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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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
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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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">
@ -312,41 +312,41 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-09-28</td>
<td align="center">S6</td>
<td align="center">Hospital A</td>
<td align="center">2014-06-06</td>
<td align="center">A5</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-08-19</td>
<td align="center">N6</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">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-05-24</td>
<td align="center">G7</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</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>
</tr>
<tr class="even">
<td align="center">2013-12-10</td>
<td align="center">H10</td>
<td align="center">2014-02-26</td>
<td align="center">R3</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2011-12-02</td>
<td align="center">H2</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-05-29</td>
<td align="center">C5</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
@ -356,19 +356,8 @@
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-04-01</td>
<td align="center">S7</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">F</td>
</tr>
<tr class="even">
<td align="center">2017-12-01</td>
<td align="center">S1</td>
<td align="center">2017-07-23</td>
<td align="center">U3</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
@ -377,6 +366,17 @@
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-11-18</td>
<td align="center">C7</td>
<td align="center">Hospital D</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>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -409,16 +409,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,499</td>
<td align="right">52.50%</td>
<td align="right">10,499</td>
<td align="right">52.50%</td>
<td align="right">10,514</td>
<td align="right">52.57%</td>
<td align="right">10,514</td>
<td align="right">52.57%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,501</td>
<td align="right">47.51%</td>
<td align="right">9,486</td>
<td align="right">47.43%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -472,9 +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 10,615 'phenotype-based' first isolates (53.1% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,709 'phenotype-based' first isolates (53.5% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.1% 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 53.5% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<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>
@ -482,10 +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 10,615 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,709 isolates for analysis. Now our data looks like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
<table style="width:100%;" class="table">
<table class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -498,7 +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>
@ -521,77 +521,29 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2014-09-28</td>
<td align="center">S6</td>
<td align="center">Hospital A</td>
<td align="center">2014-06-06</td>
<td align="center">A5</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2014-08-19</td>
<td align="center">N6</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">2016-05-24</td>
<td align="center">G7</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</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-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="center">2017-12-01</td>
<td align="center">S1</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">8</td>
<td align="center">2011-02-09</td>
<td align="center">B9</td>
<td align="center">Hospital C</td>
<tr class="even">
<td align="left">4</td>
<td align="center">2011-05-29</td>
<td align="center">C5</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -599,17 +551,65 @@ Longest: 1</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2010-02-05</td>
<td align="center">B6</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">11</td>
<td align="center">2015-02-05</td>
<td align="left">9</td>
<td align="center">2016-10-20</td>
<td align="center">F6</td>
<td align="center">Hospital B</td>
<td align="center">Hospital D</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">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">13</td>
<td align="center">2010-05-11</td>
<td align="center">G7</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">14</td>
<td align="center">2010-04-05</td>
<td align="center">T2</td>
<td align="center">Hospital D</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">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
@ -636,8 +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: 10,615<br>
Available: 10,615 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,709<br>
Available: 10,709 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -654,33 +654,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,629</td>
<td align="right">43.61%</td>
<td align="right">4,629</td>
<td align="right">43.61%</td>
