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@ -36,7 +36,7 @@
<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
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@ -109,11 +109,6 @@
Get properties of an antibiotic
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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@ -82,11 +82,6 @@
Get properties of an antibiotic
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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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
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@ -111,11 +111,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="nav-item">
@ -167,7 +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">21 August 2022</h4>
<h4 data-toc-skip class="date">25 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>
@ -175,7 +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 21 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 25 August 2022.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -206,21 +201,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-08-21</td>
<td align="center">2022-08-25</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">2022-08-21</td>
<td align="center">2022-08-25</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">2022-08-21</td>
<td align="center">2022-08-25</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -317,71 +312,71 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-06-19</td>
<td align="center">N8</td>
<td align="center">2010-03-22</td>
<td align="center">I8</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-04-13</td>
<td align="center">G1</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">R</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2014-11-21</td>
<td align="center">D5</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-07-08</td>
<td align="center">U10</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-07-14</td>
<td align="center">N3</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-07-29</td>
<td align="center">J1</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2015-03-05</td>
<td align="center">A9</td>
<td align="center">Hospital C</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>
</tr>
<tr class="even">
<td align="center">2017-10-20</td>
<td align="center">P10</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-01-18</td>
<td align="center">T4</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2012-07-14</td>
<td align="center">M9</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-02-17</td>
<td align="center">H3</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -414,16 +409,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,328</td>
<td align="right">51.64%</td>
<td align="right">10,328</td>
<td align="right">51.64%</td>
<td align="right">10,334</td>
<td align="right">51.67%</td>
<td align="right">10,334</td>
<td align="right">51.67%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,672</td>
<td align="right">48.36%</td>
<td align="right">9,666</td>
<td align="right">48.33%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -477,9 +472,9 @@ Longest: 1</p>
<span><span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span></span>
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># =&gt; Found 10,619 'phenotype-based' first isolates (53.1% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,754 'phenotype-based' first isolates (53.8% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.1% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<p>So only 53.8% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
@ -487,10 +482,10 @@ Longest: 1</p>
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>So we end up with 10,619 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,754 isolates for analysis. Now our data looks like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
<table style="width:100%;" class="table">
<table class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -503,7 +498,7 @@ Longest: 1</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@ -525,74 +520,26 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">5</td>
<td align="center">2015-03-05</td>
<td align="center">A9</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="center">2017-10-20</td>
<td align="center">P10</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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="odd">
<td align="left">8</td>
<td align="center">2013-03-11</td>
<td align="center">S7</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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">9</td>
<td align="center">2012-06-14</td>
<td align="center">I1</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<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">10</td>
<td align="center">2010-11-23</td>
<td align="center">V10</td>
<td align="left">2</td>
<td align="center">2012-04-13</td>
<td align="center">G1</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">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="even">
<td align="left">4</td>
<td align="center">2010-01-18</td>
<td align="center">T4</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
@ -604,17 +551,65 @@ Longest: 1</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">2010-02-17</td>
<td align="center">H3</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">13</td>
<td align="center">2012-03-06</td>
<td align="center">R5</td>
<td align="left">7</td>
<td align="center">2013-01-04</td>
<td align="center">C5</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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">10</td>
<td align="center">2014-12-10</td>
<td align="center">G7</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">11</td>
<td align="center">2015-10-09</td>
<td align="center">B3</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
@ -641,8 +636,8 @@ 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: 10,619<br>
Available: 10,619 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,754<br>
Available: 10,754 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -659,33 +654,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,632</td>
<td align="right">43.62%</td>
<td align="right">4,632</td>
<td align="right">43.62%</td>
<td align="right">4,654</td>
<td align="right">43.28%</td>
<td align="right">4,654</td>
<td align="right">43.28%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,742</td>
<td align="right">25.82%</td>
<td align="right">7,374</td>
<td align="right">69.44%</td>
<td align="right">2,782</td>
<td align="right">25.87%</td>
<td align="right">7,436</td>
<td align="right">69.15%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,062</td>
<td align="right">19.42%</td>
<td align="right">9,436</td>
<td align="right">88.86%</td>
<td align="right">2,109</td>
<td align="right">19.61%</td>
<td align="right">9,545</td>
<td align="right">88.76%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,183</td>
<td align="right">11.14%</td>
<td align="right">10,619</td>
<td align="right">1,209</td>
<td align="right">11.24%</td>
<td align="right">10,754</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -704,14 +699,14 @@ Longest: 24</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="10%">
<col width="11%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@ -732,9 +727,24 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-11-23</td>
<td align="center">V10</td>
<td align="center">2012-04-13</td>
<td align="center">G1</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">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="even">
<td align="center">2010-01-18</td>
<td align="center">T4</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
@ -746,24 +756,24 @@ Longest: 24</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-11-01</td>
<td align="center">B1</td>
<tr class="odd">
<td align="center">2014-06-06</td>
<td align="center">Y10</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-01-30</td>
<td align="center">H5</td>
<tr class="even">
<td align="center">2011-12-29</td>
<td align="center">J7</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
@ -776,43 +786,28 @@ Longest: 24</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-12-11</td>
<td align="center">I5</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<tr class="odd">
<td align="center">2010-05-28</td>
<td align="center">C3</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-08-04</td>
