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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
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@@ -162,7 +162,7 @@
<img src="../logo.svg" class="logo" alt=""><h1>How to conduct AMR data analysis</h1>
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
<h4 data-toc-skip class="date">29 August 2022</h4>
<h4 data-toc-skip class="date">30 August 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="d-none name"><code>AMR.Rmd</code></div>
@@ -170,7 +170,7 @@
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 29 August 2022.</p>
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 30 August 2022.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@@ -201,21 +201,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-08-29</td>
<td align="center">2022-08-30</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2022-08-29</td>
<td align="center">2022-08-30</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2022-08-29</td>
<td align="center">2022-08-30</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@@ -325,69 +325,69 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-07-19</td>
<td align="center">D10</td>
<td align="center">2012-12-24</td>
<td align="center">A3</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-10-11</td>
<td align="center">S9</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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">2016-10-24</td>
<td align="center">H3</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2013-03-15</td>
<td align="center">D4</td>
<td align="center">Hospital D</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">2015-08-08</td>
<td align="center">N3</td>
<td align="center">Hospital B</td>
<td align="center">2013-10-26</td>
<td align="center">Q7</td>
<td align="center">Hospital C</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">2015-05-24</td>
<td align="center">O2</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-06-30</td>
<td align="center">Y9</td>
<td align="center">Hospital C</td>
<td align="center">2014-03-21</td>
<td align="center">Y1</td>
<td align="center">Hospital A</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">F</td>
</tr>
<tr class="odd">
<td align="center">2016-02-25</td>
<td align="center">V4</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">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-07-02</td>
<td align="center">N6</td>
<td align="center">Hospital B</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">F</td>
</tr>
</tbody>
@@ -422,16 +422,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,459</td>
<td align="right">52.30%</td>
<td align="right">10,459</td>
<td align="right">52.30%</td>
<td align="right">10,470</td>
<td align="right">52.35%</td>
<td align="right">10,470</td>
<td align="right">52.35%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,541</td>
<td align="right">47.71%</td>
<td align="right">9,530</td>
<td align="right">47.65%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@@ -488,7 +488,7 @@ Longest: 1</p>
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,686 'phenotype-based' first isolates (53.4% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,675 'phenotype-based' first isolates (53.4% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.4% 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">
@@ -499,7 +499,7 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<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 10,686 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,675 isolates for analysis. Now our data looks like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
<table style="width:100%;" class="table">
@@ -537,15 +537,79 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2016-07-19</td>
<td align="center">D10</td>
<td align="left">4</td>
<td align="center">2014-03-21</td>
<td align="center">Y1</td>
<td align="center">Hospital A</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="left">5</td>
<td align="center">2016-02-25</td>
<td align="center">V4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">6</td>
<td align="center">2014-07-02</td>
<td align="center">N6</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2011-11-29</td>
<td align="center">Q4</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="left">14</td>
<td align="center">2013-03-07</td>
<td align="center">A2</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
@@ -553,85 +617,21 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2016-10-24</td>
<td align="center">H3</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">2013-03-15</td>
<td align="center">D4</td>
<td align="left">15</td>
<td align="center">2010-02-05</td>
<td align="center">X6</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">B_KLBSL_PNMN</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">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">4</td>
<td align="center">2015-08-08</td>
<td align="center">N3</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">2013-06-30</td>
<td align="center">Y9</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2017-03-07</td>
<td align="center">Q1</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>
</tbody>
</table>
<p>Time for the analysis!</p>
@@ -653,8 +653,8 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,686<br>
Available: 10,686 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,675<br>
Available: 10,675 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@@ -671,33 +671,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,720</td>
<td align="right">44.17%</td>
<td align="right">4,720</td>
<td align="right">44.17%</td>
<td align="right">4,591</td>
<td align="right">43.01%</td>
<td align="right">4,591</td>
<td align="right">43.01%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,738</td>
<td align="right">25.62%</td>
<td align="right">7,458</td>
<td align="right">69.79%</td>
<td align="right">25.65%</td>
<td align="right">7,329</td>
<td align="right">68.66%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,049</td>