<td align="right">4,602</td>
<td align="right">42.97%</td>
<td align="right">4,602</td>
<td align="right">42.97%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,687</td>
<td align="right">25.31%</td>
<td align="right">7,316</td>
<td align="right">68.92%</td>
<td align="right">2,816</td>
<td align="right">26.30%</td>
<td align="right">7,418</td>
<td align="right">69.27%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,137</td>
<td align="right">20.13%</td>
<td align="right">9,453</td>
<td align="right">89.05%</td>
<td align="right">2,079</td>
<td align="right">19.41%</td>
<td align="right">9,497</td>
<td align="right">88.68%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,162</td>
<td align="right">10.95%</td>
<td align="right">10,615</td>
<td align="right">1,212</td>
<td align="right">11.32%</td>
<td align="right">10,709</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -699,14 +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>
@ -727,13 +727,58 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-08-19</td>
<td align="center">N6</td>
<td align="center">2011-05-29</td>
<td align="center">C5</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-10-20</td>
<td align="center">F6</td>
<td align="center">Hospital D</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">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-12-15</td>
<td align="center">U7</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-06-08</td>
<td align="center">U7</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
@ -741,14 +786,14 @@ Longest: 24</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-02-09</td>
<td align="center">B9</td>
<td align="center">Hospital C</td>
<tr class="odd">
<td align="center">2011-07-14</td>
<td align="center">J7</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -756,64 +801,19 @@ Longest: 24</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2013-08-26</td>
<td align="center">V10</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2010-09-09</td>
<td align="center">Z10</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-09-08</td>
<td align="center">A6</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-01-11</td>
<td align="center">T7</td>
<td align="center">2017-10-13</td>
<td align="center">G8</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -837,50 +837,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2208</td>
<td align="center">124</td>
<td align="center">2297</td>
<td align="center">4629</td>
<td align="center">2159</td>
<td align="center">125</td>
<td align="center">2318</td>
<td align="center">4602</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3392</td>
<td align="center">168</td>
<td align="center">1069</td>
<td align="center">4629</td>
<td align="center">3391</td>
<td align="center">140</td>
<td align="center">1071</td>
<td align="center">4602</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3361</td>
<td align="center">3331</td>
<td align="center">0</td>
<td align="center">1268</td>
<td align="center">4629</td>
<td align="center">1271</td>
<td align="center">4602</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4051</td>
<td align="center">4013</td>
<td align="center">0</td>
<td align="center">578</td>
<td align="center">4629</td>
<td align="center">589</td>
<td align="center">4602</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">1162</td>
<td align="center">1162</td>
<td align="center">1212</td>
<td align="center">1212</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">936</td>
<td align="center">31</td>
<td align="center">195</td>
<td align="center">1162</td>
<td align="center">980</td>
<td align="center">30</td>
<td align="center">202</td>
<td align="center">1212</td>
</tr>
</tbody>
</table>
@ -903,34 +903,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4051</td>
<td align="center">4013</td>
<td align="center">0</td>
<td align="center">578</td>
<td align="center">4629</td>
<td align="center">589</td>
<td align="center">4602</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1046</td>
<td align="center">1069</td>
<td align="center">0</td>
<td align="center">116</td>
<td align="center">1162</td>
<td align="center">143</td>
<td align="center">1212</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2370</td>
<td align="center">2505</td>
<td align="center">0</td>
<td align="center">317</td>
<td align="center">2687</td>
<td align="center">311</td>
<td align="center">2816</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">2137</td>
<td align="center">2137</td>
<td align="center">2079</td>
<td align="center">2079</td>
</tr>
</tbody>
</table>
@ -944,7 +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] 0.5423457</span></span></code></pre></div>
<span><span class="co"># [1] 0.5464563</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>
@ -958,19 +958,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5395931</td>
<td align="center">0.5425565</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5418251</td>
<td align="center">0.5403611</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5406250</td>
<td align="center">0.5634772</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5486436</td>
<td align="center">0.5504023</td>
</tr>
</tbody>
</table>
