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@@ -168,7 +168,7 @@
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<h4 data-toc-skip class="author">Dr. Matthijs
|
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Berends</h4>
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|
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<h4 data-toc-skip class="date">28 November 2022</h4>
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<h4 data-toc-skip class="date">29 November 2022</h4>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
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<div class="d-none name"><code>AMR.Rmd</code></div>
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@@ -180,7 +180,7 @@ Berends</h4>
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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 28 November 2022.</p>
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generated on 29 November 2022.</p>
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<div class="section level2">
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<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
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</h2>
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@@ -236,21 +236,21 @@ make the structure of your data generally look like this:</p>
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</tr></thead>
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||||
<tbody>
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||||
<tr class="odd">
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||||
<td align="center">2022-11-28</td>
|
||||
<td align="center">2022-11-29</td>
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||||
<td align="center">abcd</td>
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||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2022-11-28</td>
|
||||
<td align="center">2022-11-29</td>
|
||||
<td align="center">abcd</td>
|
||||
<td align="center">Escherichia coli</td>
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||||
<td align="center">S</td>
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||||
<td align="center">R</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2022-11-28</td>
|
||||
<td align="center">2022-11-29</td>
|
||||
<td align="center">efgh</td>
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||||
<td align="center">Escherichia coli</td>
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||||
<td align="center">R</td>
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@@ -400,71 +400,71 @@ data set:</p>
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||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2016-12-09</td>
|
||||
<td align="center">B5</td>
|
||||
<td align="center">2016-02-08</td>
|
||||
<td align="center">L4</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Klebsiella pneumoniae</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2013-12-22</td>
|
||||
<td align="center">V7</td>
|
||||
<td align="center">2011-06-04</td>
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||||
<td align="center">B4</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2010-12-27</td>
|
||||
<td align="center">U10</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Klebsiella pneumoniae</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">2013-08-11</td>
|
||||
<td align="center">H1</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">Staphylococcus aureus</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2011-09-01</td>
|
||||
<td align="center">J7</td>
|
||||
<td align="center">2011-08-27</td>
|
||||
<td align="center">M9</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Streptococcus pneumoniae</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2015-04-24</td>
|
||||
<td align="center">L8</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">Streptococcus pneumoniae</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2010-09-10</td>
|
||||
<td align="center">N5</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2015-12-02</td>
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||||
<td align="center">E9</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Staphylococcus aureus</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2012-01-20</td>
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||||
<td align="center">V9</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Staphylococcus aureus</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
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||||
<p>Now, let’s start the cleaning and the analysis!</p>
|
||||
@@ -499,16 +499,16 @@ Longest: 1</p>
|
||||
<tr class="odd">
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||||
<td align="left">1</td>
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||||
<td align="left">M</td>
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||||
<td align="right">10,502</td>
|
||||
<td align="right">52.51%</td>
|
||||
<td align="right">10,502</td>
|
||||
<td align="right">52.51%</td>
|
||||
<td align="right">10,441</td>
|
||||
<td align="right">52.21%</td>
|
||||
<td align="right">10,441</td>
|
||||
<td align="right">52.21%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">F</td>
|
||||
<td align="right">9,498</td>
|
||||
<td align="right">47.49%</td>
|
||||
<td align="right">9,559</td>
|
||||
<td align="right">47.80%</td>
|
||||
<td align="right">20,000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
@@ -621,9 +621,9 @@ takes into account the antimicrobial susceptibility test results using
|
||||
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
|
||||
<span><span class="co"># 2</span></span>
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||||
<span><span class="co"># Including isolates from ICU.</span></span>
|
||||
<span><span class="co"># => Found 10,638 'phenotype-based' first isolates (53.2% of total where a</span></span>
|
||||
<span><span class="co"># => Found 10,709 'phenotype-based' first isolates (53.5% of total where a</span></span>
|
||||
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
|
||||
<p>So only 53.2% is suitable for resistance analysis! We can now filter
|
||||
<p>So only 53.5% 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">
|
||||
@@ -634,12 +634,13 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
|
||||
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
|
||||
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
|
||||
<p>So we end up with 10,638 isolates for analysis. Now our data looks
|
||||
<p>So we end up with 10,709 isolates for analysis. Now our data looks
|
||||
like:</p>
|
||||