<td align="right">19.17%</td>
<td align="right">9,507</td>
<td align="right">88.97%</td>
<td align="right">2,156</td>
<td align="right">20.20%</td>
<td align="right">9,485</td>
<td align="right">88.85%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,179</td>
<td align="right">11.03%</td>
<td align="right">10,686</td>
<td align="right">1,190</td>
<td align="right">11.15%</td>
<td align="right">10,675</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@@ -744,23 +744,53 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-03-15</td>
<td align="center">D4</td>
<td align="center">Hospital D</td>
<td align="center">2014-03-21</td>
<td align="center">Y1</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">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">2010-01-01</td>
<td align="center">M2</td>
<td align="center">2016-02-25</td>
<td align="center">V4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">2011-06-30</td>
<td align="center">I1</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-06-02</td>
<td align="center">D10</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
@@ -774,60 +804,30 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-02-16</td>
<td align="center">B7</td>
<td align="center">Hospital C</td>
<td align="center">2012-11-07</td>
<td align="center">W10</td>
<td align="center">Hospital A</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">2015-06-01</td>
<td align="center">D1</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-05-09</td>
<td align="center">D6</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-02-23</td>
<td align="center">I2</td>
<td align="center">Hospital A</td>
<td align="center">2017-09-12</td>
<td align="center">O7</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
@@ -854,50 +854,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2211</td>
<td align="center">120</td>
<td align="center">2389</td>
<td align="center">4720</td>
<td align="center">2171</td>
<td align="center">122</td>
<td align="center">2298</td>
<td align="center">4591</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3448</td>
<td align="center">174</td>
<td align="center">1098</td>
<td align="center">4720</td>
<td align="center">3395</td>
<td align="center">143</td>
<td align="center">1053</td>
<td align="center">4591</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3483</td>
<td align="center">3378</td>
<td align="center">0</td>
<td align="center">1237</td>
<td align="center">4720</td>
<td align="center">1213</td>
<td align="center">4591</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4124</td>
<td align="center">4022</td>
<td align="center">0</td>
<td align="center">596</td>
<td align="center">4720</td>
<td align="center">569</td>
<td align="center">4591</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">1179</td>
<td align="center">1179</td>
<td align="center">1190</td>
<td align="center">1190</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">946</td>
<td align="center">31</td>
<td align="center">202</td>
<td align="center">1179</td>
<td align="center">931</td>
<td align="center">47</td>
<td align="center">212</td>
<td align="center">1190</td>
</tr>
</tbody>
</table>
@@ -920,25 +920,25 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4124</td>
<td align="center">4022</td>
<td align="center">0</td>
<td align="center">596</td>
<td align="center">4720</td>
<td align="center">569</td>
<td align="center">4591</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1076</td>
<td align="center">1066</td>
<td align="center">0</td>
<td align="center">103</td>
<td align="center">1179</td>
<td align="center">124</td>
<td align="center">1190</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2428</td>
<td align="center">2420</td>
<td align="center">0</td>
<td align="center">310</td>
<td align="center">318</td>
<td align="center">2738</td>
</tr>
<tr class="even">
@@ -946,8 +946,8 @@ Longest: 24</p>
<td align="center">GEN</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">2049</td>
<td align="center">2049</td>
<td align="center">2156</td>
<td align="center">2156</td>
</tr>
</tbody>
</table>
@@ -961,7 +961,7 @@ Longest: 24</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5416433</span></span></code></pre></div>
<span><span class="co"># [1] 0.5525995</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@@ -975,19 +975,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5344992</td>
<td align="center">0.5429191</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5487072</td>
<td align="center">0.5560949</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5348558</td>
<td align="center">0.5516169</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5449219</td>
<td align="center">0.5619137</td>
</tr>
</tbody>
</table>
@@ -1008,23 +1008,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5344992</td>
<td align="center">3145</td>
<td align="center">0.5429191</td>
<td align="center">3227</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5487072</td>
<td align="center">3829</td>
<td align="center">0.5560949</td>
<td align="center">3708</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5348558</td>
<td align="center">1664</td>
<td align="center">0.5516169</td>
<td align="center">1608</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5449219</td>
<td align="center">2048</td>
<td align="center">0.5619137</td>
<td align="center">2132</td>
</tr>
</tbody>
</table>
@@ -1047,27 +1047,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7673729</td>
<td align="center">0.8737288</td>
<td align="center">0.9779661</td>
<td align="center">0.7706382</td>
<td align="center">0.8760619</td>
<td align="center">0.9797430</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8286684</td>
<td align="center">0.9126378</td>
<td align="center">0.9838846</td>
<td align="center">0.8218487</td>
<td align="center">0.8957983</td>
<td align="center">0.9840336</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8027757</td>
<td align="center">0.8867787</td>
<td align="center">0.9788167</td>
<td align="center">0.7797663</td>
