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@@ -162,7 +162,7 @@
<img src="../logo.svg" class="logo" alt=""><h1>How to conduct AMR data analysis</h1> <img src="../logo.svg" class="logo" alt=""><h1>How to conduct AMR data analysis</h1>
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4> <h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
<h4 data-toc-skip class="date">20 October 2022</h4> <h4 data-toc-skip class="date">21 October 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small> <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="d-none name"><code>AMR.Rmd</code></div> <div class="d-none name"><code>AMR.Rmd</code></div>
@@ -170,7 +170,7 @@
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 20 October 2022.</p> <p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 21 October 2022.</p>
<div class="section level2"> <div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a> <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2> </h2>
@@ -201,21 +201,21 @@
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">2022-10-20</td> <td align="center">2022-10-21</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</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>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2022-10-20</td> <td align="center">2022-10-21</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">2022-10-20</td> <td align="center">2022-10-21</td>
<td align="center">efgh</td> <td align="center">efgh</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">R</td> <td align="center">R</td>
@@ -325,67 +325,67 @@
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">2010-07-04</td> <td align="center">2014-10-24</td>
<td align="center">N1</td> <td align="center">Z2</td>
<td align="center">Hospital D</td> <td align="center">Hospital D</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-02-09</td>
<td align="center">T10</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2017-03-28</td>
<td align="center">P6</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td> <td align="center">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">S</td>
<td align="center">F</td> <td align="center">F</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2016-05-18</td> <td align="center">2013-05-29</td>
<td align="center">E5</td> <td align="center">G1</td>
<td align="center">Hospital A</td> <td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">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">M</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">2016-10-13</td> <td align="center">2012-08-07</td>
<td align="center">F4</td> <td align="center">U2</td>
<td align="center">Hospital D</td> <td align="center">Hospital A</td>
<td align="center">Escherichia coli</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">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-05-20</td>
<td align="center">V3</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-06-18</td>
<td align="center">M1</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">M</td> <td align="center">M</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2013-09-14</td> <td align="center">2016-02-29</td>
<td align="center">Y9</td> <td align="center">V8</td>
<td align="center">Hospital D</td> <td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td> <td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">F</td> <td align="center">F</td>
@@ -422,16 +422,16 @@ Longest: 1</p>
<tr class="odd"> <tr class="odd">
<td align="left">1</td> <td align="left">1</td>
<td align="left">M</td> <td align="left">M</td>
<td align="right">10,377</td> <td align="right">10,349</td>
<td align="right">51.89%</td> <td align="right">51.75%</td>
<td align="right">10,377</td> <td align="right">10,349</td>
<td align="right">51.89%</td> <td align="right">51.75%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">2</td> <td align="left">2</td>
<td align="left">F</td> <td align="left">F</td>
<td align="right">9,623</td> <td align="right">9,651</td>
<td align="right">48.12%</td> <td align="right">48.26%</td>
<td align="right">20,000</td> <td align="right">20,000</td>
<td align="right">100.00%</td> <td align="right">100.00%</td>
</tr> </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"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span> <span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span> <span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,663 'phenotype-based' first isolates (53.3% of total where a</span></span> <span><span class="co"># =&gt; Found 10,623 'phenotype-based' first isolates (53.1% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div> <span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<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> <p>So only 53.1% 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"> <div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> <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>
@@ -499,7 +499,7 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span> <span> <span class="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> <span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,663 isolates for analysis. Now our data looks like:</p> <p>So we end up with 10,623 isolates for analysis. Now our data looks like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> <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> <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 style="width:100%;" class="table">
@@ -538,28 +538,28 @@ Longest: 1</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="left">2</td> <td align="left">2</td>
<td align="center">2014-02-09</td> <td align="center">2013-05-29</td>
<td align="center">T10</td> <td align="center">G1</td>
<td align="center">Hospital C</td> <td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td> <td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">F</td> <td align="center">S</td>
<td align="center">Gram-positive</td> <td align="center">S</td>
<td align="center">Streptococcus</td> <td align="center">S</td>
<td align="center">pneumoniae</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> <td align="center">TRUE</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">3</td> <td align="left">3</td>
<td align="center">2017-03-28</td> <td align="center">2012-08-07</td>
<td align="center">P6</td> <td align="center">U2</td>
<td align="center">Hospital B</td> <td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td> <td align="center">B_ESCHR_COLI</td>
<td align="center">R</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">F</td> <td align="center">F</td>
@@ -569,64 +569,64 @@ Longest: 1</p>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">5</td> <td align="left">4</td>
<td align="center">2016-10-13</td> <td align="center">2012-05-20</td>
<td align="center">F4</td> <td align="center">V3</td>
<td align="center">Hospital D</td> <td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="center">2013-09-14</td>
<td align="center">Y9</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2016-09-03</td>
<td align="center">A7</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td> <td align="center">B_STPHY_AURS</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">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">M</td>
<td align="center">Gram-positive</td> <td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td> <td align="center">Staphylococcus</td>
<td align="center">aureus</td> <td align="center">aureus</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">11</td> <td align="left">5</td>
<td align="center">2012-12-21</td> <td align="center">2014-06-18</td>
<td align="center">O1</td> <td align="center">M1</td>
<td align="center">Hospital A</td> <td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</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">6</td>
<td align="center">2016-02-29</td>
<td align="center">V8</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2010-05-10</td>
<td align="center">B9</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</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">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">M</td>
<td align="center">Gram-positive</td> <td align="center">Gram-positive</td>
<td align="center">Streptococcus</td> <td align="center">Streptococcus</td>
<td align="center">pneumoniae</td> <td align="center">pneumoniae</td>
@@ -653,8 +653,8 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div> <code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p> <p><strong>Frequency table</strong></p>
<p>Class: character<br> <p>Class: character<br>
Length: 10,663<br> Length: 10,623<br>
Available: 10,663 (100.0%, NA: 0 = 0.0%)<br> Available: 10,623 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p> Unique: 4</p>
<p>Shortest: 16<br> <p>Shortest: 16<br>
Longest: 24</p> Longest: 24</p>
@@ -671,33 +671,33 @@ Longest: 24</p>
<tr class="odd"> <tr class="odd">
<td align="left">1</td> <td align="left">1</td>
