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404.html
@ -36,7 +36,7 @@
|
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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9018</small>
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||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</small>
|
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|
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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|
@ -10,7 +10,7 @@
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<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</small>
|
||||
|
||||
|
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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|
@ -38,7 +38,7 @@
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|
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<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</small>
|
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|
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|
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -162,7 +162,7 @@
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<img src="../logo.svg" class="logo" alt=""><h1>How to conduct AMR data analysis</h1>
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<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
|
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|
||||
<h4 data-toc-skip class="date">15 October 2022</h4>
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<h4 data-toc-skip class="date">19 October 2022</h4>
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<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>
|
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<div class="d-none name"><code>AMR.Rmd</code></div>
|
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@ -170,7 +170,7 @@
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<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 15 October 2022.</p>
|
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<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 19 October 2022.</p>
|
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<div class="section level2">
|
||||
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
|
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</h2>
|
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@ -201,21 +201,21 @@
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2022-10-15</td>
|
||||
<td align="center">2022-10-19</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">2022-10-15</td>
|
||||
<td align="center">2022-10-19</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">2022-10-15</td>
|
||||
<td align="center">2022-10-19</td>
|
||||
<td align="center">efgh</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
@ -325,9 +325,9 @@
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2013-11-03</td>
|
||||
<td align="center">S4</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">2010-03-04</td>
|
||||
<td align="center">Q1</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Klebsiella pneumoniae</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@ -336,20 +336,42 @@
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2010-09-09</td>
|
||||
<td align="center">P3</td>
|
||||
<td align="center">2016-12-24</td>
|
||||
<td align="center">I6</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Streptococcus pneumoniae</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2016-04-30</td>
|
||||
<td align="center">K3</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">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2014-02-16</td>
|
||||
<td align="center">W5</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">F</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2011-01-31</td>
|
||||
<td align="center">E10</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">2012-07-09</td>
|
||||
<td align="center">J8</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@ -358,38 +380,16 @@
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2012-02-03</td>
|
||||
<td align="center">D6</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">2011-07-03</td>
|
||||
<td align="center">J2</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">Streptococcus pneumoniae</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="odd">
|
||||
<td align="center">2015-06-15</td>
|
||||
<td align="center">V10</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2010-03-18</td>
|
||||
<td align="center">U8</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>Now, let’s start the cleaning and the analysis!</p>
|
||||
@ -422,16 +422,16 @@ Longest: 1</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">M</td>
|
||||
<td align="right">10,447</td>
|
||||
<td align="right">52.24%</td>
|
||||
<td align="right">10,447</td>
|
||||
<td align="right">52.24%</td>
|
||||
<td align="right">10,463</td>
|
||||
<td align="right">52.32%</td>
|
||||
<td align="right">10,463</td>
|
||||
<td align="right">52.32%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">F</td>
|
||||
<td align="right">9,553</td>
|
||||
<td align="right">47.77%</td>
|
||||
<td align="right">9,537</td>
|
||||
<td align="right">47.69%</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"># => Found 10,641 'phenotype-based' first isolates (53.2% of total where a</span></span>
|
||||
<span><span class="co"># => Found 10,669 'phenotype-based' first isolates (53.3% of total where a</span></span>
|
||||
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
|
||||
<p>So only 53.2% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
|
||||
<p>So only 53.3% 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"><-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</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"><-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</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 10,641 isolates for analysis. Now our data looks like:</p>
|
||||
<p>So we end up with 10,669 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 style="width:100%;" class="table">
|
||||
<table class="table">
|
||||
<colgroup>
|
||||
<col width="2%">
|
||||
<col width="9%">
|
||||
@ -515,7 +515,7 @@ Longest: 1</p>
|
||||
<col width="3%">
|
||||
<col width="6%">
|
||||
<col width="11%">
|
||||
<col width="12%">
|
||||
<col width="11%">
|
||||
<col width="9%">
|
||||
<col width="5%">
|
||||
</colgroup>
|
||||
@ -538,9 +538,9 @@ Longest: 1</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="center">2013-11-03</td>
|
||||
<td align="center">S4</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">2010-03-04</td>
|
||||
<td align="center">Q1</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_KLBSL_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
@ -553,77 +553,13 @@ Longest: 1</p>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">9</td>
|
||||
<td align="center">2016-10-09</td>
|
||||
<td align="center">U9</td>
|
||||
<td align="left">2</td>
|
||||
<td align="center">2016-12-24</td>
|
||||
<td align="center">I6</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_KLBSL_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">10</td>
|
||||
<td align="center">2016-12-03</td>
|
||||
<td align="center">D2</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">12</td>
|
||||
<td align="center">2017-12-08</td>
|
||||
<td align="center">C5</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">13</td>
|
||||
<td align="center">2015-07-26</td>
|
||||
<td align="center">W6</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">14</td>
|
||||
<td align="center">2014-06-06</td>
|
||||
<td align="center">I9</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">I</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>
|
||||
@ -632,6 +568,70 @@ Longest: 1</p>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">6</td>
|
||||
<td align="center">2011-07-03</td>
|
||||
<td align="center">J2</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="even">
|
||||
<td align="left">7</td>
|
||||
<td align="center">2011-05-07</td>
|
||||
<td align="center">F3</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">2017-04-03</td>
|
||||
<td align="center">O7</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="even">
|
||||
<td align="left">10</td>
|
||||
<td align="center">2012-08-29</td>
|
||||
<td align="center">O9</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">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>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>Time for the analysis!</p>
|
||||
@ -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">%>%</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: 10,641<br>
|
||||
Available: 10,641 (100.0%, NA: 0 = 0.0%)<br>
|
||||
Length: 10,669<br>
|
||||
Available: 10,669 (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">4,650</td>
|
||||
<td align="right">43.70%</td>
|
||||
<td align="right">4,650</td>
|
||||
<td align="right">43.70%</td>
|
||||
<td align="right">4,646</td>
|
||||
<td align="right">43.55%</td>
|
||||
<td align="right">4,646</td>
|
||||
<td align="right">43.55%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Staphylococcus aureus</td>
|
||||
<td align="right">2,752</td>
|
||||
<td align="right">25.86%</td>
|
||||
<td align="right">7,402</td>
|
||||
<td align="right">69.56%</td>
|
||||
<td align="right">2,725</td>
|
||||
<td align="right">25.54%</td>
|
||||
<td align="right">7,371</td>
|
||||
<td align="right">69.09%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Streptococcus pneumoniae</td>
|
||||
<td align="right">2,109</td>
|
||||
<td align="right">19.82%</td>
|
||||
<td align="right">2,140</td>
|
||||
<td align="right">20.06%</td>
|
||||
<td align="right">9,511</td>
|
||||
<td align="right">89.38%</td>
|
||||
<td align="right">89.15%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Klebsiella pneumoniae</td>
|
||||
<td align="right">1,130</td>
|
||||
<td align="right">10.62%</td>
|
||||
<td align="right">10,641</td>
|
||||
<td align="right">1,158</td>
|
||||
<td align="right">10.85%</td>
|
||||
<td align="right">10,669</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>
|
||||
@ -744,12 +744,12 @@ Longest: 24</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2014-06-06</td>
|
||||
<td align="center">I9</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">2016-12-24</td>
|
||||
<td align="center">I6</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">I</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>
|
||||