@ -989,23 +989,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5395931</td>
<td align="center">3195</td>
<td align="center">0.5425565</td>
<td align="center">3231</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5418251</td>
<td align="center">3682</td>
<td align="center">0.5403611</td>
<td align="center">3766</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5406250</td>
<td align="center">1600</td>
<td align="center">0.5634772</td>
<td align="center">1599</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5486436</td>
<td align="center">2138</td>
<td align="center">0.5504023</td>
<td align="center">2113</td>
</tr>
</tbody>
</table>
@ -1026,27 +1026,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7690646</td>
<td align="center">0.8751350</td>
<td align="center">0.9775329</td>
<td align="center">0.7672751</td>
<td align="center">0.8720122</td>
<td align="center">0.9778357</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8321859</td>
<td align="center">0.9001721</td>
<td align="center">0.9870912</td>
<td align="center">0.8333333</td>
<td align="center">0.8820132</td>
<td align="center">0.9768977</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7908448</td>
<td align="center">0.8820246</td>
<td align="center">0.9795311</td>
<td align="center">0.8004261</td>
<td align="center">0.8895597</td>
<td align="center">0.9808239</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5395414</td>
<td align="center">0.5430495</td>
<td align="center">0.0000000</td>
<td align="center">0.5395414</td>
<td align="center">0.5430495</td>
</tr>
</tbody>
</table>
@ -1071,23 +1071,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.0%</td>
<td align="right">26.6%</td>
<td align="right">54.3%</td>
<td align="right">26.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.2%</td>
<td align="right">25.7%</td>
<td align="right">54.0%</td>
<td align="right">25.3%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">54.1%</td>
<td align="right">28.1%</td>
<td align="right">56.3%</td>
<td align="right">27.4%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">54.9%</td>
<td align="right">26.4%</td>
<td align="right">55.0%</td>
<td align="right">25.8%</td>
</tr>
</tbody>
</table>
@ -1171,16 +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] 2 0.125 16 0.0625 2 0.001 0.0625 1 32 0.005 </span></span>
<span><span class="co"># [11] 8 0.0625 0.001 0.002 128 32 4 2 0.002 32 </span></span>
<span><span class="co"># [21] 128 16 1 4 256 16 128 64 0.5 8 </span></span>
<span><span class="co"># [31] 0.5 0.25 1 4 16 0.025 0.125 1 1 4 </span></span>
<span><span class="co"># [41] 0.002 16 4 16 128 0.002 8 0.001 0.001 0.005 </span></span>
<span><span class="co"># [51] 0.25 1 0.125 64 0.001 1 8 1 0.005 8 </span></span>
<span><span class="co"># [61] 2 0.025 0.001 0.125 0.025 0.001 256 0.01 2 0.002 </span></span>
<span><span class="co"># [71] 128 0.25 32 8 32 0.001 256 2 4 32 </span></span>
<span><span class="co"># [81] 64 0.002 0.25 4 8 32 0.25 0.5 0.0625 256 </span></span>
<span><span class="co"># [91] 0.25 0.025 0.002 1 0.005 0.025 1 2 0.002 64</span></span></code></pre></div>
<span><span class="co"># [1] 0.5 0.025 0.025 2 0.005 64 0.001 0.025 &gt;=256 0.025 </span></span>
<span><span class="co"># [11] 4 1 32 0.002 0.01 64 16 0.001 4 0.005 </span></span>
<span><span class="co"># [21] 0.125 2 &gt;=256 8 &gt;=256 64 0.5 64 0.0625 2 </span></span>
<span><span class="co"># [31] 128 1 4 8 &gt;=256 4 0.5 0.025 0.0625 &gt;=256 </span></span>
<span><span class="co"># [41] 0.125 64 1 &gt;=256 1 0.001 0.01 2 0.005 0.025 </span></span>
<span><span class="co"># [51] 16 0.001 8 32 0.025 1 0.025 0.25 64 0.125 </span></span>
<span><span class="co"># [61] 0.0625 0.01 128 0.5 0.025 0.001 32 0.001 0.01 0.0625</span></span>
<span><span class="co"># [71] 8 2 0.25 0.002 2 0.01 0.025 0.025 128 128 </span></span>
<span><span class="co"># [81] 0.002 1 0.25 &gt;=256 128 &gt;=256 0.5 0.0625 4 0.01 </span></span>
<span><span class="co"># [91] 0.002 0.002 0.0625 2 0.01 8 0.0625 0.01 0.025 0.25</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>
@ -1209,10 +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] 24 28 17 23 27 26 28 29 30 17 27 18 20 30 28 22 29 28 21 21 27 19 20 25 19</span></span>
<span><span class="co"># [26] 24 26 24 24 31 18 24 31 24 27 20 25 22 20 24 18 27 29 29 28 20 28 17 31 31</span></span>
<span><span class="co"># [51] 24 19 22 24 26 29 18 29 27 22 28 26 29 23 23 23 30 19 31 28 31 24 26 23 29</span></span>
<span><span class="co"># [76] 22 17 23 29 26 24 22 20 27 20 23 31 23 25 23 31 23 28 23 31 25 20 23 22 27</span></span></code></pre></div>
<span><span class="co"># [1] 21 29 21 29 23 20 17 18 24 18 26 30 24 31 18 20 19 21 19 27 28 31 17 30 25</span></span>
<span><span class="co"># [26] 20 17 21 17 23 25 29 29 30 19 31 18 29 22 28 29 28 30 25 31 20 26 22 29 22</span></span>
<span><span class="co"># [51] 23 29 20 31 30 31 28 28 19 27 28 29 17 26 29 30 27 18 17 30 24 25 30 22 26</span></span>
<span><span class="co"># [76] 31 28 26 29 20 23 20 23 27 29 21 24 17 21 29 22 29 28 27 24 23 17 22 22 30</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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@ -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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