<td align="left">Escherichia coli</td> <td align="left">Escherichia coli</td>
<td align="right">4,612</td> <td align="right">4,630</td>
<td align="right">43.25%</td> <td align="right">43.58%</td>
<td align="right">4,612</td> <td align="right">4,630</td>
<td align="right">43.25%</td> <td align="right">43.58%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">2</td> <td align="left">2</td>
<td align="left">Staphylococcus aureus</td> <td align="left">Staphylococcus aureus</td>
<td align="right">2,732</td> <td align="right">2,710</td>
<td align="right">25.62%</td> <td align="right">25.51%</td>
<td align="right">7,344</td> <td align="right">7,340</td>
<td align="right">68.87%</td> <td align="right">69.10%</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">3</td> <td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td> <td align="left">Streptococcus pneumoniae</td>
<td align="right">2,151</td> <td align="right">2,057</td>
<td align="right">20.17%</td> <td align="right">19.36%</td>
<td align="right">9,495</td> <td align="right">9,397</td>
<td align="right">89.05%</td> <td align="right">88.46%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">4</td> <td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td> <td align="left">Klebsiella pneumoniae</td>
<td align="right">1,168</td> <td align="right">1,226</td>
<td align="right">10.95%</td> <td align="right">11.54%</td>
<td align="right">10,663</td> <td align="right">10,623</td>
<td align="right">100.00%</td> <td align="right">100.00%</td>
</tr> </tr>
</tbody> </tbody>
@@ -716,14 +716,14 @@ Longest: 24</p>
<col width="9%"> <col width="9%">
<col width="9%"> <col width="9%">
<col width="9%"> <col width="9%">
<col width="11%"> <col width="10%">
<col width="3%"> <col width="3%">
<col width="3%"> <col width="3%">
<col width="3%"> <col width="3%">
<col width="3%"> <col width="3%">
<col width="6%"> <col width="6%">
<col width="11%"> <col width="11%">
<col width="11%"> <col width="12%">
<col width="9%"> <col width="9%">
<col width="5%"> <col width="5%">
</colgroup> </colgroup>
@@ -744,95 +744,95 @@ Longest: 24</p>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">2014-02-09</td> <td align="center">2010-05-10</td>
<td align="center">T10</td> <td align="center">B9</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-02-28</td>
<td align="center">B6</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">2016-03-07</td>
<td align="center">L6</td>
<td align="center">Hospital C</td> <td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td> <td align="center">B_ESCHR_COLI</td>
<td align="center">S</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</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">Gram-negative</td>
<td align="center">Streptococcus</td> <td align="center">Escherichia</td>
<td align="center">pneumoniae</td> <td align="center">coli</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2013-09-14</td> <td align="center">2011-02-04</td>
<td align="center">Y9</td> <td align="center">J2</td>
<td align="center">Hospital D</td> <td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td> <td align="center">B_STRPT_PNMN</td>
<td align="center">S</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</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">Gram-positive</td>
<td align="center">Streptococcus</td> <td align="center">Streptococcus</td>
<td align="center">pneumoniae</td> <td align="center">pneumoniae</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">2012-12-21</td> <td align="center">2015-07-22</td>
<td align="center">O1</td> <td align="center">X8</td>
<td align="center">Hospital A</td> <td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td> <td align="center">B_STPHY_AURS</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">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">F</td>
<td align="center">Gram-positive</td> <td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-03-20</td>
<td align="center">P7</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td> <td align="center">Streptococcus</td>
<td align="center">pneumoniae</td> <td align="center">pneumoniae</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="even">
<td align="center">2011-07-03</td>
<td align="center">S2</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2010-04-27</td>
<td align="center">Y1</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">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-06-16</td>
<td align="center">V4</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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> </tbody>
</table> </table>
<p>If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> function:</p> <p>If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> function:</p>
@@ -854,50 +854,50 @@ Longest: 24</p>
<tr class="odd"> <tr class="odd">
<td align="center">E. coli</td> <td align="center">E. coli</td>
<td align="center">AMX</td> <td align="center">AMX</td>
<td align="center">2181</td> <td align="center">2159</td>
<td align="center">134</td> <td align="center">145</td>
<td align="center">2297</td> <td align="center">2326</td>
<td align="center">4612</td> <td align="center">4630</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">E. coli</td> <td align="center">E. coli</td>
<td align="center">AMC</td> <td align="center">AMC</td>
<td align="center">3388</td> <td align="center">3398</td>
<td align="center">167</td> <td align="center">178</td>
<td align="center">1057</td> <td align="center">1054</td>
<td align="center">4612</td> <td align="center">4630</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">E. coli</td> <td align="center">E. coli</td>
<td align="center">CIP</td> <td align="center">CIP</td>
<td align="center">3355</td> <td align="center">3369</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">1257</td> <td align="center">1261</td>
<td align="center">4612</td> <td align="center">4630</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">E. coli</td> <td align="center">E. coli</td>
<td align="center">GEN</td> <td align="center">GEN</td>
<td align="center">4036</td> <td align="center">4053</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">576</td> <td align="center">577</td>
<td align="center">4612</td> <td align="center">4630</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">K. pneumoniae</td> <td align="center">K. pneumoniae</td>
<td align="center">AMX</td> <td align="center">AMX</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">1168</td> <td align="center">1226</td>
<td align="center">1168</td> <td align="center">1226</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">K. pneumoniae</td> <td align="center">K. pneumoniae</td>
<td align="center">AMC</td> <td align="center">AMC</td>
<td align="center">912</td> <td align="center">943</td>
<td align="center">43</td> <td align="center">48</td>
<td align="center">213</td> <td align="center">235</td>
<td align="center">1168</td> <td align="center">1226</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@@ -920,34 +920,34 @@ Longest: 24</p>
<tr class="odd"> <tr class="odd">
<td align="center">E. coli</td> <td align="center">E. coli</td>
<td align="center">GEN</td> <td align="center">GEN</td>
<td align="center">4036</td> <td align="center">4053</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">576</td> <td align="center">577</td>
<td align="center">4612</td> <td align="center">4630</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">K. pneumoniae</td> <td align="center">K. pneumoniae</td>
<td align="center">GEN</td> <td align="center">GEN</td>
<td align="center">1042</td> <td align="center">1092</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">126</td> <td align="center">134</td>
<td align="center">1168</td> <td align="center">1226</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">S. aureus</td> <td align="center">S. aureus</td>
<td align="center">GEN</td> <td align="center">GEN</td>
<td align="center">2433</td> <td align="center">2400</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">299</td> <td align="center">310</td>
<td align="center">2732</td> <td align="center">2710</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">S. pneumoniae</td> <td align="center">S. pneumoniae</td>
<td align="center">GEN</td> <td align="center">GEN</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">2151</td> <td align="center">2057</td>
<td align="center">2151</td> <td align="center">2057</td>
</tr> </tr>
</tbody> </tbody>
</table> </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> <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"> <div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span> <code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5430929</span></span></code></pre></div> <span><span class="co"># [1] 0.5488092</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> <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"> <div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@@ -975,19 +975,19 @@ Longest: 24</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">Hospital A</td> <td align="center">Hospital A</td>