@ -759,28 +759,28 @@ Longest: 24</p>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2012-11-06</td>
|
||||
<td align="center">S6</td>
|
||||
<td align="center">2011-07-03</td>
|
||||
<td align="center">J2</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">F</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">2013-06-12</td>
|
||||
<td align="center">X6</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">2017-04-03</td>
|
||||
<td align="center">O7</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">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
@ -789,48 +789,48 @@ Longest: 24</p>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2012-05-27</td>
|
||||
<td align="center">U4</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">2014-08-04</td>
|
||||
<td align="center">H1</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">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">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">2011-05-24</td>
|
||||
<td align="center">T10</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_KLBSL_PNMN</td>
|
||||
<td align="center">2010-04-30</td>
|
||||
<td align="center">J8</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">2010-07-17</td>
|
||||
<td align="center">Y3</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">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2016-12-19</td>
|
||||
<td align="center">T6</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
@ -854,50 +854,50 @@ Longest: 24</p>
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">AMX</td>
|
||||
<td align="center">2161</td>
|
||||
<td align="center">117</td>
|
||||
<td align="center">2372</td>
|
||||
<td align="center">4650</td>
|
||||
<td align="center">2135</td>
|
||||
<td align="center">140</td>
|
||||
<td align="center">2371</td>
|
||||
<td align="center">4646</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">AMC</td>
|
||||
<td align="center">3443</td>
|
||||
<td align="center">155</td>
|
||||
<td align="center">1052</td>
|
||||
<td align="center">4650</td>
|
||||
<td align="center">3388</td>
|
||||
<td align="center">166</td>
|
||||
<td align="center">1092</td>
|
||||
<td align="center">4646</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">CIP</td>
|
||||
<td align="center">3401</td>
|
||||
<td align="center">3397</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">1249</td>
|
||||
<td align="center">4650</td>
|
||||
<td align="center">4646</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">4070</td>
|
||||
<td align="center">4031</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">580</td>
|
||||
<td align="center">4650</td>
|
||||
<td align="center">615</td>
|
||||
<td align="center">4646</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">1130</td>
|
||||
<td align="center">1130</td>
|
||||
<td align="center">1158</td>
|
||||
<td align="center">1158</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center">AMC</td>
|
||||
<td align="center">902</td>
|
||||
<td align="center">47</td>
|
||||
<td align="center">181</td>
|
||||
<td align="center">1130</td>
|
||||
<td align="center">918</td>
|
||||
<td align="center">42</td>
|
||||
<td align="center">198</td>
|
||||
<td align="center">1158</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">4070</td>
|
||||
<td align="center">4031</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">580</td>
|
||||
<td align="center">4650</td>
|
||||
<td align="center">615</td>
|
||||
<td align="center">4646</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">1013</td>
|
||||
<td align="center">1057</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">117</td>
|
||||
<td align="center">1130</td>
|
||||
<td align="center">101</td>
|
||||
<td align="center">1158</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">S. aureus</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">2450</td>
|
||||
<td align="center">2431</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">302</td>
|
||||
<td align="center">2752</td>
|
||||
<td align="center">294</td>
|
||||
<td align="center">2725</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">2109</td>
|
||||
<td align="center">2109</td>
|
||||
<td align="center">2140</td>
|
||||
<td align="center">2140</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">%>%</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] 0.5466591</span></span></code></pre></div>
|
||||
<span><span class="co"># [1] 0.5476614</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">%>%</a></span></span>
|
||||
@ -975,19 +975,19 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.5511962</td>
|
||||
<td align="center">0.5541245</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.5518367</td>
|
||||
<td align="center">0.5501455</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.5463475</td>
|
||||
<td align="center">0.5269306</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.5317893</td>
|
||||
<td align="center">0.5483716</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1008,23 +1008,23 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.5511962</td>
|
||||
<td align="center">3135</td>
|
||||
<td align="center">0.5541245</td>
|
||||
<td align="center">3261</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.5518367</td>
|
||||
<td align="center">3675</td>
|
||||
<td align="center">0.5501455</td>
|
||||
<td align="center">3779</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.5463475</td>
|
||||
<td align="center">1629</td>
|
||||
<td align="center">0.5269306</td>
|
||||
<td align="center">1541</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.5317893</td>
|
||||
<td align="center">2202</td>
|
||||
<td align="center">0.5483716</td>
|
||||
<td align="center">2088</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1047,27 +1047,27 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">0.7737634</td>
|
||||
<td align="center">0.8752688</td>
|
||||
<td align="center">0.9750538</td>
|
||||
<td align="center">0.7649591</td>
|
||||
<td align="center">0.8676281</td>
|
||||
<td align="center">0.9750323</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">0.8398230</td>
|
||||
<td align="center">0.8964602</td>
|
||||
<td align="center">0.9787611</td>
|
||||
<td align="center">0.8290155</td>
|
||||
<td align="center">0.9127807</td>
|
||||
<td align="center">0.9818653</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">0.7914244</td>
|
||||
<td align="center">0.8902616</td>
|
||||
<td align="center">0.9792878</td>
|
||||
<td align="center">0.7893578</td>
|
||||
<td align="center">0.8921101</td>
|
||||
<td align="center">0.9809174</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">0.5400664</td>
|
||||
<td align="center">0.5341121</td>
|
||||
<td align="center">0.0000000</td>
|
||||
<td align="center">0.5400664</td>
|
||||
<td align="center">0.5341121</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1092,23 +1092,23 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">Hospital A</td>
|
||||
<td align="right">55.1%</td>
|
||||
<td align="right">26.5%</td>
|
||||
<td align="right">55.4%</td>
|
||||
<td align="right">27.2%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Hospital B</td>
|
||||
<td align="right">55.2%</td>
|
||||
<td align="right">26.7%</td>
|
||||
<td align="right">55.0%</td>
|
||||
<td align="right">26.8%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Hospital C</td>
|
||||
<td align="right">54.6%</td>
|
||||
<td align="right">25.0%</td>
|
||||
<td align="right">52.7%</td>
|
||||
<td align="right">27.3%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Hospital D</td>
|
||||
<td align="right">53.2%</td>
|
||||
<td align="right">25.3%</td>
|
||||
<td align="right">54.8%</td>
|
||||
<td align="right">25.9%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1205,17 +1205,17 @@ Longest: 24</p>
|
||||
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op"><-</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 <mic></span></span>
|
||||
<span><span class="co"># [1] 128 64 128 0.001 4 0.25 64 0.5 32 0.25 </span></span>
|
||||
<span><span class="co"># [11] 0.025 0.002 1 16 0.005 0.025 0.25 0.005 0.001 64 </span></span>
|
||||
<span><span class="co"># [21] 0.025 1 16 >=256 16 1 16 0.001 0.125 64 </span></span>
|
||||
<span><span class="co"># [31] 8 0.002 0.5 0.005 0.005 4 8 0.002 0.025 32 </span></span>
|
||||
<span><span class="co"># [41] 0.0625 0.001 0.125 2 8 16 0.25 1 128 4 </span></span>
|
||||
<span><span class="co"># [51] 0.001 0.125 0.005 0.25 0.5 0.0625 0.0625 0.005 0.5 1 </span></span>
|
||||
<span><span class="co"># [61] 0.005 16 4 0.025 32 16 128 0.5 16 4 </span></span>
|
||||
<span><span class="co"># [71] 0.002 1 0.5 0.5 0.025 8 32 16 64 32 </span></span>
|
||||
<span><span class="co"># [81] 4 32 2 >=256 0.125 0.025 >=256 16 2 0.01 </span></span>
|
||||
<span><span class="co"># [91] 0.5 128 0.01 0.0625 128 32 0.125 1 0.125 0.025</span></span></code></pre></div>
|
||||
<span><span class="co"># Class 'mic'</span></span>
|
||||
<span><span class="co"># [1] 0.01 128 0.005 2 0.002 0.025 128 0.001 4 128 </span></span>
|
||||
<span><span class="co"># [11] 32 128 0.002 0.025 2 128 8 16 0.002 0.005 </span></span>
|
||||
<span><span class="co"># [21] 0.005 0.0625 0.0625 2 0.5 0.25 0.001 4 32 >=256 </span></span>
|
||||
<span><span class="co"># [31] 0.25 >=256 0.125 4 0.001 32 16 0.25 0.025 0.002 </span></span>
|
||||
<span><span class="co"># [41] 32 128 64 16 0.001 64 0.025 0.125 0.025 >=256 </span></span>
|
||||
<span><span class="co"># [51] >=256 1 0.0625 32 0.025 16 8 0.025 0.025 >=256 </span></span>
|
||||
<span><span class="co"># [61] 0.0625 0.01 0.002 0.025 0.002 0.002 0.5 64 0.25 0.5 </span></span>
|
||||
<span><span class="co"># [71] 64 0.0625 1 0.0625 2 0.0625 0.25 0.25 32 1 </span></span>
|
||||
<span><span class="co"># [81] 4 0.005 128 0.5 0.001 16 0.25 16 0.5 >=256 </span></span>
|
||||
<span><span class="co"># [91] 0.002 32 0.005 16 16 128 0.025 0.0625 128 0.001</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>
|
||||
@ -1241,11 +1241,11 @@ Longest: 24</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"><-</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="va">disk_values</span></span>
|
||||
<span><span class="co"># Class <disk></span></span>
|
||||
<span><span class="co"># [1] 28 21 23 24 17 19 17 17 29 20 28 20 31 17 24 25 21 29 19 18 30 21 22 29 19</span></span>
|
||||
<span><span class="co"># [26] 24 27 18 19 28 20 19 21 30 17 29 28 26 23 19 20 30 25 19 19 28 19 25 23 19</span></span>
|
||||
<span><span class="co"># [51] 20 18 23 27 28 28 17 30 22 24 30 27 18 24 25 22 30 21 29 30 29 31 23 28 31</span></span>