<td align="center">0.8838568</td>
<td align="center">0.9762600</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5451440</td>
<td align="center">0.5245826</td>
<td align="center">0.0000000</td>
<td align="center">0.5451440</td>
<td align="center">0.5245826</td>
</tr>
</tbody>
</table>
@@ -1092,23 +1092,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">53.4%</td>
<td align="right">25.3%</td>
<td align="right">54.3%</td>
<td align="right">27.1%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.9%</td>
<td align="right">26.0%</td>
<td align="right">55.6%</td>
<td align="right">26.6%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">53.5%</td>
<td align="right">25.7%</td>
<td align="right">55.2%</td>
<td align="right">27.8%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">54.5%</td>
<td align="right">27.0%</td>
<td align="right">56.2%</td>
<td align="right">27.5%</td>
</tr>
</tbody>
</table>
@@ -1206,18 +1206,16 @@ Longest: 24</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class &lt;mic&gt;</span></span>
<span><span class="co"># [1] &lt;=0.001 64 2 0.25 64 8 32 0.125 2 </span></span>
<span><span class="co"># [10] 1 8 0.01 0.0625 8 &gt;=256 64 4 4 </span></span>
<span><span class="co"># [19] 32 128 16 0.0625 0.0625 2 16 64 128 </span></span>
<span><span class="co"># [28] 0.0625 &lt;=0.001 0.002 128 0.0625 128 64 16 0.002 </span></span>
<span><span class="co"># [37] 0.002 64 0.01 0.002 1 0.125 1 0.01 32 </span></span>
<span><span class="co"># [46] 0.002 0.0625 128 &gt;=256 2 16 0.5 0.005 0.125 </span></span>
<span><span class="co"># [55] 0.005 64 16 16 4 0.01 8 1 0.005 </span></span>
<span><span class="co"># [64] 4 0.002 32 64 0.125 &lt;=0.001 1 32 1 </span></span>
<span><span class="co"># [73] 8 0.005 &gt;=256 32 0.5 64 0.01 8 &gt;=256 </span></span>
<span><span class="co"># [82] &gt;=256 0.0625 32 64 0.01 &lt;=0.001 128 0.025 0.5 </span></span>
<span><span class="co"># [91] 1 128 16 32 128 &lt;=0.001 4 0.002 &lt;=0.001</span></span>
<span><span class="co"># [100] 2</span></span></code></pre></div>
<span><span class="co"># [1] 2 0.5 0.5 &gt;=256 0.5 1 0.002 0.025 64 0.25 </span></span>
<span><span class="co"># [11] 0.5 0.0625 0.002 0.025 16 32 8 32 0.125 4 </span></span>
<span><span class="co"># [21] 64 0.002 0.5 &gt;=256 0.001 0.001 0.01 8 0.002 128 </span></span>
<span><span class="co"># [31] 16 0.0625 0.125 0.01 2 0.25 128 2 16 0.01 </span></span>
<span><span class="co"># [41] 4 0.002 16 1 2 0.005 32 0.0625 &gt;=256 4 </span></span>
<span><span class="co"># [51] 0.01 0.01 128 0.5 0.01 0.25 0.25 0.005 2 8 </span></span>
<span><span class="co"># [61] 0.025 64 0.002 1 4 0.01 1 1 16 0.5 </span></span>
<span><span class="co"># [71] 0.005 32 &gt;=256 0.25 0.0625 16 0.125 1 0.125 128 </span></span>
<span><span class="co"># [81] 0.005 0.125 0.001 0.25 1 0.01 32 32 2 64 </span></span>
<span><span class="co"># [91] &gt;=256 0.25 0.025 4 32 16 0.0625 4 0.002 0.002</span></span></code></pre></div>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@@ -1246,10 +1244,10 @@ Longest: 24</p>
<span><span class="co"># coli). Run `mo_uncertainties()` to review this.</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class &lt;disk&gt;</span></span>
<span><span class="co"># [1] 19 21 22 30 19 24 27 19 25 31 29 25 30 17 22 31 20 27 20 24 28 23 30 31 31</span></span>
<span><span class="co"># [26] 30 23 19 29 20 17 20 25 21 25 29 17 17 18 24 21 24 18 17 24 21 18 20 23 29</span></span>
<span><span class="co"># [51] 26 25 30 27 23 24 18 22 27 31 24 25 22 27 23 18 18 22 17 19 31 30 25 24 19</span></span>
<span><span class="co"># [76] 21 28 24 18 31 20 19 29 26 29 31 17 17 18 28 18 21 26 27 23 17 21 25 30 26</span></span></code></pre></div>
<span><span class="co"># [1] 23 31 24 27 29 20 24 22 27 17 21 28 25 18 29 24 28 17 24 19 22 30 29 17 27</span></span>
<span><span class="co"># [26] 18 20 29 23 23 20 24 20 24 24 18 31 31 29 17 27 19 25 21 18 26 29 18 17 30</span></span>
<span><span class="co"># [51] 27 26 31 18 26 31 30 18 25 25 27 18 30 19 19 25 30 28 19 26 30 21 20 24 22</span></span>
<span><span class="co"># [76] 25 31 17 18 23 27 23 29 24 27 28 25 29 30 27 24 27 28 25 23 27 24 22 27 18</span></span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>
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+1 -1
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@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
articles/MDR.html
+29 -29
View File
@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -314,19 +314,19 @@ Unique: 2</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 S R R I I I</span></span>
<span><span class="co"># 2 R R I I R R</span></span>
<span><span class="co"># 3 I R S I I S</span></span>
<span><span class="co"># 4 I R S I I R</span></span>
<span><span class="co"># 5 I I S R I I</span></span>
<span><span class="co"># 6 S R S S R S</span></span>
<span><span class="co"># 1 R S I R R R</span></span>
<span><span class="co"># 2 S R R R I S</span></span>
<span><span class="co"># 3 R S I S I S</span></span>
<span><span class="co"># 4 R S R R I S</span></span>
<span><span class="co"># 5 I I R I S I</span></span>
<span><span class="co"># 6 R S R S I R</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div>
<span><span class="co"># 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 use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></span></code></pre></div>
@@ -357,40 +357,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3226</td>
<td align="right">64.52%</td>
<td align="right">3226</td>
<td align="right">64.52%</td>
<td align="right">3167</td>
<td align="right">63.34%</td>
<td align="right">3167</td>
<td align="right">63.34%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">988</td>
<td align="right">19.76%</td>
<td align="right">4214</td>
<td align="right">84.28%</td>
<td align="right">994</td>
<td align="right">19.88%</td>
<td align="right">4161</td>
<td align="right">83.22%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">440</td>
<td align="right">8.80%</td>
<td align="right">4654</td>
<td align="right">93.08%</td>