<td align="center">0.5517885</td> <td align="center">0.5565721</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital B</td> <td align="center">Hospital B</td>
<td align="center">0.5364807</td> <td align="center">0.5457235</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Hospital C</td> <td align="center">Hospital C</td>
<td align="center">0.5249089</td> <td align="center">0.5533546</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital D</td> <td align="center">Hospital D</td>
<td align="center">0.5559306</td> <td align="center">0.5385735</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@@ -1008,23 +1008,23 @@ Longest: 24</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">Hospital A</td> <td align="center">Hospital A</td>
<td align="center">0.5517885</td> <td align="center">0.5565721</td>
<td align="center">3215</td> <td align="center">3279</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital B</td> <td align="center">Hospital B</td>
<td align="center">0.5364807</td> <td align="center">0.5457235</td>
<td align="center">3728</td> <td align="center">3718</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Hospital C</td> <td align="center">Hospital C</td>
<td align="center">0.5249089</td> <td align="center">0.5533546</td>
<td align="center">1646</td> <td align="center">1565</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital D</td> <td align="center">Hospital D</td>
<td align="center">0.5559306</td> <td align="center">0.5385735</td>
<td align="center">2074</td> <td align="center">2061</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@@ -1047,27 +1047,27 @@ Longest: 24</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">Escherichia</td> <td align="center">Escherichia</td>
<td align="center">0.7708153</td> <td align="center">0.7723542</td>
<td align="center">0.8751084</td> <td align="center">0.8753780</td>
<td align="center">0.9754987</td> <td align="center">0.9790497</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Klebsiella</td> <td align="center">Klebsiella</td>
<td align="center">0.8176370</td> <td align="center">0.8083197</td>
<td align="center">0.8921233</td> <td align="center">0.8907015</td>
<td align="center">0.9803082</td> <td align="center">0.9787928</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Staphylococcus</td> <td align="center">Staphylococcus</td>
<td align="center">0.7877013</td> <td align="center">0.7911439</td>
<td align="center">0.8905564</td> <td align="center">0.8856089</td>
<td align="center">0.9802343</td> <td align="center">0.9833948</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Streptococcus</td> <td align="center">Streptococcus</td>
<td align="center">0.5281265</td> <td align="center">0.5333009</td>
<td align="center">0.0000000</td> <td align="center">0.0000000</td>
<td align="center">0.5281265</td> <td align="center">0.5333009</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@@ -1092,23 +1092,23 @@ Longest: 24</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="left">Hospital A</td> <td align="left">Hospital A</td>
<td align="right">55.2%</td> <td align="right">55.7%</td>
<td align="right">28.5%</td> <td align="right">28.5%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">Hospital B</td> <td align="left">Hospital B</td>
<td align="right">53.6%</td> <td align="right">54.6%</td>
<td align="right">25.4%</td> <td align="right">25.6%</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">Hospital C</td> <td align="left">Hospital C</td>
<td align="right">52.5%</td> <td align="right">55.3%</td>
<td align="right">26.3%</td> <td align="right">26.5%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">Hospital D</td> <td align="left">Hospital D</td>
<td align="right">55.6%</td> <td align="right">53.9%</td>
<td align="right">27.4%</td> <td align="right">24.8%</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@@ -1206,18 +1206,16 @@ Longest: 24</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span> <code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span> <span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span> <span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 32 0.025 4 0.01 32 &lt;=0.001 0.0625 0.002 0.125 </span></span> <span><span class="co"># [1] 8 64 4 0.005 32 0.125 0.005 4 &gt;=256 0.005 </span></span>
<span><span class="co"># [10] 4 64 64 0.01 0.005 64 0.125 8 1 </span></span> <span><span class="co"># [11] 0.01 &gt;=256 0.01 0.5 8 0.125 0.01 4 0.125 0.5 </span></span>
<span><span class="co"># [19] 0.25 0.002 0.01 16 0.01 256 32 2 0.005 </span></span> <span><span class="co"># [21] 1 1 0.25 0.0625 8 128 8 64 &gt;=256 0.5 </span></span>
<span><span class="co"># [28] 8 0.002 0.125 0.025 0.005 1 0.025 4 0.005 </span></span> <span><span class="co"># [31] 0.25 8 2 32 0.125 0.0625 0.25 0.025 0.001 8 </span></span>
<span><span class="co"># [37] 4 &lt;=0.001 64 32 0.025 0.125 1 64 0.002 </span></span> <span><span class="co"># [41] 128 2 64 0.25 &gt;=256 0.01 0.01 2 0.125 0.025 </span></span>
<span><span class="co"># [46] 0.005 0.5 0.005 0.0625 0.5 0.125 1 0.25 0.025 </span></span> <span><span class="co"># [51] &gt;=256 0.25 0.025 8 0.005 0.125 0.025 16 0.01 0.025 </span></span>
<span><span class="co"># [55] 1 0.005 0.002 0.0625 2 32 0.01 0.0625 16 </span></span> <span><span class="co"># [61] 1 64 8 1 64 0.025 32 &gt;=256 8 2 </span></span>
<span><span class="co"># [64] 0.005 0.125 0.01 4 0.5 4 2 0.01 0.25 </span></span> <span><span class="co"># [71] 4 0.25 0.002 0.001 1 0.001 &gt;=256 16 4 2 </span></span>
<span><span class="co"># [73] 16 &lt;=0.001 0.0625 0.0625 64 16 0.0625 0.25 0.01 </span></span> <span><span class="co"># [81] 0.125 0.125 0.125 4 64 2 0.01 0.01 0.01 4 </span></span>
<span><span class="co"># [82] 256 128 64 16 0.25 8 64 0.002 &lt;=0.001</span></span> <span><span class="co"># [91] 16 32 0.005 0.005 4 0.0625 0.125 0.005 0.01 2</span></span></code></pre></div>
<span><span class="co"># [91] 256 &lt;=0.001 32 0.5 16 &lt;=0.001 0.5 16 0.5 </span></span>
<span><span class="co"># [100] 16</span></span></code></pre></div>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span> <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> <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>
@@ -1244,10 +1242,10 @@ Longest: 24</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span> <code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span> <span><span class="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span> <span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 28 27 22 29 26 26 28 22 31 20 23 18 26 31 28 18 17 19 17 23 19 21 27 28 24</span></span> <span><span class="co"># [1] 22 18 29 23 26 26 22 22 17 28 29 31 25 28 22 27 28 30 27 26 28 29 31 19 26</span></span>
<span><span class="co"># [26] 30 27 22 21 24 28 28 24 18 31 31 17 17 30 30 17 30 26 27 21 17 28 20 21 27</span></span> <span><span class="co"># [26] 25 25 24 25 30 17 21 25 21 18 17 30 23 30 19 18 29 25 29 27 23 28 21 17 25</span></span>
<span><span class="co"># [51] 31 28 23 24 30 19 27 30 24 29 23 26 22 24 17 17 31 20 27 20 22 29 27 28 30</span></span> <span><span class="co"># [51] 27 23 17 29 28 25 30 23 21 22 20 21 28 25 23 31 29 25 31 17 22 20 21 17 19</span></span>
<span><span class="co"># [76] 20 31 25 29 20 29 27 28 29 20 30 27 21 23 24 24 26 18 26 27 19 25 26 28 24</span></span></code></pre></div> <span><span class="co"># [76] 17 21 21 18 18 20 29 30 21 18 23 18 29 25 22 27 22 22 24 24 25 27 31 26 18</span></span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span> <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> <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>
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articles/MDR.html
+28 -28
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@@ -314,19 +314,19 @@ Unique: 2</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> <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> <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"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 S I I S I S</span></span> <span><span class="co"># 1 S R R I R I</span></span>
<span><span class="co"># 2 R I I R R R</span></span> <span><span class="co"># 2 R I I R I R</span></span>
<span><span class="co"># 3 S I S S S R</span></span> <span><span class="co"># 3 I S I S I S</span></span>
<span><span class="co"># 4 R S R I R S</span></span> <span><span class="co"># 4 I I I R I I</span></span>
<span><span class="co"># 5 I R I I R I</span></span> <span><span class="co"># 5 S S R S R I</span></span>
<span><span class="co"># 6 S I I S I S</span></span> <span><span class="co"># 6 I S R R I R</span></span>
<span><span class="co"># kanamycin</span></span> <span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 R</span></span> <span><span class="co"># 1 R</span></span>