|
||||
<span><span class="co"># [76] 19 17 22 25 25 21 17 31 31 24 30 30 26 20 19 20 25 25 23 17 24 21 20 18 18</span></span></code></pre></div>
|
||||
<span><span class="co"># Class 'disk'</span></span>
|
||||
<span><span class="co"># [1] 30 17 29 30 29 30 28 21 28 19 26 17 25 30 18 21 23 29 21 18 17 18 23 27 23</span></span>
|
||||
<span><span class="co"># [26] 30 29 26 24 29 31 31 24 19 22 26 17 24 25 27 20 29 28 20 28 30 19 31 19 18</span></span>
|
||||
<span><span class="co"># [51] 23 24 23 25 22 28 29 18 26 20 23 20 23 28 18 22 19 29 30 18 28 22 30 31 18</span></span>
|
||||
<span><span class="co"># [76] 22 21 29 30 25 30 24 29 21 27 31 24 29 18 21 30 26 20 27 19 20 25 18 24 27</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>
|
||||
|
Before (image error) Size: 38 KiB After (image error) Size: 37 KiB |
Before (image error) Size: 56 KiB After (image error) Size: 52 KiB |
Before (image error) Size: 28 KiB After (image error) Size: 28 KiB |
Before (image error) Size: 38 KiB After (image error) Size: 38 KiB |
Before (image error) Size: 37 KiB After (image error) Size: 37 KiB |
Before (image error) Size: 51 KiB After (image error) Size: 51 KiB |
Before (image error) Size: 42 KiB After (image error) Size: 42 KiB |
Before (image error) Size: 28 KiB After (image error) Size: 28 KiB |
Before (image error) Size: 76 KiB After (image error) Size: 76 KiB |
Before (image error) Size: 49 KiB After (image error) Size: 49 KiB |
@ -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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -226,7 +226,7 @@
|
||||
<span><span class="co"># 3. Otherwise: Negative</span></span>
|
||||
<span><span class="co"># </span></span>
|
||||
<span><span class="co"># Unmatched rows will return NA.</span></span>
|
||||
<span><span class="co"># Results will be of class <factor>, with ordered levels: Negative < Elderly Type A < Elderly Type B</span></span></code></pre></div>
|
||||
<span><span class="co"># Results will be of class 'factor', with ordered levels: Negative < Elderly Type A < Elderly Type B</span></span></code></pre></div>
|
||||
<p>The outcome of the function can be used for the <code>guideline</code> argument in the <code><a href="../reference/mdro.html">mdro()</a></code> function:</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">example_isolates</span>, guideline <span class="op">=</span> <span class="va">custom</span><span class="op">)</span></span>
|
||||
@ -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 S R S I R</span></span>
|
||||
<span><span class="co"># 2 I S R R R S</span></span>
|
||||
<span><span class="co"># 3 S I I S I I</span></span>
|
||||
<span><span class="co"># 4 I I S S R R</span></span>
|
||||
<span><span class="co"># 5 R I R S I I</span></span>
|
||||
<span><span class="co"># 6 I I S S I S</span></span>
|
||||
<span><span class="co"># 1 R S I S I S</span></span>
|
||||
<span><span class="co"># 2 R R I R R I</span></span>
|
||||
<span><span class="co"># 3 R I S I I I</span></span>
|
||||
<span><span class="co"># 4 R R S I S S</span></span>
|
||||
<span><span class="co"># 5 R R S R I R</span></span>
|
||||
<span><span class="co"># 6 S S R I S S</span></span>
|
||||
<span><span class="co"># kanamycin</span></span>
|
||||
<span><span class="co"># 1 S</span></span>
|
||||
<span><span class="co"># 2 I</span></span>
|
||||
<span><span class="co"># 1 R</span></span>
|
||||
<span><span class="co"># 2 S</span></span>
|
||||
<span><span class="co"># 3 R</span></span>
|
||||
<span><span class="co"># 4 R</span></span>
|
||||
<span><span class="co"># 4 I</span></span>
|
||||
<span><span class="co"># 5 S</span></span>
|
||||
<span><span class="co"># 6 S</span></span></code></pre></div>
|
||||
<span><span class="co"># 6 I</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>
|
||||
@ -357,32 +357,32 @@ Unique: 5</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Mono-resistant</td>
|
||||
<td align="right">3196</td>
|
||||
<td align="right">63.92%</td>
|
||||
<td align="right">3196</td>
|
||||
<td align="right">63.92%</td>
|
||||
<td align="right">3161</td>
|
||||
<td align="right">63.22%</td>
|
||||
<td align="right">3161</td>
|
||||
<td align="right">63.22%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">989</td>
|
||||
<td align="right">19.78%</td>
|
||||
<td align="right">4185</td>
|
||||
<td align="right">83.70%</td>
|
||||
<td align="right">1035</td>
|
||||
<td align="right">20.70%</td>
|
||||
<td align="right">4196</td>
|
||||
<td align="right">83.92%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Multi-drug-resistant</td>
|
||||
<td align="right">455</td>
|
||||
<td align="right">9.10%</td>
|
||||
<td align="right">4640</td>
|
||||
<td align="right">92.80%</td>
|
||||
<td align="right">452</td>
|
||||
<td align="right">9.04%</td>
|
||||
<td align="right">4648</td>
|
||||
<td align="right">92.96%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Poly-resistant</td>
|
||||
<td align="right">249</td>
|
||||
<td align="right">4.98%</td>
|
||||
<td align="right">241</td>
|
||||
<td align="right">4.82%</td>
|
||||
<td align="right">4889</td>
|
||||
<td align="right">97.78%</td>
|
||||
</tr>
|
||||
|
@ -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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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 import data from SPSS / SAS / Stata</h1>
|
||||
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
|
||||
|
||||
<h4 data-toc-skip class="date">15 October 2022</h4>
|
||||
<h4 data-toc-skip class="date">19 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">466,054 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">466,988 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>
|
||||
@ -218,10 +218,10 @@
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="co"># not all values are valid MIC values:</span></span>
|
||||
<span><span class="fu"><a href="../reference/as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">0.125</span><span class="op">)</span></span>
|
||||
<span><span class="co"># Class <mic></span></span>
|
||||
<span><span class="co"># Class 'mic'</span></span>
|
||||
<span><span class="co"># [1] 0.125</span></span>
|
||||
<span><span class="fu"><a href="../reference/as.mic.html">as.mic</a></span><span class="op">(</span><span class="st">"testvalue"</span><span class="op">)</span></span>
|
||||
<span><span class="co"># Class <mic></span></span>
|
||||
<span><span class="co"># Class 'mic'</span></span>
|
||||
<span><span class="co"># [1] <NA></span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># the Gram stain is available for all bacteria:</span></span>
|
||||
|
@ -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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -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">15 October 2022</h4>
|
||||
<h4 data-toc-skip class="date">19 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>
|
||||
@ -177,7 +177,7 @@
|
||||
</h2>
|
||||
<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 15 October 2022 13:21:31 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 19 October 2022 09:53:44 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> (1.1 MB)<br>
|
||||
@ -449,7 +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 15 October 2022 13:21:31 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 19 October 2022 09:53:44 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>
|
||||
@ -622,7 +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 15 October 2022 13:21:31 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 19 October 2022 09:53:44 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>
|
||||
@ -754,7 +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 15 October 2022 13:21:31 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 19 October 2022 09:53:44 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>
|
||||
@ -913,7 +913,7 @@
|
||||
</h2>
|
||||
<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 15 October 2022 13:21:31 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 19 October 2022 09:53:44 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>
|
||||
@ -1185,7 +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 15 October 2022 13:21:31 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 19 October 2022 09:53:44 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>
|
||||
@ -1302,7 +1302,7 @@
|
||||
</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 15 October 2022 13:21:31 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 19 October 2022 09:53:44 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-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
|
||||
</h3>
|
||||
@ -1707,7 +1707,7 @@
|
||||
</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 15 October 2022 13:21:31 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 19 October 2022 09:53:44 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-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>
|
||||
</h3>
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -42,7 +42,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -127,10 +127,10 @@
|
||||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
<h2 class="pkg-version" data-toc-text="1.8.2.9018" id="amr-1829018">AMR 1.8.2.9018<a class="anchor" aria-label="anchor" href="#amr-1829018"></a></h2>
|
||||
<h2 class="pkg-version" data-toc-text="1.8.2.9023" id="amr-1829023">AMR 1.8.2.9023<a class="anchor" aria-label="anchor" href="#amr-1829023"></a></h2>
|
||||
<p>This version will eventually become v2.0! We’re happy to reach a new major milestone soon!</p>
|
||||
<div class="section level4">
|
||||
<h4 id="breaking-1-8-2-9018">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9018"></a></h4>
|
||||
<h4 id="breaking-1-8-2-9023">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9023"></a></h4>
|
||||
<ul><li>Removed all species of the taxonomic kingdom Chromista from the package. This was done for multiple reasons:<ul><li>CRAN allows packages to be around 5 MB maximum, some packages are exempted but this package is not one of them</li>
|
||||
<li>Chromista are not relevant when it comes to antimicrobial resistance, thus lacking the primary scope of this package</li>
|
||||
<li>Chromista are almost never clinically relevant, thus lacking the secondary scope of this package</li>
|
||||
@ -140,7 +140,7 @@
|
||||
<li>The <code><a href="../reference/mo_matching_score.html">mo_matching_score()</a></code> now count deletions and substitutions as 2 instead of 1, which impacts the outcome of <code><a href="../reference/as.mo.html">as.mo()</a></code> and any <code>mo_*()</code> function</li>