54
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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">
@ -308,19 +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 I I I S S S</span></span>
<span><span class="co"># 2 R I R I I R</span></span>
<span><span class="co"># 3 S I I S I S</span></span>
<span><span class="co"># 4 S S I R S S</span></span>
<span><span class="co"># 5 R I R S I R</span></span>
<span><span class="co"># 6 S R I R S S</span></span>
<span><span class="co"># 1 R R S R R R</span></span>
<span><span class="co"># 2 S I S R I I</span></span>
<span><span class="co"># 3 S I I S R R</span></span>
<span><span class="co"># 4 S R R S I S</span></span>
<span><span class="co"># 5 R S R S I S</span></span>
<span><span class="co"># 6 S I S S R R</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 I</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<span><span class="co"># 6 S</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>
@ -351,40 +351,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3229</td>
<td align="right">64.58%</td>
<td align="right">3229</td>
<td align="right">64.58%</td>
<td align="right">3220</td>
<td align="right">64.40%</td>
<td align="right">3220</td>
<td align="right">64.40%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">986</td>
<td align="right">19.72%</td>
<td align="right">4215</td>
<td align="right">84.30%</td>
<td align="right">4206</td>
<td align="right">84.12%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">422</td>
<td align="right">8.44%</td>
<td align="right">4637</td>
<td align="right">92.74%</td>
<td align="right">480</td>
<td align="right">9.60%</td>
<td align="right">4686</td>
<td align="right">93.72%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">256</td>
<td align="right">5.12%</td>
<td align="right">4893</td>
<td align="right">97.86%</td>
<td align="right">237</td>
<td align="right">4.74%</td>
<td align="right">4923</td>
<td align="right">98.46%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">107</td>
<td align="right">2.14%</td>
<td align="right">77</td>
<td align="right">1.54%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
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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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
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@ -169,28 +169,34 @@
<p>All reference data (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are reliable, up-to-date and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply tab separated files that are machine-readable and suitable for input in any software program, such as laboratory information systems.</p>
<p>All reference data (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are reliable, up-to-date and freely available. We continually export our data sets to formats for use in R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated text files that are machine-readable and suitable for input in any software program, such as laboratory information systems.</p>
<p>On this page, we explain how to download them and how the structure of the data sets look like.</p>
<div class="section level2">
<h2 id="microorganisms-currently-accepted-names">Microorganisms (currently accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-currently-accepted-names"></a>
<h2 id="microorganisms-microbial-taxonomy-currently-accepted-names">
<code>microorganisms</code>: Microbial Taxonomy (currently accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-microbial-taxonomy-currently-accepted-names"></a>
</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 26 August 2022 12:06:25 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 26 August 2022 21:26:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><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>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">original R Data Structure (RDS) file</a> (1.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Excel file</a> (4.8 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">tab-separated text file</a> (13.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">plain text file</a> (13.1 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Microsoft Excel workbook</a> (5.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS file</a> (0.1 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.feather" class="external-link">Apache Feather file</a> (5.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">SPSS file</a> (0.1 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.parquet" class="external-link">Apache Parquet file</a> (2.7 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata file</a> (0.1 kB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS data file</a> (69.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">IBM SPSS Statistics data file</a> (20.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata DTA file</a> (62.2 MB)</li>
</ul>
<p><strong>NOTE: The exported files for Excel, SAS, SPSS and Stata contain only the first 50 SNOMED codes per record, as their file size would otherwise exceed 100 MB; the file size limit of GitHub.</strong> Advice? Use R instead.</p>
<div class="section level3">
<h3 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a>
</h3>
@ -391,25 +397,30 @@
</div>
</div>
<div class="section level2">
<h2 id="microorganisms-previously-accepted-names">Microorganisms (previously accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-previously-accepted-names"></a>
<h2 id="microorganisms-old-microbial-taxonomy-previously-accepted-names">
<code>microorganisms.old</code>: Microbial Taxonomy (previously accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-old-microbial-taxonomy-previously-accepted-names"></a>