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
|
||||
<table class="table">
|
||||
<table style="width:100%;" class="table">
|
||||
<colgroup>
|
||||
<col width="2%">
|
||||
<col width="9%">
|
||||
<col width="9%">
|
||||
<col width="9%">
|
||||
@@ -655,6 +656,7 @@ like:</p>
|
||||
<col width="5%">
|
||||
</colgroup>
|
||||
<thead><tr class="header">
|
||||
<th align="left"></th>
|
||||
<th align="center">date</th>
|
||||
<th align="center">patient_id</th>
|
||||
<th align="center">hospital</th>
|
||||
@@ -671,90 +673,96 @@ like:</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2016-12-09</td>
|
||||
<td align="center">B5</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="left">3</td>
|
||||
<td align="center">2010-12-27</td>
|
||||
<td align="center">U10</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_KLBSL_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2013-12-22</td>
|
||||
<td align="center">V7</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2011-09-01</td>
|
||||
<td align="center">J7</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2010-09-10</td>
|
||||
<td align="center">N5</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2015-12-02</td>
|
||||
<td align="center">E9</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="left">4</td>
|
||||
<td align="center">2013-08-11</td>
|
||||
<td align="center">H1</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">7</td>
|
||||
<td align="center">2013-10-25</td>
|
||||
<td align="center">I3</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2012-01-20</td>
|
||||
<td align="center">V9</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">R</td>
|
||||
<td align="left">9</td>
|
||||
<td align="center">2011-08-23</td>
|
||||
<td align="center">Y10</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">11</td>
|
||||
<td align="center">2012-08-03</td>
|
||||
<td align="center">U10</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_KLBSL_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">12</td>
|
||||
<td align="center">2013-12-31</td>
|
||||
<td align="center">L3</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">aureus</td>
|
||||
@@ -793,8 +801,8 @@ readable:</p>
|
||||
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
|
||||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: character<br>
|
||||
Length: 10,638<br>
|
||||
Available: 10,638 (100%, NA: 0 = 0%)<br>
|
||||
Length: 10,709<br>
|
||||
Available: 10,709 (100%, NA: 0 = 0%)<br>
|
||||
Unique: 4</p>
|
||||
<p>Shortest: 16<br>
|
||||
Longest: 24</p>
|
||||
@@ -819,33 +827,33 @@ Longest: 24</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Escherichia coli</td>
|
||||
<td align="right">4,646</td>
|
||||
<td align="right">43.67%</td>
|
||||
<td align="right">4,646</td>
|
||||
<td align="right">43.67%</td>
|
||||
<td align="right">4,635</td>
|
||||
<td align="right">43.28%</td>
|
||||
<td align="right">4,635</td>
|
||||
<td align="right">43.28%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Staphylococcus aureus</td>
|
||||
<td align="right">2,743</td>
|
||||
<td align="right">25.78%</td>
|
||||
<td align="right">7,389</td>
|
||||
<td align="right">69.46%</td>
|
||||
<td align="right">2,757</td>
|
||||
<td align="right">25.74%</td>
|
||||
<td align="right">7,392</td>
|
||||
<td align="right">69.03%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Streptococcus pneumoniae</td>
|
||||
<td align="right">2,065</td>
|
||||
<td align="right">19.41%</td>
|
||||
<td align="right">9,454</td>
|
||||
<td align="right">88.87%</td>
|
||||
<td align="right">2,115</td>
|
||||
<td align="right">19.75%</td>
|
||||
<td align="right">9,507</td>
|
||||
<td align="right">88.78%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Klebsiella pneumoniae</td>
|
||||
<td align="right">1,184</td>
|
||||
<td align="right">11.13%</td>
|
||||
<td align="right">10,638</td>
|
||||
<td align="right">1,202</td>
|
||||
<td align="right">11.22%</td>
|
||||
<td align="right">10,709</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
@@ -894,8 +902,38 @@ antibiotic class they are in:</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2011-09-01</td>
|
||||
<td align="center">J7</td>
|
||||
<td align="center">2014-06-23</td>
|
||||
<td align="center">T5</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2016-09-29</td>
|
||||
<td align="center">N9</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="odd">
|
||||
<td align="center">2011-01-04</td>
|
||||
<td align="center">E8</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
@@ -909,54 +947,24 @@ antibiotic class they are in:</p>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2014-11-04</td>
|
||||
<td align="center">C7</td>
|
||||
<td align="center">2017-12-28</td>
|
||||
<td align="center">Z5</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2010-05-22</td>
|
||||
<td align="center">X1</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">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">2011-03-20</td>
|
||||
<td align="center">A1</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2016-05-13</td>
|
||||
<td align="center">K9</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">2010-08-11</td>
|
||||
<td align="center">C6</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@@ -969,9 +977,9 @@ antibiotic class they are in:</p>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2014-01-21</td>
|
||||
<td align="center">Q10</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">2012-08-24</td>
|
||||
<td align="center">Z9</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@@ -1005,50 +1013,50 @@ different bug/drug combinations, you can use the
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">AMX</td>
|
||||
<td align="center">2171</td>
|
||||
<td align="center">147</td>
|
||||
<td align="center">2328</td>
|
||||
<td align="center">4646</td>
|
||||
<td align="center">2204</td>
|
||||
<td align="center">121</td>
|
||||
<td align="center">2310</td>
|
||||
<td align="center">4635</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">AMC</td>
|
||||
<td align="center">3429</td>
|
||||
<td align="center">157</td>
|
||||
<td align="center">1060</td>
|
||||
<td align="center">4646</td>
|
||||
<td align="center">3389</td>
|
||||
<td align="center">150</td>
|
||||
<td align="center">1096</td>
|
||||
<td align="center">4635</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">CIP</td>
|
||||
<td align="center">3354</td>
|
||||
<td align="center">3408</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">1292</td>
|
||||
<td align="center">4646</td>
|
||||
<td align="center">1227</td>
|
||||
<td align="center">4635</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">4083</td>