|
||||
</ul></div>
|
||||
<div class="section level4">
|
||||
<h4 id="new-1-8-2-9018">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9018"></a></h4>
|
||||
<h4 id="new-1-8-2-9023">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9023"></a></h4>
|
||||
<ul><li>EUCAST 2022 and CLSI 2022 guidelines have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.</li>
|
||||
<li>All new algorithm for <code><a href="../reference/as.mo.html">as.mo()</a></code> (and thus internally all <code>mo_*()</code> functions) while still following our original set-up as described in our paper (DOI 10.18637/jss.v104.i03).<ul><li>A new argument <code>keep_synonyms</code> allows to <em>not</em> correct for updated taxonomy, in favour of the now deleted argument <code>allow_uncertain</code>
|
||||
</li>
|
||||
@ -157,7 +157,7 @@
|
||||
<li>Our data sets are now also continually exported to Apache Feather and Apache Parquet formats. You can find more info <a href="https://msberends.github.io/AMR/articles/datasets.html">in this article on our website</a>.</li>
|
||||
</ul></div>
|
||||
<div class="section level4">
|
||||
<h4 id="changed-1-8-2-9018">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9018"></a></h4>
|
||||
<h4 id="changed-1-8-2-9023">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9023"></a></h4>
|
||||
<ul><li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</li>
|
||||
<li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on <code>NA</code> values (e.g. <code>as.rsi(as.disk(NA), ...)</code>)</li>
|
||||
<li>Removed <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> for MIC values, since MIC are not integer values and running <code><a href="https://rdrr.io/r/base/table.html" class="external-link">table()</a></code> on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on <code>factor</code>s work)</li>
|
||||
@ -183,7 +183,7 @@
|
||||
<li>Fix for using <code><a href="../reference/as.ab.html">as.ab()</a></code> on <code>NA</code> values</li>
|
||||
</ul></div>
|
||||
<div class="section level4">
|
||||
<h4 id="other-1-8-2-9018">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9018"></a></h4>
|
||||
<h4 id="other-1-8-2-9023">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9023"></a></h4>
|
||||
<ul><li>New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions</li>
|
||||
<li>Added Peter Dutey-Magni, Dmytro Mykhailenko and Anton Mymrikov as contributors, to thank them for their valuable input</li>
|
||||
<li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>
|
||||
|
@ -11,7 +11,7 @@ articles:
|
||||
datasets: datasets.html
|
||||
resistance_predict: resistance_predict.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
last_built: 2022-10-15T13:24Z
|
||||
last_built: 2022-10-19T09:55Z
|
||||
urls:
|
||||
reference: https://msberends.github.io/AMR/reference
|
||||
article: https://msberends.github.io/AMR/articles
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -62,7 +62,7 @@ Principal component analysis for AMR
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
Before (image error) Size: 12 KiB After (image error) Size: 13 KiB |
Before (image error) Size: 12 KiB After (image error) Size: 12 KiB |
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@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -146,7 +146,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"meropenem"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] MEM</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"J01DH02"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Meropenem"</span>
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -210,13 +210,13 @@
|
||||
<span class="r-in"><span><span class="co"># straight from a true health care record:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_from_text</span><span class="op">(</span><span class="st">"28/03/2020 regular amoxicilliin 500mg po tds"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [[1]]</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] AMX</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_from_text</span><span class="op">(</span><span class="st">"500 mg amoxi po and 400mg cipro iv"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [[1]]</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] AMX CIP</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-in"><span><span class="fu">ab_from_text</span><span class="op">(</span><span class="st">"500 mg amoxi po and 400mg cipro iv"</span>, type <span class="op">=</span> <span class="st">"dose"</span><span class="op">)</span></span></span>
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -168,7 +168,7 @@
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/warning.html" class="external-link">suppressWarnings</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"test"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] <NA></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># now add a custom entry - it will be considered by as.ab() and</span></span></span>
|
||||
@ -184,7 +184,7 @@
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># "test" is now a new antibiotic:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"test"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] TEST</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"test"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Test Antibiotic"</span>
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -190,16 +190,16 @@
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> birth_date age age_exact age_at_y2k</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1959-12-08 62 62.85205 40</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1953-03-16 69 69.58356 46</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1945-02-19 77 77.65205 54</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1995-02-12 27 27.67123 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1971-01-22 51 51.72877 28</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1933-09-12 89 89.09041 66</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1953-10-17 68 68.99452 46</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1972-06-19 50 50.32329 27</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1964-01-10 58 58.76164 35</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1985-08-26 37 37.13699 14</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1980-01-01 42 42.79726 20</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1948-08-23 74 74.15616 51</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1973-10-28 48 48.97534 26</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1941-08-03 81 81.21096 58</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1991-05-15 31 31.43014 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1963-06-17 59 59.33973 36</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1972-03-23 50 50.57534 27</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1970-08-17 52 52.17260 29</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1988-10-11 34 34.02192 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1941-10-13 81 81.01644 58</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -206,7 +206,7 @@
|
||||
|
||||
|
||||
<dt>only_rsi_columns</dt>
|
||||
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only columns of class <code><rsi></code> must be selected (defaults to <code>FALSE</code>), see <code><a href="as.rsi.html">as.rsi()</a></code></p></dd>
|
||||
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only columns of class <code>rsi</code> must be selected (defaults to <code>FALSE</code>), see <code><a href="as.rsi.html">as.rsi()</a></code></p></dd>
|
||||
|
||||
|
||||
<dt>only_treatable</dt>
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -212,32 +212,32 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># these examples all return "ERY", the ID of erythromycin:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"J01FA01"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] ERY</span>
|
||||
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"J 01 FA 01"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> in like(): argument `x` must not be NULL</span>
|
||||
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"Erythromycin"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] ERY</span>
|
||||
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"eryt"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] ERY</span>
|
||||
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">" eryt 123"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> in like(): argument `x` must not be NULL</span>
|
||||
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"ERYT"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] ERY</span>
|
||||
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"ERY"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] ERY</span>
|
||||
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"eritromicine"</span><span class="op">)</span> <span class="co"># spelled wrong, yet works</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] ERY</span>
|
||||
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"Erythrocin"</span><span class="op">)</span> <span class="co"># trade name</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] ERY</span>
|
||||
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"Romycin"</span><span class="op">)</span> <span class="co"># trade name</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] ERY</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># spelling from different languages and dyslexia are no problem</span></span></span>
|
||||