</h2>
<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 26 August 2022 12:06:25 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 26 August 2022 21:26:31 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>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">original R Data Structure (RDS) file</a> (0.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.xlsx" class="external-link">Excel file</a> (0.5 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.txt" class="external-link">tab-separated text file</a> (1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.txt" class="external-link">plain text file</a> (1 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.xlsx" class="external-link">Microsoft Excel workbook</a> (0.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sas" class="external-link">SAS file</a> (0.1 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.feather" class="external-link">Apache Feather file</a> (0.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sav" class="external-link">SPSS file</a> (0.1 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.parquet" class="external-link">Apache Parquet file</a> (0.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.dta" class="external-link">Stata file</a> (0.1 kB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sas" class="external-link">SAS data file</a> (2.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sav" class="external-link">IBM SPSS Statistics data file</a> (1.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.dta" class="external-link">Stata DTA file</a> (2 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-1">Source<a class="anchor" aria-label="anchor" href="#source-1"></a>
@ -457,24 +468,29 @@
</div>
</div>
<div class="section level2">
<h2 id="antibiotic-agents">Antibiotic agents<a class="anchor" aria-label="anchor" href="#antibiotic-agents"></a>
<h2 id="antibiotics-antibiotic-agents">
<code>antibiotics</code>: Antibiotic Agents<a class="anchor" aria-label="anchor" href="#antibiotics-antibiotic-agents"></a>
</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 26 August 2022 12:06:25 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 26 August 2022 21:26:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><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>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">original R Data Structure (RDS) file</a> (36 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Excel file</a> (65 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">tab-separated text file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">plain text file</a> (0.1 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Microsoft Excel workbook</a> (65 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas" class="external-link">SAS file</a> (0.1 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.feather" class="external-link">Apache Feather file</a> (98 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">SPSS file</a> (0.1 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.parquet" class="external-link">Apache Parquet file</a> (76 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata file</a> (0.1 kB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas" class="external-link">SAS data file</a> (1.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">IBM SPSS Statistics data file</a> (0.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata DTA file</a> (0.3 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-2">Source<a class="anchor" aria-label="anchor" href="#source-2"></a>
@ -625,24 +641,29 @@
</div>
</div>
<div class="section level2">
<h2 id="antiviral-agents">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents"></a>
<h2 id="antivirals-antiviral-agents">
<code>antivirals</code>: Antiviral Agents<a class="anchor" aria-label="anchor" href="#antivirals-antiviral-agents"></a>
</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 26 August 2022 12:06:25 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 26 August 2022 21:26:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><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>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">original R Data Structure (RDS) file</a> (4 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class="external-link">Excel file</a> (14 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt" class="external-link">tab-separated text file</a> (16 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt" class="external-link">plain text file</a> (16 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class="external-link">Microsoft Excel workbook</a> (14 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas" class="external-link">SAS file</a> (0.1 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.feather" class="external-link">Apache Feather file</a> (13 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">SPSS file</a> (0.1 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.parquet" class="external-link">Apache Parquet file</a> (11 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata file</a> (0.1 kB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas" class="external-link">SAS data file</a> (80 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">IBM SPSS Statistics data file</a> (68 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata DTA file</a> (67 kB)</li>
</ul>
<div class="section level3">
<h3 id="source-3">Source<a class="anchor" aria-label="anchor" href="#source-3"></a>
@ -752,24 +773,29 @@
</div>
</div>
<div class="section level2">