<td align="center">O3</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-10-06</td>
<td align="center">V8</td>
<td align="center">Hospital A</td>
<td align="center">2012-12-04</td>
<td align="center">V6</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">F</td>
@ -842,50 +837,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2203</td>
<td align="center">123</td>
<td align="center">2306</td>
<td align="center">4632</td>
<td align="center">2225</td>
<td align="center">122</td>
<td align="center">2307</td>
<td align="center">4654</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3385</td>
<td align="center">145</td>
<td align="center">1102</td>
<td align="center">4632</td>
<td align="center">3423</td>
<td align="center">151</td>
<td align="center">1080</td>
<td align="center">4654</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3390</td>
<td align="center">3411</td>
<td align="center">0</td>
<td align="center">1242</td>
<td align="center">4632</td>
<td align="center">1243</td>
<td align="center">4654</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4049</td>
<td align="center">4041</td>
<td align="center">0</td>
<td align="center">583</td>
<td align="center">4632</td>
<td align="center">613</td>
<td align="center">4654</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">1183</td>
<td align="center">1183</td>
<td align="center">1209</td>
<td align="center">1209</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">929</td>
<td align="center">948</td>
<td align="center">54</td>
<td align="center">200</td>
<td align="center">1183</td>
<td align="center">207</td>
<td align="center">1209</td>
</tr>
</tbody>
</table>
@ -908,34 +903,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4049</td>
<td align="center">4041</td>
<td align="center">0</td>
<td align="center">583</td>
<td align="center">4632</td>
<td align="center">613</td>
<td align="center">4654</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1078</td>
<td align="center">1069</td>
<td align="center">0</td>
<td align="center">105</td>
<td align="center">1183</td>
<td align="center">140</td>
<td align="center">1209</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2430</td>
<td align="center">2474</td>
<td align="center">0</td>
<td align="center">312</td>
<td align="center">2742</td>
<td align="center">308</td>
<td align="center">2782</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">2062</td>
<td align="center">2062</td>
<td align="center">2109</td>
<td align="center">2109</td>
</tr>
</tbody>
</table>
@ -949,7 +944,7 @@ 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] 0.5432715</span></span></code></pre></div>
<span><span class="co"># [1] 0.5432397</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>
@ -963,19 +958,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5382868</td>
<td align="center">0.5458167</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5447543</td>
<td align="center">0.5334954</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5595602</td>
<td align="center">0.5404571</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5353630</td>
<td align="center">0.5580645</td>
</tr>
</tbody>
</table>
@ -994,23 +989,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5382868</td>
<td align="center">3082</td>
<td align="center">0.5458167</td>
<td align="center">3263</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5447543</td>
<td align="center">3765</td>
<td align="center">0.5334954</td>
<td align="center">3702</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5595602</td>
<td align="center">1637</td>
<td align="center">0.5404571</td>
<td align="center">1619</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5353630</td>
<td align="center">2135</td>
<td align="center">0.5580645</td>
<td align="center">2170</td>
</tr>
</tbody>
</table>
@ -1031,27 +1026,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7620898</td>
<td align="center">0.8741364</td>
<td align="center">0.9771157</td>
<td align="center">0.7679416</td>
<td align="center">0.8682853</td>
<td align="center">0.9735711</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8309383</td>
<td align="center">0.9112426</td>
<td align="center">0.9805579</td>
<td align="center">0.8287841</td>
<td align="center">0.8842018</td>
<td align="center">0.9809760</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7884756</td>
<td align="center">0.8862144</td>
<td align="center">0.9817651</td>
<td align="center">0.7890007</td>
<td align="center">0.8892883</td>
<td align="center">0.9780733</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5354025</td>
<td align="center">0.5372214</td>
<td align="center">0.0000000</td>
<td align="center">0.5354025</td>
<td align="center">0.5372214</td>
</tr>
</tbody>
</table>
@ -1076,23 +1071,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">53.8%</td>
<td align="right">26.2%</td>
<td align="right">54.6%</td>
<td align="right">26.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.5%</td>
<td align="right">27.0%</td>
<td align="right">53.3%</td>
<td align="right">25.9%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">56.0%</td>
<td align="right">27.9%</td>
<td align="right">54.0%</td>
<td align="right">25.6%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">53.5%</td>
<td align="right">26.1%</td>
<td align="right">55.8%</td>
<td align="right">27.5%</td>
</tr>
</tbody>
</table>
@ -1176,16 +1171,16 @@ 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] 256 16 0.002 0.025 8 0.025 32 0.025 0.01 256 </span></span>
<span><span class="co"># [11] 16 0.01 32 0.025 0.01 0.0625 2 0.25 128 0.005 </span></span>
<span><span class="co"># [21] 0.01 16 0.125 0.25 0.01 0.001 8 0.025 8 1 </span></span>
<span><span class="co"># [31] 0.025 0.25 0.0625 256 0.001 0.025 0.001 8 0.01 0.025 </span></span>
<span><span class="co"># [41] 0.25 8 64 8 0.25 4 1 0.0625 0.0625 0.5 </span></span>
<span><span class="co"># [51] 2 0.002 16 0.002 0.01 16 0.25 64 8 256 </span></span>
<span><span class="co"># [61] 0.005 0.0625 1 64 64 0.5 128 0.002 32 0.002 </span></span>
<span><span class="co"># [71] 128 128 0.5 0.002 0.25 0.5 0.125 1 16 64 </span></span>
<span><span class="co"># [81] 128 32 0.025 128 16 32 32 32 0.002 0.125 </span></span>
<span><span class="co"># [91] 0.5 0.0625 0.5 128 0.125 128 8 0.25 128 0.25</span></span></code></pre></div>
<span><span class="co"># [1] 2 0.01 128 2 128 0.001 0.025 0.5 2 0.025 </span></span>
<span><span class="co"># [11] 0.0625 0.125 256 0.125 4 256 4 4 0.0625 256 </span></span>
<span><span class="co"># [21] 0.125 2 64 16 0.5 0.5 0.0625 4 256 1 </span></span>
<span><span class="co"># [31] 0.005 0.125 0.002 4 32 0.01 0.01 0.002 0.25 0.125 </span></span>
<span><span class="co"># [41] 0.025 0.01 64 32 0.001 0.5 16 32 0.5 0.01 </span></span>
<span><span class="co"># [51] 0.001 4 0.001 16 8 0.001 4 0.25 64 0.002 </span></span>
<span><span class="co"># [61] 0.01 32 0.005 0.25 4 0.002 0.002 16 32 1 </span></span>
<span><span class="co"># [71] 0.0625 32 0.001 256 0.25 2 0.025 4 0.0625 16 </span></span>
<span><span class="co"># [81] 0.002 32 256 0.0625 0.125 0.001 128 0.001 0.01 64 </span></span>
<span><span class="co"># [91] 2 64 1 256 0.01 8 32 8 128 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>
@ -1214,10 +1209,10 @@ 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] 23 21 25 21 18 21 18 19 23 26 28 30 20 21 17 17 27 26 31 30 25 17 27 27 19</span></span>
<span><span class="co"># [26] 31 23 23 23 22 20 26 17 24 29 26 24 25 29 22 22 29 26 22 24 25 26 18 31 24</span></span>
<span><span class="co"># [51] 25 28 26 27 19 21 21 29 27 21 27 21 18 17 20 20 17 25 30 20 19 20 23 27 31</span></span>
<span><span class="co"># [76] 24 31 24 22 26 19 19 20 20 25 17 21 22 30 25 23 26 31 20 30 18 29 18 29 17</span></span></code></pre></div>
<span><span class="co"># [1] 25 31 18 30 19 28 18 31 17 30 31 30 20 20 25 18 30 28 18 22 25 28 17 21 22</span></span>
<span><span class="co"># [26] 22 29 30 28 29 19 21 21 30 21 28 22 19 27 26 31 21 22 31 31 29 28 31 27 28</span></span>
<span><span class="co"># [51] 28 30 24 27 21 23 26 23 22 19 25 21 30 25 26 29 31 18 18 21 26 23 19 18 24</span></span>
<span><span class="co"># [76] 20 30 28 22 31 21 28 28 24 23 21 24 17 28 18 29 28 31 21 23 24 19 17 29 17</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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7
articles/EUCAST.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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -111,11 +111,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="nav-item">