|
||||
<td align="center">4065</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">563</td>
|
||||
<td align="center">4646</td>
|
||||
<td align="center">570</td>
|
||||
<td align="center">4635</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center">AMX</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">1184</td>
|
||||
<td align="center">1184</td>
|
||||
<td align="center">1202</td>
|
||||
<td align="center">1202</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center">AMC</td>
|
||||
<td align="center">936</td>
|
||||
<td align="center">42</td>
|
||||
<td align="center">206</td>
|
||||
<td align="center">1184</td>
|
||||
<td align="center">927</td>
|
||||
<td align="center">50</td>
|
||||
<td align="center">225</td>
|
||||
<td align="center">1202</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@@ -1070,34 +1078,34 @@ different bug/drug combinations, you can use the
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">4083</td>
|
||||
<td align="center">4065</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">563</td>
|
||||
<td align="center">4646</td>
|
||||
<td align="center">570</td>
|
||||
<td align="center">4635</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">1073</td>
|
||||
<td align="center">1095</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">111</td>
|
||||
<td align="center">1184</td>
|
||||
<td align="center">107</td>
|
||||
<td align="center">1202</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">S. aureus</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">2435</td>
|
||||
<td align="center">2408</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">308</td>
|
||||
<td align="center">2743</td>
|
||||
<td align="center">349</td>
|
||||
<td align="center">2757</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">S. pneumoniae</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">2065</td>
|
||||
<td align="center">2065</td>
|
||||
<td align="center">2115</td>
|
||||
<td align="center">2115</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@@ -1129,7 +1137,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
|
||||
own:</p>
|
||||
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
|
||||
<span><span class="co"># [1] 0.5455913</span></span></code></pre></div>
|
||||
<span><span class="co"># [1] 0.5429078</span></span></code></pre></div>
|
||||
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
|
||||
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
|
||||
@@ -1144,19 +1152,19 @@ own:</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.5382918</td>
|
||||
<td align="center">0.5461974</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.5347408</td>
|
||||
<td align="center">0.5343758</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.5776965</td>
|
||||
<td align="center">0.5487149</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.5509126</td>
|
||||
<td align="center">0.5482517</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@@ -1181,23 +1189,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.5382918</td>
|
||||
<td align="center">3173</td>
|
||||
<td align="center">0.5461974</td>
|
||||
<td align="center">3182</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.5347408</td>
|
||||
<td align="center">3742</td>
|
||||
<td align="center">0.5343758</td>
|
||||
<td align="center">3709</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.5776965</td>
|
||||
<td align="center">1641</td>
|
||||
<td align="center">0.5487149</td>
|
||||
<td align="center">1673</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.5509126</td>
|
||||
<td align="center">2082</td>
|
||||
<td align="center">0.5482517</td>
|
||||
<td align="center">2145</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@@ -1222,27 +1230,27 @@ therapies very easily:</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">0.7718467</td>
|
||||
<td align="center">0.8788205</td>
|
||||
<td align="center">0.9750323</td>
|
||||
<td align="center">0.7635383</td>
|
||||
<td align="center">0.8770227</td>
|
||||
<td align="center">0.9766990</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">0.8260135</td>
|
||||
<td align="center">0.9062500</td>
|
||||
<td align="center">0.9873311</td>
|
||||
<td align="center">0.8128120</td>
|
||||
<td align="center">0.9109817</td>
|
||||
<td align="center">0.9833611</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">0.7907401</td>
|
||||
<td align="center">0.8877142</td>
|
||||
<td align="center">0.9817718</td>
|
||||
<td align="center">0.7972434</td>
|
||||
<td align="center">0.8734131</td>
|
||||
<td align="center">0.9818643</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">0.5438257</td>
|
||||
<td align="center">0.5399527</td>
|
||||
<td align="center">0.0000000</td>
|
||||
<td align="center">0.5438257</td>
|
||||
<td align="center">0.5399527</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@@ -1270,23 +1278,23 @@ classes, use a antibiotic class selector such as
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">Hospital A</td>
|
||||
<td align="right">53.8%</td>
|
||||
<td align="right">25.3%</td>
|
||||
<td align="right">54.6%</td>
|
||||
<td align="right">27.7%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Hospital B</td>
|
||||
<td align="right">53.5%</td>
|
||||
<td align="right">25.1%</td>
|
||||
<td align="right">53.4%</td>
|
||||
<td align="right">26.4%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Hospital C</td>
|
||||
<td align="right">57.8%</td>
|
||||
<td align="right">30.1%</td>
|
||||
<td align="right">54.9%</td>
|
||||
<td align="right">25.2%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Hospital D</td>
|
||||
<td align="right">55.1%</td>
|
||||
<td align="right">26.3%</td>
|
||||
<td align="right">54.8%</td>
|
||||
<td align="right">26.7%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@@ -1402,18 +1410,16 @@ classes) <code><mic></code> and <code><disk></code>:</p>
|
||||
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op"><-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
|
||||
<span><span class="va">mic_values</span></span>
|
||||
<span><span class="co"># Class 'mic'</span></span>
|
||||
<span><span class="co"># [1] 8 0.01 0.025 32 0.01 16 32 >=256 0.125 </span></span>
|
||||
<span><span class="co"># [10] 128 0.5 0.125 128 0.005 4 2 0.01 0.0625 </span></span>
|
||||
<span><span class="co"># [19] 0.025 4 <=0.001 0.025 0.002 0.125 0.0625 0.0625 0.01 </span></span>
|
||||
<span><span class="co"># [28] 0.025 <=0.001 16 8 0.005 0.0625 2 2 0.002 </span></span>
|
||||
<span><span class="co"># [37] 0.0625 64 0.025 0.005 0.125 0.002 2 16 0.005 </span></span>
|
||||
