align="center">Protozoa</td>
<td align="center">4,946</td>
</tr>
</tbody>
</table>
<p>Example rows when filtering on genus <em>Escherichia</em>:</p>
<table style="width:100%;" class="table">
<colgroup>
<col width="5%">
<col width="8%">
<col width="3%">
<col width="5%">
<col width="7%">
<col width="6%">
<col width="7%">
<col width="4%">
<col width="4%">
<col width="4%">
<col width="3%">
<col width="9%">
<col width="4%">
<col width="2%">
<col width="2%">
<col width="4%">
<col width="16%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="3%">
<col width="4%">
<col width="3%">
<col width="2%">
<col width="7%">
<col width="2%">
<col width="2%">
<col width="3%">
<col width="4%">
<col width="2%">
<col width="3%">
<col width="4%">
<col width="3%">
<col width="12%">
</colgroup>
<thead><tr class="header">
<th align="center">mo</th>
<th align="center">fullname</th>
<th align="center">status</th>
<th align="center">kingdom</th>
<th align="center">phylum</th>
<th align="center">class</th>
@ -278,8 +284,13 @@
<th align="center">subspecies</th>
<th align="center">rank</th>
<th align="center">ref</th>
<th align="center">species_id</th>
<th align="center">source</th>
<th align="center">lpsn</th>
<th align="center">lpsn_parent</th>
<th align="center">lpsn_renamed_to</th>
<th align="center">gbif</th>
<th align="center">gbif_parent</th>
<th align="center">gbif_renamed_to</th>
<th align="center">prevalence</th>
<th align="center">snomed</th>
</tr></thead>
@ -287,8 +298,9 @@
<tr class="odd">
<td align="center">B_ESCHR</td>
<td align="center">Escherichia</td>
<td align="center">accepted</td>
<td align="center">Bacteria</td>
<td align="center">Proteobacteria</td>
<td align="center">Pseudomonadota</td>
<td align="center">Gammaproteobacteria</td>
<td align="center">Enterobacterales</td>
<td align="center">Enterobacteriaceae</td>
@ -296,17 +308,47 @@
<td align="center"></td>
<td align="center"></td>
<td align="center">genus</td>
<td align="center"></td>
<td align="center">515602</td>
<td align="center">Castellani et al., 1919</td>
<td align="center">LPSN</td>
<td align="center">515602</td>
<td align="center">482</td>
<td align="center"></td>
<td align="center">3221780</td>
<td align="center">4899</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">64735005</td>
<td align="center">407310004, 407251000, 407281008, …</td>
</tr>
<tr class="even">
<td align="center">B_ESCHR_ADCR</td>
<td align="center">Escherichia adecarboxylata</td>
<td align="center">synonym</td>
<td align="center">Bacteria</td>
<td align="center">Pseudomonadota</td>
<td align="center">Gammaproteobacteria</td>
<td align="center">Enterobacterales</td>
<td align="center">Enterobacteriaceae</td>
<td align="center">Escherichia</td>
<td align="center">adecarboxylata</td>
<td align="center"></td>
<td align="center">species</td>
<td align="center">Leclerc, 1962</td>
<td align="center">LPSN</td>
<td align="center">776052</td>
<td align="center">515602</td>
<td align="center">777447</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">1</td>
<td align="center"></td>
</tr>
<tr class="odd">
<td align="center">B_ESCHR_ALBR</td>
<td align="center">Escherichia albertii</td>
<td align="center">accepted</td>
<td align="center">Bacteria</td>
<td align="center">Proteobacteria</td>
<td align="center">Pseudomonadota</td>
<td align="center">Gammaproteobacteria</td>
<td align="center">Enterobacterales</td>
<td align="center">Enterobacteriaceae</td>
@ -315,16 +357,46 @@
<td align="center"></td>
<td align="center">species</td>
<td align="center">Huys et al., 2003</td>
<td align="center">776053</td>
<td align="center">LPSN</td>
<td align="center">776053</td>
<td align="center">515602</td>
<td align="center"></td>
<td align="center">5427575</td>
<td align="center">3221780</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">419388003</td>
</tr>
<tr class="even">
<td align="center">B_ESCHR_BLTT</td>
<td align="center">Escherichia blattae</td>
<td align="center">synonym</td>
<td align="center">Bacteria</td>
<td align="center">Pseudomonadota</td>
<td align="center">Gammaproteobacteria</td>
<td align="center">Enterobacterales</td>
<td align="center">Enterobacteriaceae</td>
<td align="center">Escherichia</td>
<td align="center">blattae</td>
<td align="center"></td>
<td align="center">species</td>
<td align="center">Burgess et al., 1973</td>
<td align="center">LPSN</td>
<td align="center">776056</td>
<td align="center">515602</td>