<h2 id="interpretation-from-mic-values-disk-diameters-to-rsi">Interpretation from MIC values / disk diameters to R/SI<a class="anchor" aria-label="anchor" href="#interpretation-from-mic-values-disk-diameters-to-rsi"></a>
<h2 id="rsi_translation-interpretation-from-mic-values-disk-diameters-to-rsi">
<code>rsi_translation</code>: Interpretation from MIC values / disk diameters to R/SI<a class="anchor" aria-label="anchor" href="#rsi_translation-interpretation-from-mic-values-disk-diameters-to-rsi"></a>
</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 26 August 2022 12:06:25 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 26 August 2022 21:26:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><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>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">original R Data Structure (RDS) file</a> (49 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Excel file</a> (0.9 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">tab-separated text file</a> (2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain text file</a> (2 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Microsoft Excel workbook</a> (0.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS file</a> (0.1 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.feather" class="external-link">Apache Feather file</a> (0.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS file</a> (0.1 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.parquet" class="external-link">Apache Parquet file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata file</a> (0.1 kB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS data file</a> (4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">IBM SPSS Statistics data file</a> (2.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata DTA file</a> (3.8 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
@ -906,24 +932,29 @@
</div>
</div>
<div class="section level2">
<h2 id="intrinsic-bacterial-resistance">Intrinsic bacterial resistance<a class="anchor" aria-label="anchor" href="#intrinsic-bacterial-resistance"></a>
<h2 id="intrinsic_resistant-intrinsic-bacterial-resistance">
<code>intrinsic_resistant</code>: Intrinsic Bacterial Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intrinsic-bacterial-resistance"></a>
</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 26 August 2022 12:06:25 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 26 August 2022 21:26:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><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>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">original R Data Structure (RDS) file</a> (78 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Excel file</a> (1.3 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">tab-separated text file</a> (5.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">plain text file</a> (5.1 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Microsoft Excel workbook</a> (1.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS file</a> (0.1 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.feather" class="external-link">Apache Feather file</a> (1.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">SPSS file</a> (0.1 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.parquet" class="external-link">Apache Parquet file</a> (0.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata file</a> (0.1 kB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS data file</a> (10.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">IBM SPSS Statistics data file</a> (7.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata DTA file</a> (10.2 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></a>
@ -1173,24 +1204,29 @@
</div>
</div>
<div class="section level2">
<h2 id="dosage-guidelines-from-eucast">Dosage guidelines from EUCAST<a class="anchor" aria-label="anchor" href="#dosage-guidelines-from-eucast"></a>
<h2 id="dosage-dosage-guidelines-from-eucast">
<code>dosage</code>: Dosage Guidelines from EUCAST<a class="anchor" aria-label="anchor" href="#dosage-dosage-guidelines-from-eucast"></a>
</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 26 August 2022 12:06:25 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 26 August 2022 21:26:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p><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>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">original R Data Structure (RDS) file</a> (3 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class="external-link">Excel file</a> (14 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt" class="external-link">tab-separated text file</a> (15 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt" class="external-link">plain text file</a> (15 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class="external-link">Microsoft Excel workbook</a> (14 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class="external-link">SAS file</a> (0.1 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.feather" class="external-link">Apache Feather file</a> (12 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">SPSS file</a> (0.1 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.parquet" class="external-link">Apache Parquet file</a> (8 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata file</a> (0.1 kB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class="external-link">SAS data file</a> (52 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">IBM SPSS Statistics data file</a> (45 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata DTA file</a> (44 kB)</li>
</ul>
<div class="section level3">
<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>