<span><span class="co"># [46] 4 16 >=256 0.25 64 128 1 8 0.0625 </span></span>
|
||||
<span><span class="co"># [55] 4 0.002 32 0.0625 8 128 0.0625 64 0.0625 </span></span>
|
||||
<span><span class="co"># [64] 8 0.125 1 <=0.001 128 0.002 8 1 0.002 </span></span>
|
||||
<span><span class="co"># [73] 0.002 64 0.125 0.005 0.5 8 0.025 0.125 0.005 </span></span>
|
||||
<span><span class="co"># [82] 0.005 0.002 <=0.001 0.0625 2 0.125 2 0.25 64 </span></span>
|
||||
<span><span class="co"># [91] 0.25 4 <=0.001 0.125 0.005 0.5 4 0.0625 64 </span></span>
|
||||
<span><span class="co"># [100] 2</span></span></code></pre></div>
|
||||
<span><span class="co"># [1] 8 64 2 1 0.002 128 0.01 0.25 2 0.125 </span></span>
|
||||
<span><span class="co"># [11] 16 0.01 256 4 64 2 0.002 256 0.01 8 </span></span>
|
||||
<span><span class="co"># [21] 0.025 0.025 16 0.025 8 1 128 0.125 4 0.001 </span></span>
|
||||
<span><span class="co"># [31] 4 256 4 1 0.01 0.025 1 0.001 0.002 2 </span></span>
|
||||
<span><span class="co"># [41] 0.001 2 0.01 128 0.01 1 16 0.5 64 0.0625</span></span>
|
||||
<span><span class="co"># [51] 8 0.005 16 32 128 4 0.01 32 0.025 0.005 </span></span>
|
||||
<span><span class="co"># [61] 32 0.01 0.125 256 32 16 8 0.025 4 1 </span></span>
|
||||
<span><span class="co"># [71] 16 16 0.125 0.002 16 32 0.5 0.0625 256 2 </span></span>
|
||||
<span><span class="co"># [81] 0.005 0.01 1 0.005 0.125 0.0625 0.001 0.025 4 0.01 </span></span>
|
||||
<span><span class="co"># [91] 2 1 0.025 256 0.0625 0.001 0.125 0.005 0.0625 0.001</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
|
||||
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
|
||||
@@ -1447,10 +1453,10 @@ plotting:</p>
|
||||
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op"><-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
|
||||
<span><span class="va">disk_values</span></span>
|
||||
<span><span class="co"># Class 'disk'</span></span>
|
||||
<span><span class="co"># [1] 31 26 24 18 17 18 27 18 28 19 17 23 30 18 22 25 28 27 19 21 27 31 27 20 31</span></span>
|
||||
<span><span class="co"># [26] 20 18 24 17 17 30 18 24 25 29 29 17 25 18 18 17 31 20 29 30 18 24 29 23 27</span></span>
|
||||
<span><span class="co"># [51] 17 19 29 17 29 24 22 17 19 19 28 25 25 25 31 30 30 23 28 29 27 20 18 31 28</span></span>
|
||||
<span><span class="co"># [76] 24 30 22 27 20 20 28 23 31 25 19 30 20 19 19 21 28 27 19 31 21 28 30 17 18</span></span></code></pre></div>
|
||||
<span><span class="co"># [1] 31 26 18 31 23 20 17 17 28 29 27 20 23 19 19 24 23 29 20 17 24 26 31 21 20</span></span>
|
||||
<span><span class="co"># [26] 26 19 20 18 31 18 17 31 19 26 20 19 27 20 22 17 25 24 29 19 24 28 25 20 22</span></span>
|
||||
<span><span class="co"># [51] 30 23 18 28 29 22 18 23 30 18 18 22 24 29 26 23 31 31 21 20 31 21 26 23 25</span></span>
|
||||
<span><span class="co"># [76] 23 26 25 29 22 26 18 23 29 26 31 25 17 30 23 21 28 31 26 30 29 29 25 28 27</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
|
||||
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>
|
||||
|
||||
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+26
-26
@@ -375,17 +375,17 @@ names or codes, this would have worked exactly the same way:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
|
||||
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
|
||||
<span><span class="co"># 1 I R R S R I</span></span>
|
||||
<span><span class="co"># 2 R R S S I R</span></span>
|
||||
<span><span class="co"># 3 R S I I R S</span></span>
|
||||
<span><span class="co"># 4 S S I I R R</span></span>
|
||||
<span><span class="co"># 5 I R S R I R</span></span>
|
||||
<span><span class="co"># 6 R I I I S I</span></span>
|
||||
<span><span class="co"># 1 R R S I R I</span></span>
|
||||
<span><span class="co"># 2 S I I R I I</span></span>
|
||||
<span><span class="co"># 3 I R S R R I</span></span>
|
||||
<span><span class="co"># 4 R R R R R S</span></span>
|
||||
<span><span class="co"># 5 R I I I I R</span></span>
|
||||
<span><span class="co"># 6 S S S I S S</span></span>
|
||||
<span><span class="co"># kanamycin</span></span>
|
||||
<span><span class="co"># 1 S</span></span>
|
||||
<span><span class="co"># 1 R</span></span>
|
||||
<span><span class="co"># 2 R</span></span>
|
||||
<span><span class="co"># 3 S</span></span>
|
||||
<span><span class="co"># 4 I</span></span>
|
||||
<span><span class="co"># 4 S</span></span>
|
||||
<span><span class="co"># 5 I</span></span>
|
||||
<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
|
||||
@@ -428,40 +428,40 @@ Unique: 5</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Mono-resistant</td>
|
||||
<td align="right">3140</td>
|
||||
<td align="right">62.80%</td>
|
||||
<td align="right">3140</td>
|
||||
<td align="right">62.80%</td>
|
||||
<td align="right">3210</td>
|
||||
<td align="right">64.20%</td>
|
||||
<td align="right">3210</td>
|
||||
<td align="right">64.20%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">1047</td>
|
||||
<td align="right">20.94%</td>
|
||||
<td align="right">4187</td>
|
||||
<td align="right">83.74%</td>
|
||||
<td align="right">1010</td>
|
||||
<td align="right">20.20%</td>
|
||||
<td align="right">4220</td>
|
||||
<td align="right">84.40%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Multi-drug-resistant</td>
|
||||
<td align="right">456</td>
|
||||
<td align="right">9.12%</td>
|
||||
<td align="right">4643</td>
|
||||
<td align="right">92.86%</td>
|
||||
<td align="right">451</td>
|
||||
<td align="right">9.02%</td>
|
||||
<td align="right">4671</td>
|
||||
<td align="right">93.42%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Poly-resistant</td>
|
||||
<td align="right">254</td>
|
||||
<td align="right">5.08%</td>
|
||||
<td align="right">4897</td>
|
||||
<td align="right">97.94%</td>
|
||||
<td align="right">235</td>
|
||||
<td align="right">4.70%</td>
|
||||
<td align="right">4906</td>
|
||||
<td align="right">98.12%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="left">Extensively drug-resistant</td>
|
||||
<td align="right">103</td>
|
||||
<td align="right">2.06%</td>
|
||||
<td align="right">94</td>
|
||||
<td align="right">1.88%</td>
|
||||
<td align="right">5000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
|
||||
+1
-1
@@ -168,7 +168,7 @@
|
||||
<h4 data-toc-skip class="author">Dr. Matthijs
|
||||
Berends</h4>
|
||||
|
||||
<h4 data-toc-skip class="date">28 November 2022</h4>
|
||||
<h4 data-toc-skip class="date">29 November 2022</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
|
||||
<div class="d-none name"><code>SPSS.Rmd</code></div>
|
||||
|
||||
@@ -166,7 +166,7 @@
|
||||
<main id="main" class="col-md-9"><div class="page-header">