<span><span class="co"># 2 I</span></span> <span><span class="co"># 2 I</span></span>
<span><span class="co"># 3 R</span></span> <span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 I</span></span> <span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 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> <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"> <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> <code class="sourceCode R"><span><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></span></code></pre></div>
@@ -357,40 +357,40 @@ Unique: 5</p>
<tr class="odd"> <tr class="odd">
<td align="left">1</td> <td align="left">1</td>
<td align="left">Mono-resistant</td> <td align="left">Mono-resistant</td>
<td align="right">3202</td> <td align="right">3234</td>
<td align="right">64.04%</td> <td align="right">64.68%</td>
<td align="right">3202</td> <td align="right">3234</td>
<td align="right">64.04%</td> <td align="right">64.68%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">2</td> <td align="left">2</td>
<td align="left">Negative</td> <td align="left">Negative</td>
<td align="right">995</td> <td align="right">984</td>
<td align="right">19.90%</td> <td align="right">19.68%</td>
<td align="right">4197</td> <td align="right">4218</td>
<td align="right">83.94%</td> <td align="right">84.36%</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">3</td> <td align="left">3</td>
<td align="left">Multi-drug-resistant</td> <td align="left">Multi-drug-resistant</td>
<td align="right">443</td> <td align="right">447</td>
<td align="right">8.86%</td> <td align="right">8.94%</td>
<td align="right">4640</td> <td align="right">4665</td>
<td align="right">92.80%</td> <td align="right">93.30%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">4</td> <td align="left">4</td>
<td align="left">Poly-resistant</td> <td align="left">Poly-resistant</td>
<td align="right">260</td> <td align="right">236</td>
<td align="right">5.20%</td> <td align="right">4.72%</td>
<td align="right">4900</td> <td align="right">4901</td>
<td align="right">98.00%</td> <td align="right">98.02%</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">5</td> <td align="left">5</td>
<td align="left">Extensively drug-resistant</td> <td align="left">Extensively drug-resistant</td>
<td align="right">100</td> <td align="right">99</td>
<td align="right">2.00%</td> <td align="right">1.98%</td>
<td align="right">5000</td> <td align="right">5000</td>
<td align="right">100.00%</td> <td align="right">100.00%</td>
</tr> </tr>
articles/SPSS.html
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@@ -162,7 +162,7 @@
<img src="../logo.svg" class="logo" alt=""><h1>How to import data from SPSS / SAS / Stata</h1> <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="author">Dr. Matthijs Berends</h4>
<h4 data-toc-skip class="date">20 October 2022</h4> <h4 data-toc-skip class="date">21 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> <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> <div class="d-none name"><code>SPSS.Rmd</code></div>
articles/datasets.html
+9 -9
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@@ -161,7 +161,7 @@
<main id="main" class="col-md-9"><div class="page-header"> <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> <img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">20 October 2022</h4> <h4 data-toc-skip class="date">21 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> <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> <div class="d-none name"><code>datasets.Rmd</code></div>
@@ -177,7 +177,7 @@
</h2> </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>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>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 20 October 2022 17:39:59 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 21 October 2022 07:59:44 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> <p><strong>Direct download links:</strong></p>
<ul> <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> <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> </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>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>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 20 October 2022 17:39:59 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 21 October 2022 07:59:44 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> <p><strong>Direct download links:</strong></p>
<ul> <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> <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> </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>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>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 20 October 2022 17:39:59 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 21 October 2022 07:59:44 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> <p><strong>Direct download links:</strong></p>
<ul> <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> <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> </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>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>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 20 October 2022 17:39:59 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 21 October 2022 07:59:44 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> <p><strong>Direct download links:</strong></p>
<ul> <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> <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> </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>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>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 20 October 2022 17:39:59 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 21 October 2022 07:59:44 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> <p><strong>Direct download links:</strong></p>
<ul> <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> <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> </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>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>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 20 October 2022 17:39:59 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 21 October 2022 07:59:44 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> <p><strong>Direct download links:</strong></p>
<ul> <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> <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> </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>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>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 20 October 2022 17:39:59 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 21 October 2022 07:59:44 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"> <div class="section level3">
<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a> <h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
</h3> </h3>
@@ -1707,7 +1707,7 @@
</h2> </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>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>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 20 October 2022 17:39:59 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 21 October 2022 07:59:44 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"> <div class="section level3">
<h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a> <h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>
</h3> </h3>
pkgdown.yml
+1 -1
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@@ -11,7 +11,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2022-10-20T17:42Z last_built: 2022-10-21T08:02Z
urls: urls:
reference: https://msberends.github.io/AMR/reference reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles article: https://msberends.github.io/AMR/articles
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reference/age.html
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@@ -190,16 +190,16 @@
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span> <span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span> <span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1955-02-11 67 67.68767 44</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 1988-08-03 34 34.21644 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1965-04-20 57 57.50137 34</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 1950-05-28 72 72.40000 49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1995-01-28 27 27.72603 4</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 1968-12-14 53 53.85205 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1979-03-04 43 43.63014 20</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 1949-07-10 73 73.28219 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1975-09-03 47 47.12877 24</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 1969-05-24 53 53.41096 30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1990-02-11 32 32.68767 9</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 1966-11-13 55 55.93699 33</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1994-05-12 28 28.44110 5</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-02-11 25 25.69041 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1980-04-21 42 42.49863 19</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 1937-09-19 85 85.08767 62</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1945-01-06 77 77.78630 54</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 1989-04-24 33 33.49315 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1938-06-07 84 84.36986 61</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 1985-08-22 37 37.16438 14</span>