2
articles/index.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

2
articles/resistance_predict.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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
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11
articles/welcome_to_AMR.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -168,11 +168,12 @@
<p>Note: to keep the package size as small as possible, we only included this vignette on CRAN. You can read more vignettes on our website about how to conduct AMR data analysis, determine MDRO’s, find explanation of EUCAST rules, and much more: <a href="https://msberends.github.io/AMR/articles/" class="uri">https://msberends.github.io/AMR/articles/</a>.</p>
<p>Note: to keep the package size as small as possible, we only included this vignette on CRAN. You can read more vignettes on our website about how to conduct AMR data analysis, determine MDROs, find explanation of EUCAST rules, and much more: <a href="https://msberends.github.io/AMR/articles/" class="uri">https://msberends.github.io/AMR/articles/</a>.</p>
<hr>
<p><code>AMR</code> is a free, open-source and independent R package (see <a href="https://msberends.github.io/AMR/#copyright">Copyright</a>) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
<p>The <code>AMR</code> package is a <a href="https://msberends.github.io/AMR/#copyright">free and open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero dependencies</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
<p><img src="AMR_intro.png" width="555px"></p>
<p>After installing this package, R knows ~71,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>The <code>AMR</code> package is available in Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
<p>The <code>AMR</code> package is available in English, Chinese, Danish, Dutch, French, German, Greek, Italian, Japanese, Polish, Portuguese, Russian, Spanish, Swedish, Turkish and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
<p>This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. Since its first public release in early 2018, this package has been downloaded from more than 175 countries.</p>
<p>This package can be used for:</p>
<ul>
@ -195,6 +196,8 @@
</ul>
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
<p>This R package was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>) but is actively and durably maintained (see <a href="https://msberends.github.io/AMR/news/index.html">changelog)</a>) by two public healthcare organisations in the Netherlands.</p>
<hr>
<p><small> This AMR package for R is free, open-source software and licensed under the <a href="https://msberends.github.io/AMR/LICENSE-text.html">GNU General Public License v2.0 (GPL-2)</a>. These requirements are consequently legally binding: modifications must be released under the same license when distributing the package, changes made to the code must be documented, source code must be made available when the package is distributed, and a copy of the license and copyright notice must be included with the package. </small></p>
</main>
</div>

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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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
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2
index.html
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@ -44,7 +44,7 @@
<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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
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15
news/index.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -127,15 +127,16 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="1.8.1.9027" id="amr-1819027">AMR 1.8.1.9027<a class="anchor" aria-label="anchor" href="#amr-1819027"></a></h2>
<h2 class="pkg-version" data-toc-text="1.8.1.9030" id="amr-1819030">AMR 1.8.1.9030<a class="anchor" aria-label="anchor" href="#amr-1819030"></a></h2>
<div class="section level4">
<h4 id="new-1-8-1-9027">New<a class="anchor" aria-label="anchor" href="#new-1-8-1-9027"></a></h4>
<h4 id="new-1-8-1-9030">New<a class="anchor" aria-label="anchor" href="#new-1-8-1-9030"></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-1-8-1-9027">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9027"></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>
<h4 id="changed-1-8-1-9030">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9030"></a></h4>
<ul><li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</li>
<li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on <code>NA</code> values (e.g. <code>as.rsi(as.disk(NA), ...)</code>)</li>
<li>Removed <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> for MIC values, since MIC are not integer values and running <code><a href="https://rdrr.io/r/base/table.html" class="external-link">table()</a></code> on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on <code>factor</code>s work)</li>
<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>
@ -152,9 +153,11 @@
</li>
</ul></div>
<div class="section level4">
<h4 id="other-1-8-1-9027">Other<a class="anchor" aria-label="anchor" href="#other-1-8-1-9027"></a></h4>
<h4 id="other-1-8-1-9030">Other<a class="anchor" aria-label="anchor" href="#other-1-8-1-9030"></a></h4>
<ul><li>New website to make use of the new Bootstrap 5 and pkgdown v2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions</li>
<li>Added Peter Dutey-Magni and Anton Mymrikov as contributors, to thank them for their valuable input</li>
<li>Our data sets are now also continually exported to Apache Feather and Apache Parquet formats</li>
<li>Set up Git Large File Storage (Git LFS) for the large SAS and SPSS file formats</li>
</ul></div>
</div>
<div class="section level2">