|
||||
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
|
||||
|
||||
<h4 data-toc-skip class="date">28 November 2022</h4>
|
||||
<h4 data-toc-skip class="date">29 November 2022</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
|
||||
<div class="d-none name"><code>datasets.Rmd</code></div>
|
||||
|
||||
+1
-1
@@ -11,7 +11,7 @@ articles:
|
||||
datasets: datasets.html
|
||||
resistance_predict: resistance_predict.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
last_built: 2022-11-28T18:44Z
|
||||
last_built: 2022-11-29T18:41Z
|
||||
urls:
|
||||
reference: https://msberends.github.io/AMR/reference
|
||||
article: https://msberends.github.io/AMR/articles
|
||||
|
||||
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|
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|
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|
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|
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|
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+10
-10
@@ -195,16 +195,16 @@
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> birth_date age age_exact age_at_y2k</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1945-01-28 77 77.83288 54</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1998-08-27 24 24.25479 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1937-06-29 85 85.41644 62</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1946-11-17 76 76.03014 53</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1963-03-27 59 59.67397 36</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1952-04-02 70 70.65753 47</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1948-07-15 74 74.37260 51</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1933-10-22 89 89.10137 66</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1949-08-07 73 73.30959 50</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1959-08-15 63 63.28767 40</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1944-12-30 77 77.91507 55</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1946-04-06 76 76.64932 53</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1933-09-07 89 89.22740 66</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1992-05-18 30 30.53425 7</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1970-02-25 52 52.75890 29</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1944-11-05 78 78.06575 55</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1950-02-10 72 72.80000 49</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1995-05-07 27 27.56438 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1998-09-17 24 24.20000 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1969-01-26 53 53.84110 30</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
+10
-10
@@ -506,16 +506,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 50 × 12</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> datetime index ab_input ab_gu…¹ mo_in…² mo_guideline guide…³</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2022-11-28 <span style="color: #949494;">18:44:52</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2022-11-28 <span style="color: #949494;">18:44:52</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2022-11-28 <span style="color: #949494;">18:44:53</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2022-11-28 <span style="color: #949494;">18:44:53</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2022-11-28 <span style="color: #949494;">18:44:53</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2022-11-28 <span style="color: #949494;">18:44:54</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2022-11-28 <span style="color: #949494;">18:44:55</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2022-11-28 <span style="color: #949494;">18:44:55</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2022-11-28 <span style="color: #949494;">18:44:55</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2022-11-28 <span style="color: #949494;">18:44:55</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2022-11-29 <span style="color: #949494;">18:42:02</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2022-11-29 <span style="color: #949494;">18:42:03</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2022-11-29 <span style="color: #949494;">18:42:03</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2022-11-29 <span style="color: #949494;">18:42:03</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2022-11-29 <span style="color: #949494;">18:42:04</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2022-11-29 <span style="color: #949494;">18:42:05</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2022-11-29 <span style="color: #949494;">18:42:05</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2022-11-29 <span style="color: #949494;">18:42:05</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2022-11-29 <span style="color: #949494;">18:42:05</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2022-11-29 <span style="color: #949494;">18:42:05</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 40 more rows, 5 more variables: ref_table <chr>, method <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># input <dbl>, outcome <rsi>, breakpoint_S_R <chr>, and abbreviated variable</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># names ¹ab_guideline, ²mo_input, ³guideline</span></span>
|
||||
|
||||
+69
-74
@@ -182,45 +182,40 @@
|
||||
<span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">200</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 3 60 40 53 59 20 23 5 19 39 19 12 16 54 9 20 31 7 12 2 46 44 4 44 56</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [26] 15 58 25 39 43 9 12 35 8 18 37 58 5 46 4 17 47 10 26 11 7 34 31 11 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [51] 23 49 8 46 26 55 25 54 26 55 28 29 35 27 38 36 3 54 41 60 13 48 52 59 24</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [76] 6 6 14 15 15 1 26 19 10 62 51 10 24 16 49 22 2 25 58 12 48 19 59 34 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [101] 59 51 49 61 36 53 52 23 38 10 57 49 51 58 58 45 50 59 30 52 6 51 20 1 3</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [126] 33 38 6 14 45 42 16 54 47 4 50 22 37 59 28 40 9 43 19 61 17 51 32 54 24</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [151] 59 23 42 50 12 43 44 59 8 60 10 12 7 43 3 11 30 3 39 56 8 28 5 3 47</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [176] 54 3 16 16 9 5 43 33 58 61 21 12 10 23 59 43 29 56 59 26 10 29 15 12 32</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 53 62 32 61 13 24 5 35 42 38 15 9 6 4 24 17 13 61 29 35 46 18 27 5 29</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [26] 15 43 28 19 12 13 32 59 8 32 6 20 2 5 23 21 32 43 45 32 56 37 48 38 29</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [51] 13 18 53 7 48 52 24 7 36 52 60 6 32 29 31 5 21 12 58 15 44 31 25 8 41</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [76] 29 8 44 32 56 11 44 9 32 39 31 13 60 30 33 17 49 10 47 8 19 19 11 7 46</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [101] 31 15 47 3 25 30 61 36 1 22 55 23 20 60 60 44 63 36 46 58 58 26 51 12 41</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [126] 13 11 7 2 63 12 23 18 45 26 51 46 54 32 21 11 1 59 9 53 59 62 59 47 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [151] 54 10 15 56 39 36 50 38 40 57 42 22 31 34 14 49 34 4 26 29 63 59 62 31 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [176] 4 63 33 28 40 40 3 32 4 58 13 11 16 5 58 29 1 46 38 61 59 7 51 34 27</span>