@ -256,33 +256,34 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Erythromycin"</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"eryt"</span><span class="op">)</span> <span class="co"># "Erythromycin"</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Erythromycin"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># you can quickly rename <rsi> columns using dplyr >= 1.0.0:</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># you can quickly rename 'rsi' columns using set_ab_names() with dplyr:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/rename.html" class="external-link">rename_with</a></span><span class="op">(</span><span class="va">as.ab</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.rsi</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.rsi</span><span class="op">)</span>, property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TZP <rsi>, CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CAZ <rsi>, CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TMP <rsi>, SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MFX <rsi>, VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ERY <rsi>, CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CHL <rsi>, COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo J01CE01 J01CF04 J01CF05</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows, and 37 more variables: J01CA04 <rsi>, J01CR02 <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01CA01 <rsi>, J01CR05 <rsi>, J01DB04 <rsi>, J01DE01 <rsi>, J01DC02 <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01DC01 <rsi>, J01DD01 <rsi>, J01DD02 <rsi>, J01DD04 <rsi>, J01GB03 <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01GB01 <rsi>, J01GB06 <rsi>, J01GB04 <rsi>, J01EA01 <rsi>, J01EE01 <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01XE01 <rsi>, J01XX01 <rsi>, J01XX08 <rsi>, J01MA02 <rsi>, J01MA14 <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01XA01 <rsi>, J01XA02 <rsi>, J01AA07 <rsi>, J01AA12 <rsi>, J01AA02 <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01FA01 <rsi>, J01FF01 <rsi>, J01FA10 <rsi>, J01DH51 <rsi>, …</span></span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -165,7 +165,7 @@
|
||||
<div class="section level2">
|
||||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||||
<p>Interpret disk values as RSI values with <code><a href="as.rsi.html">as.rsi()</a></code>. It supports guidelines from EUCAST and CLSI.</p>
|
||||
<p><code>NA_disk_</code> is a missing value of the new <code><disk></code> class.</p>
|
||||
<p><code>NA_disk_</code> is a missing value of the new <code>disk</code> class.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
|
||||
@ -210,7 +210,7 @@
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'ampicillin' (AMP, ampicillin)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <rsi></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'rsi'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># interpret whole data set, pretend to be all from urinary tract infections:</span></span></span>
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -319,7 +319,7 @@
|
||||
<span class="r-in"><span> <span class="st">"VRSA"</span>, <span class="co"># Vancomycin Resistant S. aureus</span></span></span>
|
||||
<span class="r-in"><span> <span class="fl">115329001</span> <span class="co"># SNOMED CT code</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mo'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [6] B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] B_STPHY_AURS B_STPHY_AURS</span>
|
||||
@ -331,25 +331,25 @@
|
||||
<span class="r-in"><span> <span class="st">"Ureaplasmium urealytica"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="st">"Ureaplazma urealitycium"</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mo'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_URPLS_URLY B_URPLS_URLY B_URPLS_URLY B_URPLS_URLY</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Streptococcus group A"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mo'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_STRPT_GRPA</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span><span class="op">)</span> <span class="co"># will remain species: B_STPHY_EPDR</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mo'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_STPHY_EPDR</span>
|
||||
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># will not remain species: B_STPHY_CONS</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mo'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_STPHY_CONS</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. pyogenes"</span><span class="op">)</span> <span class="co"># will remain species: B_STRPT_PYGN</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mo'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_STRPT_PYGN</span>
|
||||
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. pyogenes"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># will not remain species: B_STRPT_GRPA</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mo'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_STRPT_GRPA</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># All mo_* functions use as.mo() internally too (see ?mo_property):</span></span></span>
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -239,7 +239,7 @@
|
||||
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
|
||||
|
||||
|
||||
<p>Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with new class <code><rsi></code></p>
|
||||
<p>Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with new class <code>rsi</code></p>
|
||||
|
||||
|
||||
</div>
|
||||
@ -290,11 +290,11 @@
|
||||
<h3 id="other">Other<a class="anchor" aria-label="anchor" href="#other"></a></h3>
|
||||
|
||||
|
||||
<p>The function <code>is.rsi()</code> detects if the input contains class <code><rsi></code>. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, it iterates over all columns and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
|
||||
<p>The function <code>is.rsi()</code> detects if the input contains class <code>rsi</code>. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, it iterates over all columns and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
|
||||
<p>The function <code>is.rsi.eligible()</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> argument. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, it iterates over all columns and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
|
||||
</div>
|
||||
|
||||
<p><code>NA_rsi_</code> is a missing value of the new <code><rsi></code> class, analogous to e.g. base <span style="R">R</span>'s <code><a href="https://rdrr.io/r/base/NA.html" class="external-link">NA_character_</a></code>.</p>
|
||||
<p><code>NA_rsi_</code> is a missing value of the new <code>rsi</code> class, analogous to e.g. base <span style="R">R</span>'s <code><a href="https://rdrr.io/r/base/NA.html" class="external-link">NA_character_</a></code>.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="interpretation-of-r-and-s-i">Interpretation of R and S/I<a class="anchor" aria-label="anchor" href="#interpretation-of-r-and-s-i"></a></h2>
|
||||
@ -474,7 +474,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of column 'TOB' (tobramycin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Assigning class <rsi> to already clean column 'ERY' (erythromycin)...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Assigning class 'rsi' to already clean column 'ERY' (erythromycin)...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> microorganism AMP CIP GEN TOB ERY</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli S I S S R</span>
|
||||
@ -484,16 +484,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 50 × 13</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> datetime index ab_input ab_consid…¹ mo_in…² mo_conside…³ guide…⁴</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2022-10-15 <span style="color: #949494;">13:24:55</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2022-10-15 <span style="color: #949494;">13:24:56</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2022-10-15 <span style="color: #949494;">13:24:56</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2022-10-15 <span style="color: #949494;">13:24:56</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2022-10-15 <span style="color: #949494;">13:24:56</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2022-10-15 <span style="color: #949494;">13:24:57</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2022-10-15 <span style="color: #949494;">13:24:57</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2022-10-15 <span style="color: #949494;">13:24:57</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2022-10-15 <span style="color: #949494;">13:24:57</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2022-10-15 <span style="color: #949494;">13:24:57</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2022-10-19 <span style="color: #949494;">09:56:17</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2022-10-19 <span style="color: #949494;">09:56:17</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2022-10-19 <span style="color: #949494;">09:56:17</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2022-10-19 <span style="color: #949494;">09:56:18</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2022-10-19 <span style="color: #949494;">09:56:18</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2022-10-19 <span style="color: #949494;">09:56:18</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2022-10-19 <span style="color: #949494;">09:56:19</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2022-10-19 <span style="color: #949494;">09:56:19</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2022-10-19 <span style="color: #949494;">09:56:19</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2022-10-19 <span style="color: #949494;">09:56:19</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 40 more rows, 6 more variables: ref_table <chr>, method <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># breakpoint_S <dbl>, breakpoint_R <dbl>, input <dbl>, interpretation <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># and abbreviated variable names ¹ab_considered, ²mo_input, ³mo_considered,</span></span>
|
||||
@ -509,7 +509,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <rsi></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'rsi'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.rsi</span><span class="op">(</span></span></span>
|
||||
@ -521,7 +521,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'ampicillin' (AMP, ampicillin)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <rsi></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'rsi'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
@ -645,10 +645,10 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-in"><span><span class="fu">as.rsi</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: 3 results in column '24' truncated (50%) that were invalid</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> antimicrobial interpretations: "A", "B" and "C"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <rsi></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'rsi'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S I R <NA> <NA> <NA></span>
|
||||