<td align="right">487</td>
<td align="right">9.74%</td>
<td align="right">4648</td>
<td align="right">92.96%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">238</td>
<td align="right">4.76%</td>
<td align="right">4892</td>
<td align="right">97.84%</td>
<td align="right">246</td>
<td align="right">4.92%</td>
<td align="right">4894</td>
<td align="right">97.88%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">108</td>
<td align="right">2.16%</td>
<td align="right">106</td>
<td align="right">2.12%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>
articles/PCA.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
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@@ -162,7 +162,7 @@
<img src="../logo.svg" class="logo" alt=""><h1>How to import data from SPSS / SAS / Stata</h1>
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
<h4 data-toc-skip class="date">29 August 2022</h4>
<h4 data-toc-skip class="date">30 August 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>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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articles/datasets.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
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@@ -161,7 +161,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">29 August 2022</h4>
<h4 data-toc-skip class="date">30 August 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
@@ -177,7 +177,7 @@
</h2>
<p>A data set with 70,764 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 August 2022 07:59:26 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p>It was last updated on 30 August 2022 20:17:48 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">original R Data Structure (RDS) file</a> (1.3 MB)<br>
@@ -403,7 +403,7 @@
<p>A data set with 14,338 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>prevalence</em>.</p>
<p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
<p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 August 2022 07:59:26 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p>It was last updated on 30 August 2022 20:17:48 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">original R Data Structure (RDS) file</a> (0.2 MB)<br>
@@ -473,7 +473,7 @@
</h2>
<p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 August 2022 07:59:26 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 30 August 2022 20:17:48 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">original R Data Structure (RDS) file</a> (36 kB)<br>
@@ -646,7 +646,7 @@
</h2>
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 August 2022 07:59:26 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 30 August 2022 20:17:48 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">original R Data Structure (RDS) file</a> (4 kB)<br>
@@ -778,7 +778,7 @@
</h2>
<p>A data set with 20,369 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 August 2022 07:59:26 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p>It was last updated on 30 August 2022 20:17:48 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">original R Data Structure (RDS) file</a> (49 kB)<br>
@@ -937,7 +937,7 @@
</h2>
<p>A data set with 134,956 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 August 2022 07:59:26 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p>It was last updated on 30 August 2022 20:17:48 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">original R Data Structure (RDS) file</a> (78 kB)<br>
@@ -1209,7 +1209,7 @@
</h2>
<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 August 2022 07:59:26 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p>It was last updated on 30 August 2022 20:17:48 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">original R Data Structure (RDS) file</a> (3 kB)<br>
@@ -1326,7 +1326,7 @@
</h2>
<p>A data set with 2,000 rows and 46 columns, containing the following column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>, <em>ward</em>, <em>mo</em>, <em>PEN</em>, <em>OXA</em>, <em>FLC</em>, <em>AMX</em>, <em>AMC</em>, <em>AMP</em>, <em>TZP</em>, <em>CZO</em>, <em>FEP</em>, <em>CXM</em>, <em>FOX</em>, <em>CTX</em>, <em>CAZ</em>, <em>CRO</em>, <em>GEN</em>, <em>TOB</em>, <em>AMK</em>, <em>KAN</em>, <em>TMP</em>, <em>SXT</em>, <em>NIT</em>, <em>FOS</em>, <em>LNZ</em>, <em>CIP</em>, <em>MFX</em>, <em>VAN</em>, <em>TEC</em>, <em>TCY</em>, <em>TGC</em>, <em>DOX</em>, <em>ERY</em>, <em>CLI</em>, <em>AZM</em>, <em>IPM</em>, <em>MEM</em>, <em>MTR</em>, <em>CHL</em>, <em>COL</em>, <em>MUP</em> and <em>RIF</em>.</p>
<p>This data set is in R available as <code>example_isolates</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 August 2022 07:59:26 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
<p>It was last updated on 30 August 2022 20:17:48 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
<div class="section level3">
<h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>
</h3>
@@ -1731,7 +1731,7 @@
</h2>
<p>A data set with 3,000 rows and 8 columns, containing the following column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>, <em>bacteria</em>, <em>AMX</em>, <em>AMC</em>, <em>CIP</em> and <em>GEN</em>.</p>
<p>This data set is in R available as <code>example_isolates_unclean</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 August 2022 07:59:26 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
<p>It was last updated on 30 August 2022 20:17:48 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
<div class="section level3">
<h3 id="source-8">Source<a class="anchor" aria-label="anchor" href="#source-8"></a>
</h3>
articles/index.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
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articles/welcome_to_AMR.html
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@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
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authors.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -153,7 +153,7 @@
</p>
</li>
<li>
<p><strong>Judith M Fonville</strong>. Contributor.
<p><strong>Judith M. Fonville</strong>. Contributor.