</code></pre></div> </code></pre></div>
</div> </div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
reference/as.rsi.html
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@@ -484,16 +484,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 13</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 13</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-10-20 <span style="color: #949494;">17:43:03</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-10-21 <span style="color: #949494;">08:03:03</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-10-20 <span style="color: #949494;">17:43:03</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-10-21 <span style="color: #949494;">08:03:03</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-10-20 <span style="color: #949494;">17:43:03</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-10-21 <span style="color: #949494;">08:03:03</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-10-20 <span style="color: #949494;">17:43:04</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-10-21 <span style="color: #949494;">08:03:03</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-10-20 <span style="color: #949494;">17:43:04</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-10-21 <span style="color: #949494;">08:03:04</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-10-20 <span style="color: #949494;">17:43:04</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-10-21 <span style="color: #949494;">08:03:04</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-10-20 <span style="color: #949494;">17:43:05</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-10-21 <span style="color: #949494;">08:03:05</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-10-20 <span style="color: #949494;">17:43:05</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-10-21 <span style="color: #949494;">08:03:05</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-10-20 <span style="color: #949494;">17:43:05</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-10-21 <span style="color: #949494;">08:03:05</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-10-20 <span style="color: #949494;">17:43:05</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-10-21 <span style="color: #949494;">08:03:05</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 6 more variables: ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 6 more variables: ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S &lt;dbl&gt;, breakpoint_R &lt;dbl&gt;, input &lt;dbl&gt;, interpretation &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S &lt;dbl&gt;, breakpoint_R &lt;dbl&gt;, input &lt;dbl&gt;, interpretation &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># and abbreviated variable names ¹​ab_considered, ²​mo_input, ³​mo_considered,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># and abbreviated variable names ¹​ab_considered, ²​mo_input, ³​mo_considered,</span></span>
reference/get_episode.html
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@@ -177,42 +177,42 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</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 class="va">df</span> <span class="op">&lt;-</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></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span> <span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</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">#&gt;</span> [1] 51 1 30 33 57 38 63 41 55 28 20 27 45 11 12 55 39 3 21 59 25 21 9 2 42</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 21 6 27 50 51 28 39 19 14 34 23 43 60 21 1 44 39 11 2 30 34 24 1 46 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 5 49 24 11 32 51 28 21 38 57 36 11 54 24 36 60 6 50 31 60 47 43 20 54 10</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [26] 21 27 50 8 49 11 54 5 24 26 21 38 11 8 56 1 51 26 13 36 18 59 15 37 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 40 35 12 62 31 42 41 37 9 20 1 2 34 48 46 45 51 36 59 45 62 28 54 26 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [51] 63 39 37 52 1 60 17 4 53 42 62 42 47 6 30 15 25 61 44 24 11 43 60 65 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 44 49 28 19 17 10 62 40 6 8 38 51 32 5 37 46 7 61 51 38 27 52 33 58 39</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [76] 4 14 3 3 21 53 18 62 10 38 7 53 23 65 30 34 7 31 28 28 54 43 40 49 49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 38 1 41 7 48 43 9 17 14 31 16 60 19 54 54 28 24 31 54 35 54 3 6 15 18</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [101] 21 64 64 63 39 44 46 56 25 63 21 37 2 49 44 13 4 1 1 6 56 9 35 11 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 48 34 34 60 29 41 12 19 57 54 50 45 17 56 62 10 28 13 28 4 33 53 54 47 22</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [126] 4 32 13 23 63 55 7 17 54 20 4 9 17 12 1 65 2 60 31 25 7 35 20 57 48</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 56 31 9 49 40 61 33 11 50 27 23 24 44 15 4 8 30 48 28 61 62 3 40 60 26</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [151] 45 13 15 42 17 60 56 17 3 34 22 56 55 23 58 48 28 39 29 44 27 61 15 25 56</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 21 26 25 4 13 10 3 8 54 63 48 64 64 44 42 47 58 53 14 8 52 22 13 17 23</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [176] 2 7 40 1 32 62 9 62 33 12 56 9 61 41 43 13 11 12 2 39 11 3 17 53 24</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">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span> <span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</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">#&gt;</span> [1] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [145] TRUE FALSE FALSE TRUE TRUE TRUE TRUE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [169] TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-in"><span></span></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="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">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span> <span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</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">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-10-11 974319 78 M Outpatie… B_STPHY_EPDR S NA S NA </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</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">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-08-31 149442 80 F ICU B_STPHY_AURS R NA S R </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-07-16 241328 78 M Outpatie… B_STPHY_CONS R NA S R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-10-18 E55128 57 F ICU B_STPHY_AURS R NA S R </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-08-19 A49852 70 M Clinical B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2002-09-23 F35553 51 M ICU B_STPHY_AURS S NA S NA </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2002-07-21 955940 82 F Clinical B_PSDMN_AERG R NA NA R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 36 more variables: AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;, CZO &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 36 more variables: AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;, CZO &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FEP &lt;rsi&gt;, CXM &lt;rsi&gt;, FOX &lt;rsi&gt;, CTX &lt;rsi&gt;, CAZ &lt;rsi&gt;, CRO &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FEP &lt;rsi&gt;, CXM &lt;rsi&gt;, FOX &lt;rsi&gt;, CTX &lt;rsi&gt;, CAZ &lt;rsi&gt;, CRO &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># GEN &lt;rsi&gt;, TOB &lt;rsi&gt;, AMK &lt;rsi&gt;, KAN &lt;rsi&gt;, TMP &lt;rsi&gt;, SXT &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># GEN &lt;rsi&gt;, TOB &lt;rsi&gt;, AMK &lt;rsi&gt;, KAN &lt;rsi&gt;, TMP &lt;rsi&gt;, SXT &lt;rsi&gt;,</span></span>