59
articles/MDR.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -111,11 +111,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="nav-item">
@ -313,19 +308,19 @@ 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 S R I R I</span></span>
<span><span class="co"># 2 I R S S S S</span></span>
<span><span class="co"># 3 I R S I S S</span></span>
<span><span class="co"># 4 R I S I S R</span></span>
<span><span class="co"># 5 I I S R S R</span></span>
<span><span class="co"># 6 S I S S R R</span></span>
<span><span class="co"># 1 R S I R I I</span></span>
<span><span class="co"># 2 S R R S R S</span></span>
<span><span class="co"># 3 R R S R S S</span></span>
<span><span class="co"># 4 I R S R I I</span></span>
<span><span class="co"># 5 S R S I S I</span></span>
<span><span class="co"># 6 R S R R S R</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div>
<span><span class="co"># 6 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></span></code></pre></div>
@ -356,40 +351,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3182</td>
<td align="right">63.64%</td>
<td align="right">3182</td>
<td align="right">63.64%</td>
<td align="right">3214</td>
<td align="right">64.28%</td>
<td align="right">3214</td>
<td align="right">64.28%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">993</td>
<td align="right">19.86%</td>
<td align="right">4175</td>
<td align="right">83.50%</td>
<td align="right">977</td>
<td align="right">19.54%</td>
<td align="right">4191</td>
<td align="right">83.82%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">477</td>
<td align="right">9.54%</td>
<td align="right">4652</td>
<td align="right">93.04%</td>
<td align="right">450</td>
<td align="right">9.00%</td>
<td align="right">4641</td>
<td align="right">92.82%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">250</td>
<td align="right">5.00%</td>
<td align="right">4902</td>
<td align="right">98.04%</td>
<td align="right">255</td>
<td align="right">5.10%</td>
<td align="right">4896</td>
<td align="right">97.92%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">98</td>
<td align="right">1.96%</td>
<td align="right">104</td>
<td align="right">2.08%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