</p>
</li>
<li>
index.html
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
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news/index.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
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@@ -127,16 +127,17 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="1.8.1.9046" id="amr-1819046">AMR 1.8.1.9046<a class="anchor" aria-label="anchor" href="#amr-1819046"></a></h2>
<h2 class="pkg-version" data-toc-text="1.8.1.9047" id="amr-1819047">AMR 1.8.1.9047<a class="anchor" aria-label="anchor" href="#amr-1819047"></a></h2>
<div class="section level4">
<h4 id="new-1-8-1-9046">New<a class="anchor" aria-label="anchor" href="#new-1-8-1-9046"></a></h4>
<h4 id="new-1-8-1-9047">New<a class="anchor" aria-label="anchor" href="#new-1-8-1-9047"></a></h4>
<ul><li>EUCAST 2022 and CLSI 2022 guidelines have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.</li>
<li>Function to calculate the mean AMR distance: <code><a href="../reference/mean_amr_distance.html">mean_amr_distance()</a></code>. The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand.</li>
<li>Support for <code>data.frame</code>-enhancing R packages, more specifically: <code>data.table</code>, <code>tibble</code>, and <code>tsibble</code>. AMR package functions that have a data set as output (such as <code><a href="../reference/proportion.html">rsi_df()</a></code> and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code>), will now return the same data type as the input. Furthermore, all our data sets are now in <code>tibble</code> format.</li>
<li>Our data sets are now also continually exported to Apache Feather and Apache Parquet formats. You can find more info <a href="https://msberends.github.io/AMR/articles/datasets.html">in this article on our website</a>.</li>
<li>Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. We are very grateful for the valuable input by our colleagues from other countries. The <code>AMR</code> package is now available in 16 languages.</li>
</ul></div>
<div class="section level4">
<h4 id="changed-1-8-1-9046">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9046"></a></h4>
<h4 id="changed-1-8-1-9047">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9047"></a></h4>
<ul><li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</li>
<li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on <code>NA</code> values (e.g. <code>as.rsi(as.disk(NA), ...)</code>)</li>
<li>Removed <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> for MIC values, since MIC are not integer values and running <code><a href="https://rdrr.io/r/base/table.html" class="external-link">table()</a></code> on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on <code>factor</code>s work)</li>
@@ -159,7 +160,7 @@
<li>Fix for using <code><a href="../reference/ab_property.html">ab_atc()</a></code> on non-existing ATC codes</li>
</ul></div>
<div class="section level4">
<h4 id="other-1-8-1-9046">Other<a class="anchor" aria-label="anchor" href="#other-1-8-1-9046"></a></h4>
<h4 id="other-1-8-1-9047">Other<a class="anchor" aria-label="anchor" href="#other-1-8-1-9047"></a></h4>
<ul><li>New website to make use of the new Bootstrap 5 and pkgdown v2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions</li>
<li>Added Peter Dutey-Magni and Anton Mymrikov as contributors, to thank them for their valuable input</li>
<li>Set up Git Large File Storage (Git LFS) for the large SAS and SPSS file formats</li>
pkgdown.yml
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datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2022-08-29T08:02Z
last_built: 2022-08-30T20:19Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles
reference/AMR-deprecated.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
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reference/AMR.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
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reference/WHOCC.html
+1 -1
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/WHONET.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/ab_from_text.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/ab_property.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/age.html
+11 -11
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -190,16 +190,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1948-07-12 74 74.13151 51</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1948-04-22 74 74.35342 51</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1980-01-02 42 42.65479 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1976-12-28 45 45.66849 23</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1974-05-24 48 48.26575 25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1940-07-01 82 82.16164 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1967-07-22 55 55.10411 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1939-09-26 82 82.92329 60</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1942-07-20 80 80.10959 57</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1993-11-03 28 28.81918 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1948-08-18 74 74.03288 51</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1996-10-11 25 25.88493 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1968-11-21 53 53.77260 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1962-11-19 59 59.77808 37</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1961-12-24 60 60.68219 38</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1943-01-20 79 79.60822 56</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1934-03-25 88 88.43288 65</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1989-07-16 33 33.12329 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1988-11-22 33 33.76986 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1961-11-12 60 60.79726 38</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
reference/age_groups.html
+1 -1
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/antibiotic_class_selectors.html
+1 -1
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/antibiotics.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/as.ab.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/as.disk.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/as.mic.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/as.mo.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/as.rsi.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/atc_online.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/availability.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/bug_drug_combinations.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/catalogue_of_life.html
+2 -2
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -163,7 +163,7 @@ Function <code><a href="as.mo.html">as.mo()</a></code> to use the data for intel
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Get version info of included data set</span></span></span>
<span class="r-in"><span><span class="fu"><a href="catalogue_of_life_version.html">catalogue_of_life_version</a></span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Included in this AMR package (v1.8.1.9046) are:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Included in this AMR package (v1.8.1.9047) are:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Catalogue of Life: 2019 Annual Checklist</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Available at: http://www.catalogueoflife.org</span>
reference/catalogue_of_life_version.html
+1 -1
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/count.html
+1 -1
View File
@@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/custom_eucast_rules.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/dosage.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/eucast_rules.html
+1 -1
View File
@@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/example_isolates.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/example_isolates_unclean.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/first_isolate.html
+1 -1
View File
@@ -12,7 +12,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/g.test.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/get_episode.html