|
||||
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] TRUE TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE TRUE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] TRUE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [109] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [121] FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [133] FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [145] TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [157] TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [169] FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [181] FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [193] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [109] TRUE FALSE TRUE TRUE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [121] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [133] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [145] TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [157] TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE TRUE TRUE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [169] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [181] TRUE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [193] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 7 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-07-30 218912 76 F ICU B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-09-08 B8CB09 60 F Outpatie… B_STPHY_CONS S NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">#></span> <span style="color: #BCBCBC;">4</span> 2002-07-23 F35553 51 M ICU B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> 2002-07-15 426426 67 F ICU B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">6</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">#></span> <span style="color: #BCBCBC;">7</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">#></span> <span style="color: #949494;"># A tibble: 2 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-06-22 FD8039 75 F ICU B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-06-18 012595 30 M ICU B_CRYNB I NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 36 more variables: AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>,</span></span>
|
||||
@@ -256,16 +251,16 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: condition [3]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient date condition new_episode</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 218912 2002-07-30 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> C72224 2017-08-09 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 207804 2012-10-04 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 329C35 2016-04-03 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 647993 2017-05-16 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> E19253 2006-08-22 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> F37316 2007-07-07 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 151041 2003-01-31 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> C34072 2006-07-05 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> C2846C 2012-06-29 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> F76601 2015-09-20 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> D20588 2017-08-17 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 48BB05 2010-03-15 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 871020 2017-07-20 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 554965 2005-08-29 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 451990 2008-03-22 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> E44854 2003-03-22 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> D91230 2010-12-06 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 743093 2012-09-14 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> BC9909 2011-07-08 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 190 more rows</span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
@@ -277,19 +272,19 @@
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 200 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [184]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward date patient new_index new_logical</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> ICU 2002-07-30 218912 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical 2017-08-09 C72224 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical 2012-10-04 207804 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical 2016-04-03 329C35 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2017-05-16 647993 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Clinical 2006-08-22 E19253 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> ICU 2007-07-07 F37316 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Clinical 2003-01-31 151041 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Clinical 2006-07-05 C34072 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> ICU 2012-06-29 C2846C 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [182]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward date patient new_index new_logical</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> ICU 2015-09-20 F76601 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> ICU 2017-08-17 D20588 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical 2010-03-15 48BB05 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical 2017-07-20 871020 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2005-08-29 554965 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Clinical 2008-03-22 451990 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> ICU 2003-03-22 E44854 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Clinical 2010-12-06 D91230 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Outpatient 2012-09-14 743093 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Clinical 2011-07-08 BC9909 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 190 more rows</span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