7
articles/PCA.html
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@ -38,7 +38,7 @@
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@ -38,7 +38,7 @@
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@ -111,11 +111,6 @@
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@ -167,7 +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">21 August 2022</h4>
<h4 data-toc-skip class="date">25 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>

7
articles/WHONET.html
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@ -38,7 +38,7 @@
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@ -111,11 +111,6 @@
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articles/datasets.html
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@ -38,7 +38,7 @@
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@ -111,11 +111,6 @@
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</a>
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@ -166,7 +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">21 August 2022</h4>
<h4 data-toc-skip class="date">25 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>
@ -184,7 +179,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</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 21 August 2022 15:23:37 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 25 August 2022 17:23:20 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">R file</a> (1.3 MB)<br>
@ -405,7 +400,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<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 21 August 2022 15:23:37 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 25 August 2022 17:23:20 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">R file</a> (0.2 MB)<br>
@ -470,7 +465,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</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 21 August 2022 15:23:37 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 25 August 2022 17:23:20 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">R file</a> (33 kB)<br>
@ -638,7 +633,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</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 21 August 2022 15:23:37 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 25 August 2022 17:23:20 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">R file</a> (5 kB)<br>
@ -765,7 +760,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</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 21 August 2022 15:23:37 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 25 August 2022 17:23:20 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">R file</a> (49 kB)<br>
@ -919,7 +914,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</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 21 August 2022 15:23:37 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 25 August 2022 17:23:20 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">R file</a> (78 kB)<br>
@ -1186,7 +1181,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</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 21 August 2022 15:23:37 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 25 August 2022 17:23:20 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">R file</a> (3 kB)<br>