@@ -248,16 +248,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: condition [3]</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: condition [3]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_episode</span> <span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> D53062 2014-07-28 B FALSE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 0E2483 2007-05-29 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 495616 2002-01-17 C TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 114570 2003-04-08 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 534816 2008-10-28 A TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 189795 2008-10-19 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> D30712 2009-04-10 B FALSE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> C48417 2014-02-07 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 092034 2016-08-07 C FALSE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 658640 2014-05-30 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 080086 2010-08-08 A FALSE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B65162 2008-12-29 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 470001 2017-10-04 C FALSE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> E53320 2011-07-04 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> F15984 2011-04-01 B FALSE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 418311 2006-11-10 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> D41749 2015-12-15 A FALSE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2B1C03 2005-10-23 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 945BD5 2008-05-06 A FALSE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 192353 2010-04-05 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</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="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">%&gt;%</a></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">%&gt;%</a></span></span></span>
@@ -269,19 +269,19 @@
<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-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">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 5</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [185]</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [182]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span> <span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2014-07-28 D53062 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2007-05-29 0E2483 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2002-01-17 495616 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU 2003-04-08 114570 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2008-10-28 534816 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2008-10-19 189795 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2009-04-10 D30712 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2014-02-07 C48417 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2016-08-07 092034 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2014-05-30 658640 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2010-08-08 080086 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2008-12-29 B65162 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2017-10-04 470001 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2011-07-04 E53320 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Outpatient 2011-04-01 F15984 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ICU 2006-11-10 418311 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2015-12-15 D41749 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2005-10-23 2B1C03 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2008-05-06 945BD5 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2010-04-05 192353 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</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="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">%&gt;%</a></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">%&gt;%</a></span></span></span>
@@ -296,9 +296,9 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span> <span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 116 14 53 71</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 113 14 49 70</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 52 11 32 40</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 58 13 34 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 17 10 16 17</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 11 5 11 11</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="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></span>
<span class="r-in"><span> <span class="co"># grouping on patients and microorganisms leads to the same</span></span></span> <span class="r-in"><span> <span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
@@ -317,7 +317,7 @@
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">y</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="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Including isolates from ICU.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Including isolates from ICU.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</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="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></span>
<span class="r-in"><span> <span class="co"># but is_new_episode() has a lot more flexibility than first_isolate(),</span></span></span> <span class="r-in"><span> <span class="co"># but is_new_episode() has a lot more flexibility than first_isolate(),</span></span></span>
@@ -328,19 +328,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</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="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 4</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [190]</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [193]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span> <span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> D53062 B_HMPHL_INFL Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 0E2483 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 495616 B_STPHY_EPDR Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 114570 B_STRPT_PYGN ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 534816 F_CANDD_ALBC Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 189795 B_AERCC_URNQ Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> D30712 B_STRPT_PNMN Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> C48417 B_LCTBC_DLBR_LCTS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 092034 B_ESCHR_COLI Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 658640 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 080086 B_STPHY_CONS Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B65162 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 470001 B_KLBSL_PNMN Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> E53320 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> F15984 B_STPHY_CONS Outpatient TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 418311 B_STPHY_CONS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> D41749 B_ESCHR_COLI Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2B1C03 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 945BD5 B_ENTRBC_CLOC Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 192353 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div> </code></pre></div>
reference/kurtosis.html
+2 -2
View File
@@ -167,9 +167,9 @@
<div class="section level2"> <div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <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> <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">#&gt;</span> [1] 2.993252</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.960986</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-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">#&gt;</span> [1] 0.03411978</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.03795045</span>
</code></pre></div> </code></pre></div>
</div> </div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
reference/mean_amr_distance.html
+38 -38
View File
@@ -195,10 +195,10 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</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> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</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-in"><span><span class="va">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 64 128 0.01 0.001 128 0.025 16 4 64 0.25 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.025 8 0.0625 16 16 1 0.125 &gt;=32 0.25 0.002 </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-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">#&gt;</span> [1] 0.8219432 0.9802175 -1.1792542 -1.7050300 0.9802175 -0.9700270</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.9782837 0.7941806 -0.6967299 1.0071679 1.0071679 0.1552190</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.5053947 0.1888461 0.8219432 -0.4442511</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.4837427 1.2201551 -0.2707555 -1.7543786</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</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><span class="va">y</span> <span class="op">&lt;-</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> <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>