@@ -304,9 +299,9 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 112 14 54 72</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 62 14 34 43</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 10 6 9 10</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 112 15 51 70</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 61 13 37 43</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 9 6 9 9</span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
|
||||
@@ -336,19 +331,19 @@
|
||||
<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="op">}</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 200 × 4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, mo, ward [189]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient mo ward flag_episode</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 218912 B_ESCHR_COLI ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> C72224 B_STRPT_AGLC Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 207804 B_STRPT_PNMN Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 329C35 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 647993 B_STPHY_AURS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> E19253 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> F37316 B_STRPT_PNMN ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 151041 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> C34072 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> C2846C B_ESCHR_COLI ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, mo, ward [188]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient mo ward flag_episode</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> F76601 B_ESCHR_COLI ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> D20588 B_STPHY_HMNS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 48BB05 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 871020 B_STPHY_EPDR Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 554965 B_STPHY_AURS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 451990 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> E44854 B_STRPT_PNMN ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> D91230 B_STPHY_EPDR Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 743093 B_ENTRBC_CLOC Outpatient TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> BC9909 B_ENTRBC_CLOC Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 190 more rows</span></span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
|
||||
@@ -172,9 +172,9 @@
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 2.94123</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 3.060168</span>
|
||||
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.05912825</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.01364338</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
@@ -200,10 +200,10 @@
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">x</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 64 1 8 0.025 0.002 0.005 0.0625 16 0.01 32 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.5 32 1 4 256 64 4 0.002 0.025 0.5 </span>
|
||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1.3091844 0.2558741 0.7825293 -0.6783995 -1.3180848 -1.0860180</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.4463328 0.9580810 -0.9104663 1.1336327</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.3241709 0.8396588 -0.1301993 0.2577439 1.4215736 1.0336304</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.2577439 -1.8693070 -1.1625023 -0.3241709</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">y</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
|
||||
@@ -213,38 +213,38 @@
|
||||
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">y</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 8 0.025 1 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B <=4 0.125 0.5 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C <=4 >=1 4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D <=4 0.125 1 >=8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E >=16 >=1 2 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F >=16 0.025 1 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G <=4 0.25 4 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H >=16 0.125 0.5 >=8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 8 0.5 0.5 >=8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J <=4 0.25 1 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 4 <=0.125 <=0.5 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.25 1 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C 32 0.25 1 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 2 <=0.125 <=0.5 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 8 <=0.125 8 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 32 0.25 2 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 8 0.5 1 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 2 >=1 8 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 32 <=0.125 4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 16 0.25 2 2</span>
|
||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> "id" and "tobr"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.55426393 -0.42949279 0.62941387 -0.05490015 0.49015830 -0.12782528</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.09926391 0.26899945 0.26246847 -0.38529402</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.51912782 -0.09831951 0.63538430 -1.20290099 -0.21181627 0.27774576</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.04628481 0.49245479 0.45927606 0.12101887</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 8 0.025 1 1 -0.55426393</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B <=4 0.125 0.5 4 -0.42949279</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J <=4 0.25 1 1 -0.38529402</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F >=16 0.025 1 2 -0.12782528</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G <=4 0.25 4 0.5 -0.09926391</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D <=4 0.125 1 >=8 -0.05490015</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 8 0.5 0.5 >=8 0.26246847</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H >=16 0.125 0.5 >=8 0.26899945</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E >=16 >=1 2 0.5 0.49015830</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C <=4 >=1 4 4 0.62941387</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D 2 <=0.125 <=0.5 1 -1.20290099</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A 4 <=0.125 <=0.5 4 -0.51912782</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E 8 <=0.125 8 1 -0.21181627</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.25 1 4 -0.09831951</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G 8 0.5 1 2 0.04628481</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J 16 0.25 2 2 0.12101887</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F 32 0.25 2 2 0.27774576</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I 32 <=0.125 4 4 0.45927606</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H 2 >=1 8 2 0.49245479</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C 32 0.25 1 8 0.63538430</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