<span class="r-in"><span><span class="fu">as.rsi</span><span class="op">(</span><span class="st">"<= 0.002; S"</span><span class="op">)</span> <span class="co"># will return "S"</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <rsi></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'rsi'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S</span>
|
||||
<span class="r-in"><span><span class="va">rsi_data</span> <span class="op"><-</span> <span class="fu">as.rsi</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="fl">474</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"I"</span>, <span class="fl">36</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"R"</span>, <span class="fl">370</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">is.rsi</span><span class="op">(</span><span class="va">rsi_data</span><span class="op">)</span></span></span>
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -201,7 +201,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
|
||||
|
||||
|
||||
<dt>only_rsi_columns</dt>
|
||||
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antibiotic columns must be detected that were transformed to class <code><rsi></code> (see <code><a href="as.rsi.html">as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></dd>
|
||||
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antibiotic columns must be detected that were transformed to class <code>rsi</code> (see <code><a href="as.rsi.html">as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></dd>
|
||||
|
||||
|
||||
<dt>custom_rules</dt>
|
||||
@ -299,7 +299,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
|
||||
<span class="r-in"><span><span class="co"># apply EUCAST rules: some results wil be changed</span></span></span>
|
||||
<span class="r-in"><span><span class="va">b</span> <span class="op"><-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span><span class="op">)</span></span></span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `eucast_rules()`: not all columns with antimicrobial results are of</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> class <rsi> . Transform them on beforehand, with e.g.:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> class 'rsi'. Transform them on beforehand, with e.g.:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> - a %>% as.rsi(CXM:AMX)</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> - a %>% mutate_if(is.rsi.eligible, as.rsi)</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> - a %>% mutate(across(where(is.rsi.eligible), as.rsi))</span>
|
||||
@ -317,7 +317,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
|
||||
<span class="r-in"><span><span class="co"># containing all details about the transformations:</span></span></span>
|
||||
<span class="r-in"><span><span class="va">c</span> <span class="op"><-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `eucast_rules()`: not all columns with antimicrobial results are of</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> class <rsi> . Transform them on beforehand, with e.g.:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> class 'rsi'. Transform them on beforehand, with e.g.:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> - a %>% as.rsi(CXM:AMX)</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> - a %>% mutate_if(is.rsi.eligible, as.rsi)</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> - a %>% mutate(across(where(is.rsi.eligible), as.rsi))</span>
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -12,7 +12,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -250,7 +250,7 @@
|
||||
|
||||
|
||||
<dt>include_untested_rsi</dt>
|
||||
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether also rows without antibiotic results are still eligible for becoming a first isolate. Use <code>include_untested_rsi = FALSE</code> to always return <code>FALSE</code> for such rows. This checks the data set for columns of class <code><rsi></code> and consequently requires transforming columns with antibiotic results using <code><a href="as.rsi.html">as.rsi()</a></code> first.</p></dd>
|
||||
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether also rows without antibiotic results are still eligible for becoming a first isolate. Use <code>include_untested_rsi = FALSE</code> to always return <code>FALSE</code> for such rows. This checks the data set for columns of class <code>rsi</code> and consequently requires transforming columns with antibiotic results using <code><a href="as.rsi.html">as.rsi()</a></code> first.</p></dd>
|
||||
|
||||
|
||||
<dt>...</dt>
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -177,40 +177,41 @@
|
||||
<span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">200</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 14 30 51 63 66 3 25 25 10 50 17 32 20 64 19 41 45 62 25 18 24 26 28 6 63</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [26] 47 32 10 16 28 23 2 4 66 62 8 41 13 15 56 9 22 34 51 15 65 45 1 53 57</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [51] 29 39 12 52 12 33 58 57 48 51 40 27 30 18 36 43 13 7 65 60 13 25 16 21 62</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [76] 66 39 22 39 7 8 24 60 19 27 27 58 5 49 6 62 23 15 39 10 66 63 7 50 5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [101] 60 29 67 51 52 57 34 48 60 18 65 55 48 51 66 12 20 49 41 65 41 67 53 39 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [126] 55 65 66 68 13 27 43 34 46 51 3 13 11 23 31 65 34 11 37 10 54 16 66 24 50</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [151] 38 10 5 8 59 30 49 63 59 9 36 44 38 28 30 65 5 6 66 10 30 5 26 1 42</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [176] 18 63 66 14 60 64 35 55 47 13 43 21 66 61 8 61 54 41 64 12 65 16 40 10 52</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 54 9 4 2 23 7 29 14 21 37 18 58 61 29 16 13 27 63 35 56 9 8 52 60 12</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [26] 14 19 62 16 61 48 34 46 59 48 31 2 5 30 25 9 3 56 53 4 31 32 6 23 49</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [51] 55 57 32 3 64 63 14 4 30 65 61 62 14 58 48 17 11 13 1 52 21 51 61 56 52</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [76] 21 60 17 49 37 43 42 48 63 21 43 63 1 62 11 58 64 58 49 11 10 21 56 48 63</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [101] 53 20 4 23 6 55 30 42 6 6 39 37 28 8 33 42 39 47 55 7 43 6 43 1 60</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [126] 43 24 56 19 48 32 16 4 38 28 29 14 44 53 39 23 20 51 13 53 3 45 60 20 24</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [151] 35 36 36 29 41 33 10 46 51 1 40 41 17 22 8 26 52 21 27 31 1 52 64 38 64</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [176] 63 53 16 34 8 50 57 12 10 59 64 6 10 15 43 65 25 9 48 9 32 17 15 4 43</span>
|
||||
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] FALSE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] TRUE FALSE TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [109] FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [121] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [133] FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [145] TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [157] TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [169] FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [181] FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [193] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] FALSE TRUE TRUE TRUE FALSE TRUE TRUE TRUE FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [109] TRUE FALSE TRUE TRUE TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [121] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [133] FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [145] FALSE FALSE TRUE TRUE FALSE TRUE TRUE FALSE TRUE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [157] FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [169] TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [181] TRUE TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [193] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-10-20 F35553 51 M ICU B_STPHY_AURS S NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-11-18 956065 89 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-07-15 C42193 84 M ICU B_STPHY_HMNS R NA R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-07-28 F54261 69 M Clinical B_STPHY_CONS R NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2002-07-23 F35553 51 M ICU B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 36 more variables: AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>,</span></span>
|
||||
@ -246,16 +247,16 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: condition [3]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient date condition new_episode</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 219024 2005-02-17 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> A31059 2008-12-04 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> D53062 2014-07-28 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 305134 2016-10-28 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> D80438 2017-07-03 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> F35553 2002-10-20 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> ED4982 2007-07-13 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 122506 2007-08-11 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 05B00F 2004-05-11 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 8F77B2 2014-01-14 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> E99D61 2015-04-07 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 394107 2004-01-16 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> F35553 2002-09-23 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> F41248 2002-04-04 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 5B78D5 2007-02-21 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 032343 2003-06-09 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> D43890 2008-11-28 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> F41D7B 2005-01-12 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 94BB11 2006-08-14 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> D82303 2010-12-11 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 190 more rows</span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
@ -267,19 +268,19 @@