<td align="center">788468</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">1</td>
<td align="center"></td>
</tr>
<tr class="odd">
<td align="center">B_ESCHR_COLI</td>
<td align="center">Escherichia coli</td>
<td align="center">accepted</td>
<td align="center">Bacteria</td>
<td align="center">Proteobacteria</td>
<td align="center">Pseudomonadota</td>
<td align="center">Gammaproteobacteria</td>
<td align="center">Enterobacterales</td>
<td align="center">Enterobacteriaceae</td>
@ -333,135 +405,39 @@
<td align="center"></td>
<td align="center">species</td>
<td align="center">Castellani et al., 1919</td>
<td align="center">776057</td>
<td align="center">LPSN</td>
<td align="center">776057</td>
<td align="center">515602</td>
<td align="center"></td>
<td align="center">6110934</td>
<td align="center">3221780</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">1095001000112106, 715307006, 737528008, …</td>
</tr>
<tr class="even">
<td align="center">B_ESCHR_FRGS</td>
<td align="center">Escherichia fergusonii</td>
<td align="center">B_ESCHR_DYSN</td>
<td align="center">Escherichia dysenteriae</td>
<td align="center">accepted</td>
<td align="center">Bacteria</td>
<td align="center">Proteobacteria</td>
<td align="center">Pseudomonadota</td>
<td align="center">Gammaproteobacteria</td>
<td align="center">Enterobacterales</td>
<td align="center">Enterobacteriaceae</td>
<td align="center">Escherichia</td>
<td align="center">fergusonii</td>
<td align="center">dysenteriae</td>
<td align="center"></td>
<td align="center">species</td>
<td align="center">Farmer et al., 1985</td>
<td align="center">776059</td>
<td align="center">LPSN</td>
<td align="center">1</td>
<td align="center">72461005</td>
</tr>
<tr class="odd">
<td align="center">B_ESCHR_HRMN</td>
<td align="center">Escherichia hermannii</td>
<td align="center">Bacteria</td>
<td align="center">Proteobacteria</td>
<td align="center">Gammaproteobacteria</td>
<td align="center">Enterobacterales</td>
<td align="center">Enterobacteriaceae</td>
<td align="center">Escherichia</td>
<td align="center">hermannii</td>
<td align="center"></td>
<td align="center">species</td>
<td align="center">Brenner et al., 1983</td>
<td align="center">776060</td>
<td align="center">LPSN</td>
<td align="center">1</td>
<td align="center">85786000</td>
</tr>
<tr class="even">
<td align="center">B_ESCHR_MRMT</td>
<td align="center">Escherichia marmotae</td>
<td align="center">Bacteria</td>
<td align="center">Proteobacteria</td>
<td align="center">Gammaproteobacteria</td>
<td align="center">Enterobacterales</td>
<td align="center">Enterobacteriaceae</td>
<td align="center">Escherichia</td>
<td align="center">marmotae</td>
<td align="center">GBIF</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">10862979</td>
<td align="center">3221780</td>
<td align="center"></td>
<td align="center">species</td>
<td align="center">Liu et al., 2015</td>
<td align="center">792928</td>
<td align="center">LPSN</td>
<td align="center">1</td>
<td align="center">14961000146107</td>
</tr>
</tbody>
</table>
</div>
</div>
<div class="section level2">
<h2 id="microorganisms-old-microbial-taxonomy-previously-accepted-names">
<code>microorganisms.old</code>: Microbial Taxonomy (previously accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-old-microbial-taxonomy-previously-accepted-names"></a>
</h2>
<p>A data set with 14,338 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>prevalence</em>.</p>
<p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
<p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 1 September 2022 13:33:21 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">original R Data Structure (RDS) file</a> (0.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.txt" class="external-link">tab-separated text file</a> (1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.xlsx" class="external-link">Microsoft Excel workbook</a> (0.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.feather" class="external-link">Apache Feather file</a> (0.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.parquet" class="external-link">Apache Parquet file</a> (0.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sas" class="external-link">SAS data file</a> (2.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sav" class="external-link">IBM SPSS Statistics data file</a> (1.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.dta" class="external-link">Stata DTA file</a> (2 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-1">Source<a class="anchor" aria-label="anchor" href="#source-1"></a>