@@ -208,38 +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> 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="op">)</span></span></span>
<span class="r-in"><span><span class="va">y</span></span></span> <span class="r-in"><span><span class="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span> <span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 4 0.125 2 &gt;=4</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 16 &lt;=0.0625 &lt;=0.25 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 8 0.25 8 &lt;=0.5</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 B &gt;=32 0.125 1 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &lt;=2 1 2 &gt;=4</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 4 &lt;=0.0625 &lt;=0.25 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 1 8 &gt;=4</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 D &gt;=32 &gt;=1 0.5 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E &lt;=2 1 2 &lt;=0.5</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 8 0.125 2 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F &lt;=2 &lt;=0.025 1 &lt;=0.5</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 4 0.25 &lt;=0.25 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 0.0625 1 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 16 &lt;=0.0625 &lt;=0.25 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H &lt;=2 2 8 &gt;=4</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 0.25 &gt;=4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 8 0.125 0.5 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 4 &gt;=1 &lt;=0.25 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &gt;=16 0.5 16 &gt;=4</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &lt;=2 &gt;=1 2 8</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-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">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "id" and "tobr"</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> "id" and "tobr"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NAs introduced by coercion</span> <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.07272768 0.02436854 0.07054523 0.81400616 -0.47677206 -1.27310062</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.04787176 0.30260331 -0.98864537 0.73456530 0.25539334 -0.10496162</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.30764224 0.49475116 -0.33800496 1.06457646</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.63509198 -0.05402839 0.19150191 0.34653525</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</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">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span> <span class="r-msg co"><span class="r-pr">#&gt;</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">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span> <span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</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">#&gt;</span> id amox cipr gent tobr amr_distance</span> <span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F &lt;=2 &lt;=0.025 1 &lt;=0.5 -1.27310062</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 4 &lt;=0.0625 &lt;=0.25 1 -0.98864537</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E &lt;=2 1 2 &lt;=0.5 -0.47677206</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 16 &lt;=0.0625 &lt;=0.25 1 -0.63509198</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 8 0.125 0.5 2 -0.33800496</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 4 0.25 &lt;=0.25 &gt;=16 -0.10496162</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 0.0625 1 2 -0.30764224</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 0.25 &gt;=4 1 -0.05402839</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 4 0.125 2 &gt;=4 -0.07272768</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 16 &lt;=0.0625 &lt;=0.25 &gt;=16 -0.04787176</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 8 0.25 8 &lt;=0.5 0.02436854</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 4 &gt;=1 &lt;=0.25 &gt;=16 0.19150191</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &lt;=2 1 2 &gt;=4 0.07054523</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 8 0.125 2 8 0.25539334</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H &lt;=2 2 8 &gt;=4 0.49475116</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 B &gt;=32 0.125 1 4 0.30260331</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 1 8 &gt;=4 0.81400616</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &lt;=2 &gt;=1 2 8 0.34653525</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &gt;=16 0.5 16 &gt;=4 1.06457646</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 D &gt;=32 &gt;=1 0.5 8 0.73456530</span>
<span class="r-in"><span></span></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="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">%&gt;%</a></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">%&gt;%</a></span></span></span>
@@ -251,17 +251,17 @@
<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-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span> <span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C &lt;=2 1 2 &gt;=4 0.07054523 0.00000000</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 C 4 &lt;=0.0625 &lt;=0.25 1 -0.98864537 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 8 0.25 8 &lt;=0.5 0.02436854 0.04617669</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 G 16 &lt;=0.0625 &lt;=0.25 1 -0.63509198 0.3535534</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 A 4 0.125 2 &gt;=4 -0.07272768 0.14327291</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 F 4 0.25 &lt;=0.25 &gt;=16 -0.10496162 0.8836838</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 G 8 0.0625 1 2 -0.30764224 0.37818747</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 H 4 0.25 &gt;=4 1 -0.05402839 0.9346170</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 I 8 0.125 0.5 2 -0.33800496 0.40855018</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 A 16 &lt;=0.0625 &lt;=0.25 &gt;=16 -0.04787176 0.9407736</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 H &lt;=2 2 8 &gt;=4 0.49475116 0.42420593</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 I 4 &gt;=1 &lt;=0.25 &gt;=16 0.19150191 1.1801473</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 E &lt;=2 1 2 &lt;=0.5 -0.47677206 0.54731729</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 E 8 0.125 2 8 0.25539334 1.2440387</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 D 8 1 8 &gt;=4 0.81400616 0.74346093</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 B &gt;=32 0.125 1 4 0.30260331 1.2912487</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 J &gt;=16 0.5 16 &gt;=4 1.06457646 0.99403123</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 J &lt;=2 &gt;=1 2 8 0.34653525 1.3351806</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 F &lt;=2 &lt;=0.025 1 &lt;=0.5 -1.27310062 1.34364585</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 D &gt;=32 &gt;=1 0.5 8 0.73456530 1.7232107</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="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="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">%&gt;%</a></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">%&gt;%</a></span></span></span>
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reference/random.html
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@@ -178,42 +178,43 @@
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <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> <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">#&gt;</span> Class 'mic'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 0.01 64 0.5 &lt;=0.001 64 4 8 64 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 1 0.025 0.002 64 0.005 1 &lt;=0.001 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.5 16 0.25 0.005 0.125 0.005 &lt;=0.001 4 0.25 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.5 0.5 &gt;=256 128 0.01 0.002 0.005 64 0.002 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.002 0.01 0.125 4 64 0.002 &gt;=128 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [19] 1 32 &lt;=0.001 &gt;=256 32 0.5 0.5 </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-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">#&gt;</span> Class 'disk'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 19 48 50 43 37 6 35 42 37 19 33 47 50 45 48 44 47 26 15 23 42 15 38 30 38</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 40 50 26 30 33 38 49 50 44 43 44 44 23 48 16 23 10 16 44 22 15 45 40 22 42</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-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">#&gt;</span> Class 'rsi'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'rsi'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I R S I I S S I S R R S I S I I R R I S S R S I I</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] I I S I R S R S R I I R S I R R R I I R I S I I R</span>