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 200 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [180]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward date patient new_index new_logical</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical 2005-02-17 219024 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical 2008-12-04 A31059 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical 2014-07-28 D53062 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> ICU 2016-10-28 305134 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2017-07-03 D80438 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> ICU 2002-10-20 F35553 2 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> ICU 2007-07-13 ED4982 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Clinical 2007-08-11 122506 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> ICU 2004-05-11 05B00F 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Clinical 2014-01-14 8F77B2 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [182]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward date patient new_index new_logical</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> ICU 2015-04-07 E99D61 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> ICU 2004-01-16 394107 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> ICU 2002-09-23 F35553 2 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical 2002-04-04 F41248 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2007-02-21 5B78D5 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Clinical 2003-06-09 032343 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Outpatient 2008-11-28 D43890 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> ICU 2005-01-12 F41D7B 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Clinical 2006-08-14 94BB11 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> ICU 2010-12-11 D82303 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 190 more rows</span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
@ -294,9 +295,9 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 112 14 55 73</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 56 12 36 46</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 12 8 11 12</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 105 14 52 67</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 64 12 38 46</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 13 7 11 12</span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
|
||||
@ -327,18 +328,18 @@
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 200 × 4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, mo, ward [188]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient mo ward flag_episode</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 219024 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> A31059 B_STRPT_MTNS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> D53062 B_HMPHL_INFL Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 305134 B_PROTS_VLGR ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> D80438 B_STPHY_AURS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> F35553 B_STPHY_AURS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> ED4982 B_ESCHR_COLI ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 122506 B_STPHY_AURS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 05B00F F_CANDD_ALBC ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 8F77B2 B_ENTRC_FACM Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient mo ward flag_episode</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> E99D61 B_STPHY_EPDR ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 394107 B_STPHY_CONS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> F35553 B_STPHY_AURS ICU FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> F41248 B_STPHY_AURS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 5B78D5 B_STPHY_AURS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 032343 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> D43890 UNKNOWN Outpatient TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> F41D7B B_STRPT_PNMN ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 94BB11 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> D82303 B_ESCHR_COLI ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 190 more rows</span></span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -156,7 +156,7 @@
|
||||
|
||||
|
||||
<dt>only_rsi_columns</dt>
|
||||
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antibiotic columns must be detected that were transformed to class <code><rsi></code> (see <code><a href="as.rsi.html">as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></dd>
|
||||
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antibiotic columns must be detected that were transformed to class <code>rsi</code> (see <code><a href="as.rsi.html">as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></dd>
|
||||
|
||||
</dl></div>
|
||||
<div class="section level2">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -187,7 +187,7 @@
|
||||
|
||||
|
||||
<dt>only_rsi_columns</dt>
|
||||
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only columns must be included that were transformed to class <code><rsi></code> (see <code><a href="as.rsi.html">as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></dd>
|
||||
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only columns must be included that were transformed to class <code>rsi</code> (see <code><a href="as.rsi.html">as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></dd>
|
||||
|
||||
|
||||
<dt>...</dt>
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -167,9 +167,9 @@
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 3.023296</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 3.078481</span>
|
||||
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.1095747</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.07857002</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -193,7 +193,7 @@
|
||||
|
||||
|
||||
<dt>only_rsi_columns</dt>
|
||||
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antibiotic columns must be detected that were transformed to class <code><rsi></code> (see <code><a href="as.rsi.html">as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></dd>
|
||||
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antibiotic columns must be detected that were transformed to class <code>rsi</code> (see <code><a href="as.rsi.html">as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></dd>
|
||||
|
||||
|
||||
<dt>...</dt>
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -194,12 +194,11 @@
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">x</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.25 32 0.01 32 0.01 1 0.125 >=256 <=0.002</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 128 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1 >=128 >=128 0.001 4 0.125 0.25 0.01 0.001 2 </span>
|
||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.28698184 0.84500052 -1.03794802 0.84500052 -1.03794802 0.03644169</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.44869360 1.33013581 -1.41343111 1.16842405</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.23800503 1.38104904 1.38104904 -1.38932783 0.56458903 -0.25187098</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.08857897 -0.84688355 -1.38932783 0.40129703</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">y</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
|
||||
@ -209,38 +208,38 @@
|
||||
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">y</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 4 <=0.125 2 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 16 0.5 0.25 >=4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C 16 >=1 16 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 16 <=0.125 16 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 4 0.5 8 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 32 0.5 0.25 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G <=2 <=0.125 0.5 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 32 <=0.125 8 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 16 <=0.125 16 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 16 >=1 0.5 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 16 <=0.025 >=4 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.5 1 <=0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C 4 0.0625 1 <=0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D >=32 1 >=4 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 4 0.125 2 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 8 0.0625 >=4 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.0625 2 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H >=32 0.0625 1 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 8 0.25 <=0.25 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J >=32 0.0625 <=0.25 2</span>
|
||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> "id" and "tobr"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.55656226 0.35659439 0.44544165 0.10294421 0.24387145 -0.14027373</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.70751904 -0.03633100 0.33011266 -0.03827833</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.14091001 -0.32396107 -0.78118181 0.85710543 0.08049237 0.41685866</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.07191455 0.18697943 -0.07834229 -0.14512615</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G <=2 <=0.125 0.5 2 -0.70751904</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 4 <=0.125 2 1 -0.55656226</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 32 0.5 0.25 0.5 -0.14027373</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 16 >=1 0.5 0.5 -0.03827833</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 32 <=0.125 8 0.5 -0.03633100</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 16 <=0.125 16 1 0.10294421</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 4 0.5 8 2 0.24387145</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 16 <=0.125 16 2 0.33011266</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 16 0.5 0.25 >=4 0.35659439</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C 16 >=1 16 0.5 0.44544165</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C 4 0.0625 1 <=0.25 -0.78118181</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.5 1 <=0.25 -0.32396107</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J >=32 0.0625 <=0.25 2 -0.14512615</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 16 <=0.025 >=4 0.5 -0.14091001</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 8 0.25 <=0.25 4 -0.07834229</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.0625 2 4 -0.07191455</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 4 0.125 2 4 0.08049237</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H >=32 0.0625 1 2 0.18697943</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 8 0.0625 >=4 8 0.41685866</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D >=32 1 >=4 0.5 0.85710543</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