</h3>
<p>This data set contains old, previously accepted taxonomic names. The data sources are the same as the <code>microorganisms</code> data set:</p>
<ul>
<li>
<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (included version: 2019)</li>
<li>
<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
</ul>
</div>
<div class="section level3">
<h3 id="example-content-1">Example content<a class="anchor" aria-label="anchor" href="#example-content-1"></a>
</h3>
<p>Example rows when filtering on <em>Escherichia</em>:</p>
<table class="table">
<thead><tr class="header">
<th align="center">fullname</th>
<th align="center">fullname_new</th>
<th align="center">ref</th>
<th align="center">prevalence</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">Escherichia adecarboxylata</td>
<td align="center">Leclercia adecarboxylata</td>
<td align="center">Leclerc, 1962</td>
<td align="center">1</td>
</tr>
<tr class="even">
<td align="center">Escherichia blattae</td>
<td align="center">Shimwellia blattae</td>
<td align="center">Burgess et al., 1973</td>
<td align="center">1</td>
</tr>
<tr class="odd">
<td align="center">Escherichia vulneris</td>
<td align="center">Pseudescherichia vulneris</td>
<td align="center">Brenner et al., 1983</td>
<td align="center">1</td>
<td align="center"></td>
</tr>
</tbody>
</table>
@ -473,7 +449,7 @@
</h2>
<p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 1 September 2022 13:33:21 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 5 October 2022 10:27:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">original R Data Structure (RDS) file</a> (36 kB)<br>
@ -493,7 +469,7 @@
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata DTA file</a> (0.3 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-2">Source<a class="anchor" aria-label="anchor" href="#source-2"></a>
<h3 id="source-1">Source<a class="anchor" aria-label="anchor" href="#source-1"></a>
</h3>
<p>This data set contains all EARS-Net and ATC codes gathered from WHO and WHONET, and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
<ul>
@ -504,7 +480,7 @@
</ul>
</div>
<div class="section level3">
<h3 id="example-content-2">Example content<a class="anchor" aria-label="anchor" href="#example-content-2"></a>
<h3 id="example-content-1">Example content<a class="anchor" aria-label="anchor" href="#example-content-1"></a>
</h3>
<table style="width:100%;" class="table">
<colgroup>
@ -646,7 +622,7 @@
</h2>
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 1 September 2022 13:33:21 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 5 October 2022 10:27:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">original R Data Structure (RDS) file</a> (4 kB)<br>
@ -666,7 +642,7 @@
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata DTA file</a> (67 kB)</li>
</ul>
<div class="section level3">
<h3 id="source-3">Source<a class="anchor" aria-label="anchor" href="#source-3"></a>
<h3 id="source-2">Source<a class="anchor" aria-label="anchor" href="#source-2"></a>
</h3>
<p>This data set contains all ATC codes gathered from WHO and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
<ul>
@ -676,7 +652,7 @@
</ul>
</div>
<div class="section level3">
<h3 id="example-content-3">Example content<a class="anchor" aria-label="anchor" href="#example-content-3"></a>
<h3 id="example-content-2">Example content<a class="anchor" aria-label="anchor" href="#example-content-2"></a>
</h3>
<table class="table">
<colgroup>
@ -778,7 +754,7 @@
</h2>
<p>A data set with 20,369 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 1 September 2022 13:33:21 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p>It was last updated on 5 October 2022 10:27:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">original R Data Structure (RDS) file</a> (49 kB)<br>
@ -798,12 +774,12 @@
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata DTA file</a> (3.8 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
<h3 id="source-3">Source<a class="anchor" aria-label="anchor" href="#source-3"></a>
</h3>
<p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2011-2022) and EUCAST (2011-2022).</p>
</div>
<div class="section level3">
<h3 id="example-content-4">Example content<a class="anchor" aria-label="anchor" href="#example-content-4"></a>