+67 -70
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9047</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -177,42 +177,39 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">200</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 31 3 57 44 3 12 59 6 2 52 18 35 56 59 21 41 52 6 51 45 16 4 7 51 56</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 20 50 9 59 41 5 5 27 7 8 43 44 16 57 1 60 33 23 7 40 63 18 59 32 39</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 42 31 7 6 60 2 48 58 41 40 12 59 55 24 40 17 60 37 16 9 47 56 51 17 9</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 15 26 14 40 38 14 9 59 59 15 6 11 18 36 18 55 60 3 40 59 12 53 36 43 44</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 34 21 10 31 44 33 39 12 44 55 11 34 46 20 9 33 52 30 29 59 3 26 21 36 40</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 43 36 58 9 52 17 61 6 48 22 28 8 41 52 27 45 46 63 19 58 46 44 27 13 9</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 25 22 54 23 36 50 5 14 39 56 57 26 60 36 30 62 16 44 49 4 5 8 34 47 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 27 16 52 52 49 26 23 59 29 29 31 62 12 30 62 10 28 57 15 37 26 20 31 50 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 53 18 52 33 48 33 11 63 36 51 38 25 17 19 32 18 28 9 65 43 38 17 51 1 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 12 35 40 22 10 37 48 49 53 41 19 30 7 54 19 28 25 20 25 14 57 1 47 49 29</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 34 66 27 18 10 28 54 51 52 6 34 26 4 35 64 29 32 25 14 35 28 22 27 33 55</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 44 45 12 46 13 59 53 46 60 13 41 53 42 10 30 64 18 25 59 3 65 32 44 15 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 58 2 44 23 21 42 26 41 14 17 16 64 25 50 8 11 63 37 30 28 27 52 53 4 25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 35 28 45 9 7 61 50 1 53 19 1 58 11 39 21 43 6 24 40 2 63 6 27 16 63</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 41 36 20 23 57 5 64 47 29 58 2 30 57 8 25 11 15 13 14 52 7 31 1 27 62</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 65 60 25 29 7 1 56 55 49 65 28 64 33 26 46 1 18 22 64 14 63 10 66 59 13</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] TRUE TRUE FALSE TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE TRUE TRUE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE TRUE FALSE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE FALSE TRUE FALSE FALSE TRUE TRUE TRUE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] TRUE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE FALSE TRUE TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE TRUE FALSE FALSE FALSE FALSE TRUE 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">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-11-16 762305 87 F Clinical B_BCTRD_FRGL R NA NA R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-10-14 FCC668 54 F ICU B_ACNTB R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-10-20 F35553 51 M ICU B_STPHY_AURS S NA S NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2002-11-21 450741 77 F ICU B_STPHY_EPDR R NA S NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-07-21 955940 82 F Clinical B_PSDMN_AERG R NA NA R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 36 more variables: AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;, CZO &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FEP &lt;rsi&gt;, CXM &lt;rsi&gt;, FOX &lt;rsi&gt;, CTX &lt;rsi&gt;, CAZ &lt;rsi&gt;, CRO &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># GEN &lt;rsi&gt;, TOB &lt;rsi&gt;, AMK &lt;rsi&gt;, KAN &lt;rsi&gt;, TMP &lt;rsi&gt;, SXT &lt;rsi&gt;,</span></span>
@@ -248,16 +245,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: condition [3]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 291882 2010-05-01 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 762305 2002-11-16 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 644292 2016-10-26 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> B86399 2013-08-13 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> FCC668 2002-10-14 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> F41D7B 2005-01-12 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> CD8C33 2017-02-25 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> A59636 2003-07-24 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> E52286 2002-05-16 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B6F683 2015-11-15 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 534091 2015-02-15 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 968584 2005-12-29 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 419568 2014-10-19 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 291882 2010-05-01 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> A97263 2013-11-23 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 192353 2010-04-05 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 189363 2004-06-22 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 422833 2017-03-21 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> C34429 2011-01-02 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> C11627 2014-09-11 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -269,19 +266,19 @@
<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">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [183]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2010-05-01 291882 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2002-11-16 762305 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ICU 2016-10-26 644292 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU 2013-08-13 B86399 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2002-10-14 FCC668 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU 2005-01-12 F41D7B 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2017-02-25 CD8C33 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2003-07-24 A59636 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2002-05-16 E52286 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Outpatient 2015-11-15 B6F683 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [182]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2015-02-15 534091 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2005-12-29 968584 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2014-10-19 419568 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2010-05-01 291882 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2013-11-23 A97263 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2010-04-05 192353 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2004-06-22 189363 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ICU 2017-03-21 422833 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU 2011-01-02 C34429 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2014-09-11 C11627 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -296,9 +293,9 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 102 13 47 71</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 65 13 40 48</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 16 8 14 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 124 14 54 72</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 48 13 33 39</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 10 7 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>
@@ -328,19 +325,19 @@