@ -252,17 +251,17 @@
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C 16 >=1 16 0.5 0.44544165 0.00000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 16 0.5 0.25 >=4 0.35659439 0.08884727</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 I 16 <=0.125 16 2 0.33011266 0.11532899</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 E 4 0.5 8 2 0.24387145 0.20157020</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 D 16 <=0.125 16 1 0.10294421 0.34249744</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 H 32 <=0.125 8 0.5 -0.03633100 0.48177265</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 J 16 >=1 0.5 0.5 -0.03827833 0.48371999</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 F 32 0.5 0.25 0.5 -0.14027373 0.58571538</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 A 4 <=0.125 2 1 -0.55656226 1.00200391</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 G <=2 <=0.125 0.5 2 -0.70751904 1.15296069</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C 4 0.0625 1 <=0.25 -0.78118181 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.5 1 <=0.25 -0.32396107 0.4572207</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 J >=32 0.0625 <=0.25 2 -0.14512615 0.6360557</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 A 16 <=0.025 >=4 0.5 -0.14091001 0.6402718</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 I 8 0.25 <=0.25 4 -0.07834229 0.7028395</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 G 4 0.0625 2 4 -0.07191455 0.7092673</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 E 4 0.125 2 4 0.08049237 0.8616742</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H >=32 0.0625 1 2 0.18697943 0.9681612</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 F 8 0.0625 >=4 8 0.41685866 1.1980405</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 D >=32 1 >=4 0.5 0.85710543 1.6382872</span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -184,7 +184,7 @@
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mo'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_ESCHR_COLI</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Matching scores are based on the resemblance between the input and the full</span>
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -182,7 +182,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
<p>It has now created a file <code>"~/mo_source.rds"</code> with the contents of our Excel file. Only the first column with foreign values and the 'mo' column will be kept when creating the RDS file.</p>
|
||||
<p>And now we can use it in our functions:</p>
|
||||
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">as.mo</span>(<span class="st">"lab_mo_ecoli"</span>)</span>
|
||||
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="co">#> Class <mo></span></span>
|
||||
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="co">#> Class 'mo'</span></span>
|
||||
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="co">#> [1] B_ESCHR_COLI</span></span>
|
||||
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="fu">mo_genus</span>(<span class="st">"lab_mo_kpneumoniae"</span>)</span>
|
||||
@ -192,7 +192,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a><span class="fu">as.mo</span>(<span class="fu">c</span>(<span class="st">"Escherichia coli"</span>, <span class="st">"E. coli"</span>, <span class="st">"lab_mo_ecoli"</span>))</span>
|
||||
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Translation to one microorganism was guessed with uncertainty.</span></span>
|
||||
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a><span class="co">#> Use mo_uncertainties() to review it.</span></span>
|
||||
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a><span class="co">#> Class <mo></span></span>
|
||||
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a><span class="co">#> Class 'mo'</span></span>
|
||||
<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a><span class="co">#> [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI</span></span></code></pre><p></p></div>
|
||||
<p>If we edit the Excel file by, let's say, adding row 4 like this:</p>
|
||||
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a> <span class="sc">|</span> A <span class="sc">|</span> B <span class="sc">|</span></span>
|
||||
@ -207,7 +207,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from</span></span>
|
||||
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="co">#> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns</span></span>
|
||||
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="co">#> "Organisation XYZ" and "mo"</span></span>
|
||||
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="co">#> Class <mo></span></span>
|
||||
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="co">#> Class 'mo'</span></span>
|
||||
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="co">#> [1] B_ESCHR_COLI</span></span>
|
||||
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a><span class="fu">mo_genus</span>(<span class="st">"lab_Staph_aureus"</span>)</span>
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
Before (image error) Size: 26 KiB After (image error) Size: 25 KiB |
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@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -166,7 +166,7 @@
|
||||
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
|
||||
|
||||
|
||||
<p>class <code><mic></code> for <code>random_mic()</code> (see <code><a href="as.mic.html">as.mic()</a></code>) and class <code><disk></code> for <code>random_disk()</code> (see <code><a href="as.disk.html">as.disk()</a></code>)</p>
|
||||
<p>class <code>mic</code> for <code>random_mic()</code> (see <code><a href="as.mic.html">as.mic()</a></code>) and class <code>disk</code> for <code>random_disk()</code> (see <code><a href="as.disk.html">as.disk()</a></code>)</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||||
@ -177,44 +177,43 @@
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 32 1 0.001 0.25 1 16 0.0625 64 0.25 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] 4 0.01 0.125 8 128 0.0625 >=256 0.025 >=256 0.125 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] 64 32 0.0625 1 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 8 0.25 0.002 0.0625 128 256 1 4 1 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 128 <=0.001 0.0625 64 0.0625 0.125 0.025 0.25 0.002 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] 0.5 8 64 128 0.025 8 256 </span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <disk></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 15 46 30 46 39 44 18 22 8 28 24 30 14 20 47 46 10 41 46 21 23 47 13 25 49</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 50 37 18 41 39 28 16 24 31 40 13 12 46 25 6 27 21 45 13 43 15 21 36 27 21</span>
|
||||
<span class="r-in"><span><span class="fu">random_rsi</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <rsi></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R R R I S S S S S R R R I R S S S I R S I R S I I</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'rsi'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R S I R R R R S I S I S S S R S I I S S R R S S I</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.5 64 0.005 32 4 0.005 128 0.25 64 0.025 0.5 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] 0.025 0.025 2 0.125 64 8 2 1 0.125 64 32 32 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] 0.5 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 4 64 0.025 0.025 64 0.01 128 >=256 0.5 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 2 0.125 0.0625 16 0.005 0.002 0.25 0.002 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] 0.25 8 <=0.001 4 <=0.001 0.125 2 </span>
|
||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 8 4 8 8 2 8 1 0.5 16 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] 8 16 <=0.25 0.5 8 8 1 2 2 <=0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] 8 8 2 2 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 4 2 4 <=1 <=1 8 8 16 4 4 2 <=1 <=1 16 4 <=1 16 16 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [20] <=1 8 16 16 16 4 </span>
|
||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.25 8 0.125 8 16 4 8 0.025 8 4 8 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] 0.125 0.125 0.25 1 0.025 8 0.025 1 2 4 4 0.25 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.5 1 0.5 0.5 0.0625 2 1 0.5 0.5 0.0625</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] 1 0.25 0.125 2 0.25 2 0.125 1 0.0625 0.25 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] >=4 1 0.125 1 0.0625</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <disk></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 35 48 23 48 32 44 49 43 11 18 41 37 30 22 19 26 40 50 15 30 41 41 42 21 15</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 42 48 22 13 8 14 38 49 12 38 37 21 41 11 48 44 34 27 33 41 10 44 36 11 42</span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <disk></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 15 16 13 12 16 11 12 16 17 15 14 13 12 13 15 16 15 13 16 14 16 16 17 16 15</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 11 17 12 17 17 14 15 17 16 16 16 15 16 12 13 12 15 12 12 11 13 14 17 13 16</span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <disk></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 25 18 18 18 24 15 20 19 20 21 26 22 18 15 23 21 19 22 26 25 21 23 20 16 23</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 19 27 24 21 24 19 16 17 19 22 26 24 18 25 22 27 20 24 24 19 27 26 21 27 21</span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
|
@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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">
|
||||
@ -166,7 +166,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.02786978</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.03698095</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9018</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</small>
|
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|
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|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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