7
articles/index.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -38,7 +38,7 @@
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@ -38,7 +38,7 @@
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@ -10,7 +10,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
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@ -131,37 +126,6 @@
<small>Source: <a href="https://github.com/msberends/AMR/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="1.8.1.9021" id="amr-1819021">AMR 1.8.1.9021<a class="anchor" aria-label="anchor" href="#amr-1819021"></a></h2>
<div class="section level4">
<h4 id="new-1-8-1-9021">New<a class="anchor" aria-label="anchor" href="#new-1-8-1-9021"></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>Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. The <code>AMR</code> package is now available in 16 languages.</li>
</ul></div>
<div class="section level4">
<h4 id="changed-1-8-1-9021">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9021"></a></h4>
<ul><li>Fix for <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</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>
<li>
<code><a href="https://rdrr.io/r/base/droplevels.html" class="external-link">droplevels()</a></code> on MIC will now return a common <code>factor</code> at default and will lose the <code>&lt;mic&gt;</code> class. Use <code>droplevels(..., as.mic = TRUE)</code> to keep the <code>&lt;mic&gt;</code> class.</li>
<li>Small fix for using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>
</li>
<li>Fixes for reading in text files using <code><a href="../reference/mo_source.html">set_mo_source()</a></code>, which now also allows the source file to contain valid taxonomic names instead of only valid microorganism ID of this package</li>
<li>Using any <code>random_*()</code> function (such as <code><a href="../reference/random.html">random_mic()</a></code>) is now possible by directly calling the package without loading it first: <code>AMR::random_mic(10)</code>
</li>
<li>Added <em>Toxoplasma gondii</em> (<code>P_TXPL_GOND</code>) to the <code>microorganisms</code> data set, together with its genus, family, and order</li>
<li>Changed value in column <code>prevalence</code> of the <code>microorganisms</code> data set from 3 to 2 for these genera: <em>Acholeplasma</em>, <em>Alistipes</em>, <em>Alloprevotella</em>, <em>Bergeyella</em>, <em>Borrelia</em>, <em>Brachyspira</em>, <em>Butyricimonas</em>, <em>Cetobacterium</em>, <em>Chlamydia</em>, <em>Chlamydophila</em>, <em>Deinococcus</em>, <em>Dysgonomonas</em>, <em>Elizabethkingia</em>, <em>Empedobacter</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Myroides</em>, <em>Odoribacter</em>, <em>Ornithobacterium</em>, <em>Parabacteroides</em>, <em>Pedobacter</em>, <em>Phocaeicola</em>, <em>Porphyromonas</em>, <em>Riemerella</em>, <em>Sphingobacterium</em>, <em>Streptobacillus</em>, <em>Tenacibaculum</em>, <em>Terrimonas</em>, <em>Victivallis</em>, <em>Wautersiella</em>, <em>Weeksella</em>
</li>
<li>Fix for using the form <code>df[carbapenems() == "R", ]</code> using the latest <code>vctrs</code> package</li>
<li>Fix for using <code>info = FALSE</code> in <code><a href="../reference/mdro.html">mdro()</a></code>
</li>
</ul></div>
<div class="section level4">
<h4 id="other-1-8-1-9021">Other<a class="anchor" aria-label="anchor" href="#other-1-8-1-9021"></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>
</ul></div>
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="1.8.1" id="amr-181">
<code>AMR</code> 1.8.1<a class="anchor" aria-label="anchor" href="#amr-181"></a></h2><p class="text-muted">CRAN release: 2022-03-24</p>

2
pkgdown.yml
View File

@ -11,7 +11,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2022-08-21T15:26Z
last_built: 2022-08-25T17:26Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

7
reference/AMR-deprecated.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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

7
reference/AMR.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

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7
reference/WHOCC.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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

7
reference/WHONET.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

7
reference/ab_from_text.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

7
reference/ab_property.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="nav-item">

27
reference/age.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">
@ -195,16 +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 1955-03-05 67 67.46301 44</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1969-09-23 52 52.90959 30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1952-10-15 69 69.84932 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1940-09-07 81 81.95342 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1956-10-12 65 65.85753 43</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1997-03-26 25 25.40548 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1946-04-17 76 76.34521 53</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1987-04-28 35 35.31507 12</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1957-09-27 64 64.89863 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1949-07-17 73 73.09589 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1964-06-04 58 58.22466 35</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1982-09-15 39 39.94247 17</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1966-11-08 55 55.79452 33</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1971-11-11 50 50.78630 28</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1960-06-12 62 62.20274 39</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1992-06-01 30 30.23288 7</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1953-06-03 69 69.22740 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1977-05-25 45 45.25205 22</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1945-02-11 77 77.53425 54</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1972-07-19 50 50.10137 27</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