<h3 id="example-content-3">Example content<a class="anchor" aria-label="anchor" href="#example-content-3"></a>
</h3>
<table style="width:100%;" class="table">
<colgroup>
@ -935,9 +911,9 @@
<h2 id="intrinsic_resistant-intrinsic-bacterial-resistance">
<code>intrinsic_resistant</code>: Intrinsic Bacterial Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intrinsic-bacterial-resistance"></a>
</h2>
<p>A data set with 134,956 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
<p>A data set with 134,659 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 1 September 2022 13:33:21 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p>It was last updated on 5 October 2022 10:27:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">original R Data Structure (RDS) file</a> (78 kB)<br>
@ -950,19 +926,19 @@
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.parquet" class="external-link">Apache Parquet file</a> (0.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS data file</a> (10.4 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS data file</a> (9.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">IBM SPSS Statistics data file</a> (7.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata DTA file</a> (10.2 MB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata DTA file</a> (9.6 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></a>
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
</h3>
<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes/" class="external-link">‘EUCAST Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ v3.3</a> (2021).</p>
</div>
<div class="section level3">
<h3 id="example-content-5">Example content<a class="anchor" aria-label="anchor" href="#example-content-5"></a>
<h3 id="example-content-4">Example content<a class="anchor" aria-label="anchor" href="#example-content-4"></a>
</h3>
<p>Example rows when filtering on <em>Enterobacter cloacae</em>:</p>
<table class="table">
@ -1209,7 +1185,7 @@
</h2>
<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 1 September 2022 13:33:21 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p>It was last updated on 5 October 2022 10:27:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">original R Data Structure (RDS) file</a> (3 kB)<br>
@ -1229,13 +1205,13 @@
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata DTA file</a> (44 kB)</li>
</ul>
<div class="section level3">
<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
<h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></a>
</h3>
<p>EUCAST breakpoints used in this package are based on the dosages in this data set.</p>
<p>Currently included dosages in the data set are meant for: <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical Breakpoint Tables’ v11.0</a> (2021).</p>
</div>
<div class="section level3">
<h3 id="example-content-6">Example content<a class="anchor" aria-label="anchor" href="#example-content-6"></a>
<h3 id="example-content-5">Example content<a class="anchor" aria-label="anchor" href="#example-content-5"></a>
</h3>
<table class="table">
<thead><tr class="header">
@ -1326,14 +1302,14 @@
</h2>
<p>A data set with 2,000 rows and 46 columns, containing the following column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>, <em>ward</em>, <em>mo</em>, <em>PEN</em>, <em>OXA</em>, <em>FLC</em>, <em>AMX</em>, <em>AMC</em>, <em>AMP</em>, <em>TZP</em>, <em>CZO</em>, <em>FEP</em>, <em>CXM</em>, <em>FOX</em>, <em>CTX</em>, <em>CAZ</em>, <em>CRO</em>, <em>GEN</em>, <em>TOB</em>, <em>AMK</em>, <em>KAN</em>, <em>TMP</em>, <em>SXT</em>, <em>NIT</em>, <em>FOS</em>, <em>LNZ</em>, <em>CIP</em>, <em>MFX</em>, <em>VAN</em>, <em>TEC</em>, <em>TCY</em>, <em>TGC</em>, <em>DOX</em>, <em>ERY</em>, <em>CLI</em>, <em>AZM</em>, <em>IPM</em>, <em>MEM</em>, <em>MTR</em>, <em>CHL</em>, <em>COL</em>, <em>MUP</em> and <em>RIF</em>.</p>
<p>This data set is in R available as <code>example_isolates</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 1 September 2022 13:33:21 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
<p>It was last updated on 5 October 2022 10:27:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
<div class="section level3">
<h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>
<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
</h3>
<p>This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis.</p>
</div>
<div class="section level3">
<h3 id="example-content-7">Example content<a class="anchor" aria-label="anchor" href="#example-content-7"></a>