<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">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [193]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 291882 B_STPHY_EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 762305 B_BCTRD_FRGL Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 644292 B_STPHY_AURS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> B86399 B_LISTR_MNCY ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> FCC668 B_ACNTB ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> F41D7B B_STRPT_PNMN ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> CD8C33 B_STPHY_HMNS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> A59636 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> E52286 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B6F683 B_STPHY_HMNS Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [190]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 534091 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 968584 B_PSDMN_AERG Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 419568 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 291882 B_STPHY_EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> A97263 B_KLBSL_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 192353 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 189363 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 422833 B_STPHY_EPDR ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> C34429 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> C11627 B_STRPT_GRPC Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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<dd>Antibiotic Selectors</dd>
</dl><dl><dt>
<code><a href="mean_amr_distance.html">mean_amr_distance()</a></code> <code><a href="mean_amr_distance.html">distance_from_row()</a></code>
</dt>
<dd>Mean AMR Distance</dd>
</dl><dl><dt>
<code><a href="resistance_predict.html">resistance_predict()</a></code> <code><a href="resistance_predict.html">rsi_predict()</a></code> <code><a href="resistance_predict.html">plot(<i>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_predict()</a></code> <code><a href="resistance_predict.html">autoplot(<i>&lt;resistance_predict&gt;</i>)</a></code>
</dt>
<dd>Predict Antimicrobial Resistance</dd>
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<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">#&gt;</span> [1] 3.004254</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.958293</span>
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.07839509</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.007432764</span>
</code></pre></div>
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<img src="../logo.svg" class="logo" alt=""><h1>Mean AMR Distance</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/mean_amr_distance.R" class="external-link"><code>R/mean_amr_distance.R</code></a></small>
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<p>This function calculates a normalised mean for antimicrobial resistance between multiple observations.</p>
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for default</span></span>
<span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for mic</span></span>
<span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for disk</span></span>
<span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for rsi</span></span>
<span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for data.frame</span></span>
<span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">distance_from_row</span><span class="op">(</span><span class="va">mean_distance</span>, <span class="va">row</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dd><p>a vector of class <a href="as.rsi.html">rsi</a>, <a href="as.rsi.html">rsi</a> or <a href="as.rsi.html">rsi</a>, or a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing columns of any of these classes</p></dd>
<dt>...</dt>
<dd><p>variables to select (supports tidy selection such as <code>column1:column4</code> and <code><a href="https://tidyselect.r-lib.org/reference/language.html" class="external-link">where(is.mic)</a></code>), and can thus also be <a href="antibiotic_class_selectors.html">antibiotic selectors</a></p></dd>
<dt>combine_SI</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S and I must be merged into one, so the input only consists of S+I vs. R (susceptible vs. resistant), defaults to <code>TRUE</code></p></dd>
<dt>mean_distance</dt>
<dd><p>the outcome of <code>mean_amr_distance()</code></p></dd>
<dt>row</dt>
<dd><p>an index, such as a row number</p></dd>
</dl></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand. For common numeric data this distance is equal to <a href="https://en.wikipedia.org/wiki/Standard_score" class="external-link">Z scores</a> (the number of standard deviations from the mean).</p>
<p>MIC values (see <code><a href="as.mic.html">as.mic()</a></code>) are transformed with <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2()</a></code> first; their distance is calculated as <code>(log2(x) - mean(log2(x))) / sd(log2(x))</code>.</p>
<p>R/SI values (see <code><a href="as.rsi.html">as.rsi()</a></code>) are transformed using <code>"S"</code> = 1, <code>"I"</code> = 2, and <code>"R"</code> = 3. If <code>combine_SI</code> is <code>TRUE</code> (default), the <code>"I"</code> will be considered to be 1.</p>
<p>For data sets, the mean AMR distance will be calculated per variable, after which the mean of all columns will returned per row (using <code><a href="https://rdrr.io/r/base/colSums.html" class="external-link">rowMeans()</a></code>), see <em>Examples</em>.</p>
<p>Use <code>distance_from_row()</code> to subtract distances from the distance of one row, see <em>Examples</em>.</p>
</div>
<div class="section level2">
<h2 id="interpretation">Interpretation<a class="anchor" aria-label="anchor" href="#interpretation"></a></h2>
<p>Isolates with distances less than 0.01 difference from each other should be considered similar. Differences lower than 0.025 should be considered suspicious.</p>
</div>
<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="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5 4 &gt;=128 &lt;=0.002 0.25 32 0.25 0.025 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.005 </span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01781163 0.59141290 1.54741502 -1.50524970 -0.17338879 1.16501418</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.17338879 -0.80854285 0.59141290 -1.25249649</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
<span class="r-in"><span> amox <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">"amox"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> cipr <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">"cipr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> gent <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">"gent"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span><span 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">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 8 0.25 1 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 32 0.5 &lt;=0.5 &lt;=0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 8 0.0625 &lt;=0.5 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 16 1 1 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 16 0.125 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 8 1 1 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 32 0.0625 1 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 16 0.25 &lt;=0.5 &lt;=0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 4 0.25 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 0.0625 2 1</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "id" and "tobr"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.1021142 -0.0512292 -0.4408420 0.5640747 0.2717444 -0.0723823</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.3064119 -0.4761266 -0.0939276 -0.1098375</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "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">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 16 0.25 &lt;=0.5 &lt;=0.25 -0.4761266</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 8 0.0625 &lt;=0.5 8 -0.4408420</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 0.0625 2 1 -0.1098375</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 4 0.25 4 1 -0.0939276</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 8 1 1 0.5 -0.0723823</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 32 0.5 &lt;=0.5 &lt;=0.25 -0.0512292</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 8 0.25 1 8 0.1021142</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 16 0.125 4 1 0.2717444</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 32 0.0625 1 8 0.3064119</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 16 1 1 4 0.5640747</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">%&gt;%</a></span> </span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>amr_distance <span class="op">=</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">.