7
reference/age_groups.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

18
reference/antibiotic_class_selectors.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">
@ -315,7 +310,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'</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/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mo"</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span></span>
@ -335,7 +329,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B_STPHY_EPDR NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B_STPHY_EPDR NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># select only antibiotic columns with DDDs for oral treatment</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span>, <span class="fu">administrable_per_os</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
@ -356,7 +349,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> NA NA R R S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> NA NA S R S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter using any() or all()</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/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span></span>
@ -376,7 +368,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> A B_PROTS_MRBL NA S S S S S S R R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 45 more rows, 3 more variables: MEM &lt;rsi&gt;, TEC &lt;rsi&gt;, VAN &lt;rsi&gt;, and</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># abbreviated variable name ¹​hospital_id</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">df</span>, <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span></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-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 55 × 14</span></span>
@ -394,7 +385,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> A B_PROTS_MRBL NA S S S S S S R R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 45 more rows, 3 more variables: MEM &lt;rsi&gt;, TEC &lt;rsi&gt;, VAN &lt;rsi&gt;, and</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># abbreviated variable name ¹​hospital_id</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter on any or all results in the carbapenem columns (i.e., IPM, MEM):</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/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span>
@ -415,7 +405,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> C B_ESCHR_COLI R R NA R S S NA NA S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 952 more rows, 3 more variables: MEM &lt;rsi&gt;, TEC &lt;rsi&gt;, VAN &lt;rsi&gt;, and</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># abbreviated variable name ¹​hospital_id</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</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/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></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 Filtering all of columns 'IPM' and 'MEM' to contain value "R", "S" or "I"</span>
@ -434,7 +423,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B B_ESCHR_COLI NA S S S S S S NA S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 746 more rows, 3 more variables: MEM &lt;rsi&gt;, TEC &lt;rsi&gt;, VAN &lt;rsi&gt;, and</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># abbreviated variable name ¹​hospital_id</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter with multiple antibiotic selectors using c()</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/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span></span>
@ -456,7 +444,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> D B_STPHY_CONS R R R R R R R R R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 16 more rows, 3 more variables: MEM &lt;rsi&gt;, TEC &lt;rsi&gt;, VAN &lt;rsi&gt;, and</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># abbreviated variable name ¹​hospital_id</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter + select in one go: get penicillins in carbapenems-resistant strains</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/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="fu">penicillins</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
@ -477,7 +464,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> NA S S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> NA S S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 45 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># You can combine selectors with '&amp;' to be more specific. For example,</span></span></span>
<span class="r-in"><span><span class="co"># penicillins() would select benzylpenicillin ('peni G') and</span></span></span>
@ -504,7 +490,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># ab_selector() applies a filter in the `antibiotics` data set and is thus very</span></span></span>
<span class="r-in"><span><span class="co"># flexible. For instance, to select antibiotic columns with an oral DDD of at</span></span></span>
@ -526,7 +511,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> NA NA S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> NA NA S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># dplyr -------------------------------------------------------------------</span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>

7
reference/antibiotics.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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

8
reference/as.ab.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">
@ -290,7 +285,6 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>

7
reference/as.disk.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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

7
reference/as.mic.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

7
reference/as.mo.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

9
reference/as.rsi.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">
@ -340,7 +335,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span> <span class="co"># see all R/SI results at a glance</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date hospital_id ward_icu ward_clinical </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Min. :2002-01-02 A:321 Mode :logical Mode :logical </span>
@ -736,7 +730,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>

7
reference/atc_online.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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

7
reference/availability.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

7
reference/bug_drug_combinations.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

9
reference/catalogue_of_life.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">
@ -168,7 +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 (v1.8.1.9021) are:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Included in this AMR package (v1.8.1.9026) 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>

7
reference/catalogue_of_life_version.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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

7
reference/count.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -84,11 +84,6 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

7
reference/custom_eucast_rules.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

7
reference/dosage.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

7
reference/eucast_rules.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -84,11 +84,6 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

8
reference/example_isolates.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">
@ -180,7 +175,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;, TCY &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;, IPM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, RIF &lt;rsi&gt;, and …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `colnames()` to see all variable names</span></span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