<h3 id="example-content-6">Example content<a class="anchor" aria-label="anchor" href="#example-content-6"></a>
</h3>
<table class="table">
<colgroup>
@ -1731,14 +1707,14 @@
</h2>
<p>A data set with 3,000 rows and 8 columns, containing the following column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>, <em>bacteria</em>, <em>AMX</em>, <em>AMC</em>, <em>CIP</em> and <em>GEN</em>.</p>
<p>This data set is in R available as <code>example_isolates_unclean</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 1 September 2022 13:33:21 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
<p>It was last updated on 5 October 2022 10:27:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
<div class="section level3">
<h3 id="source-8">Source<a class="anchor" aria-label="anchor" href="#source-8"></a>
<h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>
</h3>
<p>This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis.</p>
</div>
<div class="section level3">
<h3 id="example-content-8">Example content<a class="anchor" aria-label="anchor" href="#example-content-8"></a>
<h3 id="example-content-7">Example content<a class="anchor" aria-label="anchor" href="#example-content-7"></a>
</h3>
<table class="table">
<thead><tr class="header">
@ -1829,7 +1805,7 @@
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<p>Note: to keep the package size as small as possible, we only included this vignette on CRAN. You can read more vignettes on our website about how to conduct AMR data analysis, determine MDROs, find explanation of EUCAST rules, and much more: <a href="https://msberends.github.io/AMR/articles/" class="uri">https://msberends.github.io/AMR/articles/</a>.</p>
<hr>
<p>The <code>AMR</code> package is a <a href="https://msberends.github.io/AMR/#copyright">free and open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero dependencies</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
<p>After installing this package, R knows ~71,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>This work was published in the Journal of Statistical Software (Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">DOI 10.18637/jss.v104.i03</a>) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>).</p>
<p>After installing this package, R knows ~49,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>The <code>AMR</code> package is available in English, Chinese, Danish, Dutch, French, German, Greek, Italian, Japanese, Polish, Portuguese, Russian, Spanish, Swedish, Turkish and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
<p>This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. Since its first public release in early 2018, this package has been downloaded from more than 175 countries.</p>
<p>This package can be used for:</p>
<ul>
<li>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the Catalogue of Life and List of Prokaryotic names with Standing in Nomenclature</li>
<li>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF)</li>
<li>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines</li>
<li>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records</li>
<li>Determining first isolates to be used for AMR data analysis</li>
@ -194,7 +195,7 @@
<li>Principal component analysis for AMR</li>
</ul>
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
<p>This R package was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>) but is actively and durably maintained (see <a href="https://msberends.github.io/AMR/news/index.html">changelog)</a>) by two public healthcare organisations in the Netherlands.</p>
<p>This R package was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>, and is being <a href="./news">actively and durably maintained</a> by two public healthcare organisations in the Netherlands.</p>
<hr>
<p><small> This AMR package for R is free, open-source software and licensed under the <a href="https://msberends.github.io/AMR/LICENSE-text.html">GNU General Public License v2.0 (GPL-2)</a>. These requirements are consequently legally binding: modifications must be released under the same license when distributing the package, changes made to the code must be documented, source code must be made available when the package is distributed, and a copy of the license and copyright notice must be included with the package. </small></p>
</main>
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