</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> check_id_C <span class="op">=</span> <span class="fu">distance_from_row</span><span class="op">(</span><span class="va">amr_distance</span>, <span class="va">id</span> <span class="op">==</span> <span class="st">"C"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">check_id_C</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C 8 0.0625 &lt;=0.5 8 -0.4408420 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 H 16 0.25 &lt;=0.5 &lt;=0.25 -0.4761266 0.0352847</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 J 16 0.0625 2 1 -0.1098375 0.3310044</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 I 4 0.25 4 1 -0.0939276 0.3469144</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 F 8 1 1 0.5 -0.0723823 0.3684596</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 B 32 0.5 &lt;=0.5 &lt;=0.25 -0.0512292 0.3896127</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 A 8 0.25 1 8 0.1021142 0.5429562</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 E 16 0.125 4 1 0.2717444 0.7125863</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 G 32 0.0625 1 8 0.3064119 0.7472539</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 D 16 1 1 4 0.5640747 1.0049167</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">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Enterococcus"</span> <span class="op">&amp;</span> <span class="fu"><a href="mo_property.html">mo_species</a></span><span class="op">(</span><span class="op">)</span> <span class="op">!=</span> <span class="st">""</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="va">TCY</span>, <span class="fu"><a href="antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>d <span class="op">=</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">.</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.rsi</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">mo</span>, <span class="va">d</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for `mo_genus()`</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for `mo_species()`</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "IPM", "MEM" and "TCY"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 63 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: mo [4]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo TCY IPM MEM d</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> B_ENTRC_AVIM S S NA <span style="color: #BB0000;">NaN</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> B_ENTRC_AVIM S S NA <span style="color: #BB0000;">NaN</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B_ENTRC_CSSL NA S NA <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> B_ENTRC_FACM S S NA -<span style="color: #BB0000;">2.66</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> B_ENTRC_FACM S R R -<span style="color: #BB0000;">0.423</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B_ENTRC_FACM S R R -<span style="color: #BB0000;">0.423</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B_ENTRC_FACM NA R R 0.224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B_ENTRC_FACM NA R R 0.224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B_ENTRC_FACM NA R R 0.224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B_ENTRC_FACM NA R R 0.224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 53 more rows</span></span>
</code></pre></div>
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<p></p><p><code>AMR</code> (for R). Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><a target="_blank" href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
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@@ -178,42 +178,43 @@
<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">#&gt;</span> Class &lt;mic&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 16 &gt;=256 2 0.5 0.01 0.5 16 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &lt;=0.001 1 &lt;=0.001 &gt;=256 2 0.5 &gt;=256 0.002 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 128 &lt;=0.001 0.01 64 128 16 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 256 1 0.001 128 0.001 64 256 0.001 0.002 16 128 256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.001 64 8 0.025 2 0.002 128 64 128 0.001 0.01 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 0.025</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 44 7 48 45 20 42 10 37 32 44 27 23 36 11 29 11 21 32 38 19 34 18 10 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 6 22 25 8 47 50 15 46 23 33 41 11 48 17 36 28 15 6 11 44 34 19 9 48 29</span>
<span class="r-in"><span><span class="fu">random_rsi</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;rsi&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I S R S R I I S I S I R S R I S I R R I S I S I R</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I R R R R R I R I R S R S S S I S S S S I R I I S</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">#&gt;</span> Class &lt;mic&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.005 0.001 0.002 1 0.5 &gt;=128 0.01 0.002 0.5 0.005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 64 0.001 0.0625 0.125 1 0.0625 0.001 0.5 0.5 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.002 8 32 4 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.025 32 0.125 32 0.0625 0.25 0.125 0.002 0.125 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.0625 2 2 0.01 0.5 0.001 0.025 0.25 4 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.0625 0.002 32 8 &gt;=64 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &gt;=16 0.25 4 4 8 8 &gt;=16 0.5 2 0.25 2 1 &gt;=16 2 0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] 0.25 0.5 1 0.5 0.25 0.25 2 1 1 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 32 8 &lt;=1 16 8 4 32 32 8 &lt;=1 16 8 &lt;=1 4 8 &lt;=1 8 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [20] 16 2 4 8 32 16 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4 0.0625 4 1 16 8 4 1 1 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.5 2 1 2 1 4 0.5 1 2 0.0625</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.125 1 0.0625 16 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=0.0625 1 0.5 0.125 &lt;=0.0625 0.5 4 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] 4 0.25 2 2 &lt;=0.0625 0.25 0.125 &lt;=0.0625</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [17] 1 1 &gt;=8 2 0.125 4 &lt;=0.0625 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 1 </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">#&gt;</span> Class &lt;disk&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 14 20 12 27 44 48 50 12 30 17 17 41 35 27 46 44 39 9 46 40 14 47 32 23 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 27 46 48 46 45 11 8 45 45 13 31 50 41 43 24 16 32 41 42 42 42 46 41 26 26</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 15 12 16 16 16 12 12 16 12 14 14 11 17 13 13 17 12 16 15 15 13 11 14 16 17</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 12 15 14 15 17 12 14 15 11 11 16 15 16 17 13 16 11 17 14 15 16 15 12 16 17</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 23 15 25 24 25 27 22 23 18 24 17 18 19 25 25 15 23 15 25 19 25 26 23 26 23</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 27 16 15 19 18 15 24 26 25 18 22 17 20 26 19 18 23 26 16 24 19 22 21 20 20</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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@@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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@@ -166,7 +166,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<div class="section level2">
<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">#&gt;</span> [1] 0.0004346661</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.06936305</span>
</code></pre></div>
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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
[{"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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