7
reference/example_isolates_unclean.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

9
reference/first_isolate.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -84,11 +84,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">
@ -349,7 +344,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># get all first Gram-negatives</span></span></span>
<span class="r-in"><span><span class="va">example_isolates</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">first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu"><a href="mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span>
@ -374,7 +368,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># filter on first isolates using dplyr:</span></span></span>

7
reference/g.test.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

65
reference/get_episode.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">
@ -182,41 +177,40 @@
<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] 63 42 61 46 22 21 21 10 46 12 31 47 53 64 9 27 12 7 30 25 15 61 52 20 18</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 46 53 39 38 54 61 58 12 58 39 21 27 35 66 46 59 57 13 43 30 29 60 51 25 35</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 22 4 56 20 5 18 18 22 9 21 50 9 58 38 59 44 46 11 41 55 55 5 14 56 26</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 53 63 33 20 5 31 32 10 1 51 46 2 28 24 40 10 13 26 55 12 49 54 16 43 26</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 51 37 60 27 49 23 42 63 5 60 7 23 4 37 47 22 52 45 65 56 11 38 17 36 12</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 9 47 25 14 1 56 38 66 42 53 19 51 10 34 16 11 15 62 31 40 22 63 49 32 62</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 45 6 48 5 58 57 7 56 46 13 58 65 15 21 7 42 8 5 6 6 28 29 4 26 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 3 56 3 60 61 63 63 56 65 16 21 40 57 23 16 47 58 61 21 32 9 60 3 17 62</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 6 17 60 34 7 61 19 35 61 38 26 59 25 61 25 20 50 2 20 5 53 35 67 48 5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 11 17 20 59 66 54 26 60 44 48 20 12 23 37 4 5 36 21 28 59 20 44 11 60 49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 6 12 16 16 62 40 4 17 64 52 33 20 3 1 55 46 12 12 30 64 22 8 2 30 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 28 61 31 52 63 35 15 7 45 51 65 41 36 33 14 53 18 40 12 42 55 2 15 14 38</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 23 9 9 23 22 58 3 26 20 6 1 68 43 39 24 46 12 40 56 29 39 1 8 59 65</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 57 14 64 65 37 41 42 37 20 24 32 59 14 61 52 10 13 59 18 24 40 52 62 30 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 10 35 65 61 10 16 20 4 53 16 24 47 2 67 27 58 64 1 11 62 12 40 47 1 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 22 54 21 29 11 23 59 61 40 39 42 14 14 17 66 17 2 52 23 29 2 68 24 46 14</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] TRUE TRUE FALSE TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE TRUE FALSE TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] TRUE TRUE TRUE FALSE TRUE FALSE FALSE TRUE</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: 3 × 49</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 49</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date hospita…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo </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;fct&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-06-06 D FALSE TRUE FALSE 20 F 24D393 B_ESCHR_COLI</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-06-18 B TRUE FALSE FALSE 30 M 012595 B_CRYNB </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-07-23 B TRUE FALSE FALSE 51 M F35553 B_STPHY_AURS</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-06-04 B TRUE FALSE FALSE 78 M 082413 B_STRPT_PNMN</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-06-06 D FALSE TRUE FALSE 20 F 24D393 B_ESCHR_COLI</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more variables: PEN &lt;rsi&gt;, OXA &lt;rsi&gt;, FLC &lt;rsi&gt;, AMX &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;, CZO &lt;rsi&gt;, FEP &lt;rsi&gt;, CXM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOX &lt;rsi&gt;, CTX &lt;rsi&gt;, CAZ &lt;rsi&gt;, CRO &lt;rsi&gt;, GEN &lt;rsi&gt;, TOB &lt;rsi&gt;,</span></span>
@ -224,7 +218,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;, TCY &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;, IPM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, RIF &lt;rsi&gt;, and …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `colnames()` to see all variable names</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># the functions also work for less than a day, e.g. to include one per hour:</span></span></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span>,</span></span>

7
reference/ggplot_pca.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

7
reference/ggplot_rsi.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

7
reference/guess_ab_col.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

7
reference/index.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

7
reference/intrinsic_resistant.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
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7
reference/italicise_taxonomy.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
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7
reference/join.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
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7
reference/key_antimicrobials.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
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11
reference/kurtosis.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
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@ -172,9 +167,9 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.031812</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.056791</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] -0.03994734</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.006309202</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