@@ -256,17 +256,17 @@
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C <=4 >=1 4 4 0.62941387 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 E >=16 >=1 2 0.5 0.49015830 0.1392556</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 H >=16 0.125 0.5 >=8 0.26899945 0.3604144</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 I 8 0.5 0.5 >=8 0.26246847 0.3669454</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 D <=4 0.125 1 >=8 -0.05490015 0.6843140</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 G <=4 0.25 4 0.5 -0.09926391 0.7286778</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 F >=16 0.025 1 2 -0.12782528 0.7572391</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 J <=4 0.25 1 1 -0.38529402 1.0147079</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 B <=4 0.125 0.5 4 -0.42949279 1.0589067</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 A 8 0.025 1 1 -0.55426393 1.1836778</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C 32 0.25 1 8 0.63538430 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 H 2 >=1 8 2 0.49245479 0.1429295</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 I 32 <=0.125 4 4 0.45927606 0.1761082</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 F 32 0.25 2 2 0.27774576 0.3576385</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 J 16 0.25 2 2 0.12101887 0.5143654</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 G 8 0.5 1 2 0.04628481 0.5890995</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 B 4 0.25 1 4 -0.09831951 0.7337038</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 E 8 <=0.125 8 1 -0.21181627 0.8472006</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 A 4 <=0.125 <=0.5 4 -0.51912782 1.1545121</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 D 2 <=0.125 <=0.5 1 -1.20290099 1.8382853</span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
|
||||
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+16
-16
@@ -183,42 +183,42 @@
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 2 64 0.25 2 1 2 0.125 4 0.25 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 1 0.025 <=0.002 0.25 64 0.0625 0.005 0.01 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] 8 1 2 0.025 <=0.002 >=256 0.25 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 32 4 0.001 8 2 0.025 4 128 128 0.5 0.025 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] 0.025 16 64 1 64 8 0.125 128 0.25 >=256 2 0.025</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] 16 </span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 30 26 41 36 23 42 33 16 10 41 21 24 39 49 34 47 32 44 20 33 41 48 15 9 6</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 29 13 31 34 33 32 7 8 18 32 46 16 14 41 10 26 10 45 41 39 40 13 18 13 35</span>
|
||||
<span class="r-in"><span><span class="fu">random_rsi</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'rsi'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S S S I S I R I S I R I I R R I S S I S I I I I S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S I R S I R S R I R S R S I I I I I R R R R S I I</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.125 0.25 0.025 16 0.005 0.125 0.5 0.0625 4 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] 16 1 2 1 0.01 0.005 0.125 0.002 0.01 0.25 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] 0.5 0.002 0.0625 >=32 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 32 128 0.025 0.125 1 64 0.5 16 0.025 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 0.25 0.25 0.25 0.25 0.0625 <=0.001 0.005 0.25 0.0625 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] 0.0625 0.025 <=0.001 16 2 32 0.0625 </span>
|
||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 2 2 1 >=16 2 >=16 2 4 8 2 2 8 2 2 1 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [16] >=16 >=16 4 2 2 1 2 4 >=16 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.5 1 8 2 2 16 8 8 16 0.5 4 8 4 8 0.5 2 16 0.5 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [20] 8 0.5 16 2 8 0.5</span>
|
||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.25 0.5 8 0.0625 1 0.5 <=0.025 0.125 <=0.025</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 4 0.0625 0.25 0.0625 <=0.025 0.25 0.0625 1 0.125 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] 2 <=0.025 2 0.25 8 1 0.125 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.125 0.0625 0.125 0.25 2 0.25 0.0625 2 0.125 0.125 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] 0.125 >=4 >=4 0.5 0.125 >=4 0.25 0.125 1 0.5 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] 0.0625 1 >=4 0.0625 >=4 </span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 16 50 45 44 44 18 37 24 21 47 26 16 15 43 43 15 40 35 30 15 21 41 8 29 15</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 17 36 40 30 8 48 50 21 28 8 12 20 34 17 20 47 46 49 25 20 47 42 36 25 47</span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 15 11 14 15 11 16 16 14 17 13 14 11 16 12 14 12 17 12 15 11 14 11 14 13 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 12 14 14 13 14 14 17 14 14 14 12 17 13 11 14 11 13 11 14 13 11 12 16 14 14</span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 21 16 18 21 25 26 19 21 26 17 18 15 24 15 18 20 17 24 17 19 26 18 17 16 15</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 23 23 16 26 18 20 22 15 18 19 27 15 16 21 21 21 25 23 22 18 17 17 25 18 16</span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
@@ -171,7 +171,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.01809232</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.0009022991</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
+1
-1
@@ -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
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[{"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
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