<span class="r-in"><span></span></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"># \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="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-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">#&gt;</span> Class 'mic'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.005 0.5 1 0.005 2 0.01 16 0.25 128 0.002 8 0.025</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.125 &gt;=256 0.25 0.002 4 16 0.125 0.5 8 0.002 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 32 16 16 0.001 4 0.005 16 0.125 0.25 8 0.5 64 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.01 16 0.0625 128 2 0.5 0.0625 8 2 0.025 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 32 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [21] 16 32 1 &gt;=256 0.01 </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-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">#&gt;</span> Class 'mic'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 &lt;=1 2 16 &lt;=1 &gt;=64 &lt;=1 32 4 &lt;=1 2 16 2 2 &gt;=64</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 16 16 4 4 1 16 2 1 1 8 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] &gt;=64 2 8 32 &gt;=64 8 8 4 &lt;=1 16 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [13] 32 2 1 &lt;=0.5 1 4 4 1 2 2 8 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 8 </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-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">#&gt;</span> Class 'mic'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 8 2 &lt;=0.125 0.5 &lt;=0.125 0.5 1 0.5 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 0.5 0.5 0.25 &lt;=0.125 8 4 2 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.5 8 &lt;=0.125 2 1 2 0.25 1 2 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [10] 2 4 8 2 1 8 4 0.25 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 2 2 1 0.25 0.5 8 0.25 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [19] &lt;=0.125 &lt;=0.125 0.25 8 0.25 0.5 &lt;=0.125</span>
<span class="r-in"><span></span></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-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">#&gt;</span> Class 'disk'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 14 49 37 14 42 20 48 28 49 28 47 21 35 34 35 36 49 31 18 39 25 50 23 32 26</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 44 47 50 45 9 46 47 39 36 41 45 22 49 50 28 50 28 13 16 44 17 10 15 44 23</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-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">#&gt;</span> Class 'disk'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 11 11 14 12 16 13 15 11 12 14 14 13 13 12 16 14 11 12 11 11 13 15 17 13 16</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 11 14 11 11 14 16 16 11 11 12 14 15 13 14 16 12 17 15 11 12 15 14 11 16 12</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-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">#&gt;</span> Class 'disk'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 22 23 20 17 18 15 20 26 22 26 16 23 23 27 20 18 18 17 25 27 27 15 19 19 19</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 23 25 15 17 25 18 22 20 24 17 15 24 22 23 15 16 27 19 24 21 25 15 15 23 23</span>
<span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div> </code></pre></div>
</div> </div>
reference/skewness.html
+1 -1
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@@ -166,7 +166,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<div class="section level2"> <div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <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> <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">#&gt;</span> [1] -0.0958419</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.007945776</span>
</code></pre></div> </code></pre></div>
</div> </div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
search.json
+1 -1
View File
@@ -1 +1 @@
[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations RSI values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables.","code":"library(dplyr) library(ggplot2) library(AMR) library(cleaner) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\", \"cleaner\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"creation-of-data","dir":"Articles","previous_headings":"","what":"Creation of data","title":"How to conduct AMR data analysis","text":"create fake example data use analysis. AMR data analysis, need least: patient ID, name code microorganism, date antimicrobial results (antibiogram). also include specimen type (e.g. filter blood urine), ward type (e.g. filter ICUs). additional columns (like hospital name, patients gender even [well-defined] clinical properties) can comparative analysis, tutorial demonstrate .","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"patients","dir":"Articles","previous_headings":"Creation of data","what":"Patients","title":"How to conduct AMR data analysis","text":"start patients, need unique list patients. LETTERS object available R - ’s vector 26 characters: Z. patients object just created now vector length 260, values (patient IDs) varying A1 Z10. Now also set gender patients, putting ID gender table: first 135 patient IDs now male, 125 female.","code":"patients <- unlist(lapply(LETTERS, paste0, 1:10)) patients_table <- data.frame( patient_id = patients, gender = c( rep(\"M\", 135), rep(\"F\", 125) ) )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"dates","dir":"Articles","previous_headings":"Creation of data","what":"Dates","title":"How to conduct AMR data analysis","text":"Let’s pretend data consists blood cultures isolates 1 January 2010 1 January 2018. dates object now contains days date range.","code":"dates <- seq(as.Date(\"2010-01-01\"), as.Date(\"2018-01-01\"), by = \"day\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"microorganisms","dir":"Articles","previous_headings":"Creation of data > Dates","what":"Microorganisms","title":"How to conduct AMR data analysis","text":"tutorial, uses four different microorganisms: Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae:","code":"bacteria <- c( \"Escherichia coli\", \"Staphylococcus aureus\", \"Streptococcus pneumoniae\", \"Klebsiella pneumoniae\" )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"put-everything-together","dir":"Articles","previous_headings":"CreatLine truncated [{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations RSI values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables.","code":"library(dplyr) library(ggplot2) library(AMR) library(cleaner) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\", \"cleaner\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"creation-of-data","dir":"Articles","previous_headings":"","what":"Creation of data","title":"How to conduct AMR data analysis","text":"create fake example data use analysis. AMR data analysis, need least: patient ID, name code microorganism, date antimicrobial results (antibiogram). also include specimen type (e.g. filter blood urine), ward type (e.g. filter ICUs). additional columns (like hospital name, patients gender even [well-defined] clinical properties) can comparative analysis, tutorial demonstrate .","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"patients","dir":"Articles","previous_headings":"Creation of data","what":"Patients","title":"How to conduct AMR data analysis","text":"start patients, need unique list patients. LETTERS object available R - ’s vector 26 characters: Z. patients object just created now vector length 260, values (patient IDs) varying A1 Z10. Now also set gender patients, putting ID gender table: first 135 patient IDs now male, 125 female.","code":"patients <- unlist(lapply(LETTERS, paste0, 1:10)) patients_table <- data.frame( patient_id = patients, gender = c( rep(\"M\", 135), rep(\"F\", 125) ) )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"dates","dir":"Articles","previous_headings":"Creation of data","what":"Dates","title":"How to conduct AMR data analysis","text":"Let’s pretend data consists blood cultures isolates 1 January 2010 1 January 2018. dates object now contains days date range.","code":"dates <- seq(as.Date(\"2010-01-01\"), as.Date(\"2018-01-01\"), by = \"day\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"microorganisms","dir":"Articles","previous_headings":"Creation of data > Dates","what":"Microorganisms","title":"How to conduct AMR data analysis","text":"tutorial, uses four different microorganisms: Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae:","code":"bacteria <- c( \"Escherichia coli\", \"Staphylococcus aureus\", \"Streptococcus pneumoniae\", \"Klebsiella pneumoniae\" )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"put-everything-together","dir":"Articles","previous_headings":"CreatLine truncated