10
reference/like.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">
@ -230,7 +225,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># faster way, since mo_name() is context-aware:</span></span></span>
<span class="r-in"><span><span class="va">example_isolates</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"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%like%</span> <span class="st">"^ent"</span><span class="op">)</span>, <span class="op">]</span></span></span>
@ -255,7 +249,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@ -282,7 +275,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>

7
reference/mdro.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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

7
reference/microorganisms.codes.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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
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<li class="active nav-item">

7
reference/microorganisms.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

7
reference/microorganisms.old.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

7
reference/mo_matching_score.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

8
reference/mo_property.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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="nav-item">
@ -470,7 +465,6 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># get a list with the complete taxonomy (from kingdom to subspecies)</span></span></span>

7
reference/mo_source.html
View File

@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -84,11 +84,6 @@ This is the fastest way to have your organisation (or analysis) specific codes p
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
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<li class="active nav-item">

7
reference/pca.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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

BIN
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7
reference/plot.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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

7
reference/proportion.html
View File

@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -84,11 +84,6 @@ resistance() should be used to calculate resistance, susceptibility() should be
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">

40
reference/random.html
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="">1.8.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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">
@ -82,11 +82,6 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div>
</li>
<li class="active nav-item">
@ -183,42 +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] 8 64 8 0.25 8 2 0.005 16 256 32 16 0.125</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.125 64 32 0.25 256 4 1 0.125 32 0.5 0.025 128 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=0.001 1 0.25 128 0.01 0.025 0.025 16 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 128 64 16 &lt;=0.001 0.01 0.0625 0.0625 0.5 0.0625 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.025 8 128 32 0.025 0.0625 0.01 </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] 27 41 44 30 6 49 34 45 48 31 48 31 31 41 49 46 14 24 31 12 45 24 44 36 38</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 30 11 11 41 49 41 47 7 44 29 15 18 25 6 30 49 24 38 15 23 15 17 43 45 6</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 I R S S R S S S I I R I R I I S R R R S I S I S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S I I S R R I I S R S I S R R R R I S I R I I S I</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.125 0.25 0.125 0.002 4 2 8 32 0.0625 0.002 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.125 0.005 1 0.002 0.001 16 0.025 0.25 0.5 128 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 2 0.005 128 4 0.002 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01 0.025 8 2 1 0.002 0.125 2 64 0.25 16 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.005 0.125 0.01 256 0.5 1 4 0.25 0.125 0.001 256 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 128 </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] &lt;=1 4 8 8 8 8 8 &gt;=16 2 2 4 2 &lt;=1 8 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] &lt;=1 &gt;=16 2 2 8 4 4 8 &lt;=1 &lt;=1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5 &gt;=64 2 4 8 0.5 &gt;=64 2 1 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] &gt;=64 16 8 &lt;=0.25 &lt;=0.25 4 &lt;=0.25 16 16 &lt;=0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 16 32 32 &lt;=0.25 &lt;=0.25</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] 0.125 0.25 2 0.5 0.0625 8 0.25 0.25 0.125 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 2 0.125 0.0625 4 0.5 0.125 2 8 4 0.0625</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.5 0.25 0.5 8 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.25 1 &gt;=8 &lt;=0.125 0.25 4 0.5 &gt;=8 &gt;=8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.25 0.25 0.25 1 4 &lt;=0.125 1 &gt;=8 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 4 0.5 2 &gt;=8 &gt;=8 &gt;=8 0.25 </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] 42 30 13 25 19 37 49 26 38 8 46 40 23 25 44 11 40 13 22 34 15 36 47 49 49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 19 46 14 40 42 13 26 42 12 21 41 26 21 12 24 27 40 21 45 37 24 13 41 17 41</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 14 17 16 15 16 15 11 16 16 15 15 13 13 15 11 15 15 15 17 13 11 15 17 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 16 17 11 13 14 13 17 17 16 17 12 17 11 16 11 13 15 13 11 16 12 14 16 13</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] 20 25 18 16 15 19 16 21 23 19 25 18 16 16 16 18 16 27 17 27 23 22 17 19 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 22 17 19 18 25 20 18 23 18 15 23 20 24 23 21 20 18 21 18 21 23 15 18 25 22</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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@ -10,7 +10,7 @@
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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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@ -171,7 +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] 0.06804385</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.04631559</span>
</code></pre></div>
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