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datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2022-08-26T12:08Z
last_built: 2022-08-26T21:28Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9027</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9027</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/ab_from_text.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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

2
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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

22
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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -190,16 +190,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1975-05-28 47 47.24658 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1943-01-19 79 79.60000 56</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1996-10-04 25 25.89315 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1949-06-23 73 73.17534 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1973-11-22 48 48.75890 26</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1946-02-08 76 76.54521 53</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1971-03-30 51 51.40822 28</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-12-20 33 33.68219 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1983-01-17 39 39.60548 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1933-02-25 89 89.49863 66</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1941-07-07 81 81.13699 58</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1938-12-21 83 83.67945 61</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1986-07-22 36 36.09589 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1959-10-17 62 62.85753 40</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1975-01-14 47 47.61370 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1973-12-13 48 48.70137 26</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1954-03-31 68 68.40548 45</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1961-10-20 60 60.84932 38</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1959-01-07 63 63.63288 40</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1967-08-20 55 55.01644 32</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

2
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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
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2
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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

2
reference/antibiotics.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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

2
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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

2
reference/as.disk.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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

2
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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

2
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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

2
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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

2
reference/atc_online.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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

2
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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

2
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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

4
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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -163,7 +163,7 @@ Function <code><a href="as.mo.html">as.mo()</a></code> to use the data for intel
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Get version info of included data set</span></span></span>
<span class="r-in"><span><span class="fu"><a href="catalogue_of_life_version.html">catalogue_of_life_version</a></span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Included in this AMR package (v1.8.1.9027) are:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Included in this AMR package (v1.8.1.9030) 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>

2
reference/catalogue_of_life_version.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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

2
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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

2
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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

2
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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

2
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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

2
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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

2
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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

2
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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

2
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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</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">

59
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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -177,40 +177,41 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&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] 28 28 18 40 67 67 29 37 63 60 40 26 15 63 46 7 50 54 7 37 7 43 19 30 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 59 42 12 27 46 2 47 22 64 41 18 15 14 31 55 49 63 47 67 43 47 6 30 7 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 13 2 60 30 10 17 34 1 57 24 10 22 11 22 61 44 15 2 11 26 64 31 10 12 33</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 23 49 8 12 50 6 57 29 51 28 59 48 6 35 60 12 25 17 15 40 62 61 64 2 7</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 56 10 24 66 30 65 47 54 31 64 7 13 41 60 23 35 11 37 24 12 53 58 39 31 26</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 34 60 56 62 31 58 36 17 13 54 67 53 37 23 60 15 30 61 43 61 45 5 20 34 33</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 47 10 20 29 15 39 38 34 65 7 40 57 23 59 3 9 60 62 54 66 40 26 42 63 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 23 16 15 67 48 65 63 27 33 52 6 60 44 41 54 64 32 4 16 3 5 21 19 49 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 37 22 35 49 56 34 5 24 8 19 29 58 1 25 23 2 63 43 7 18 52 35 30 50 39</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 51 60 35 37 36 7 26 55 12 28 31 29 21 12 26 39 11 5 43 15 45 32 11 51 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 12 1 59 39 10 26 46 1 57 46 44 61 17 59 17 53 39 4 27 48 51 10 16 52 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 45 16 56 39 34 34 36 30 15 28 53 3 12 29 32 7 10 20 38 12 61 16 1 59 29</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 34 2 39 35 14 49 41 28 48 58 54 6 7 38 46 50 54 25 34 49 54 3 18 5 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 42 63 24 13 42 26 19 8 36 54 56 18 11 13 14 58 43 13 9 54 32 52 50 49 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 22 4 40 49 27 22 55 43 38 1 33 47 9 30 5 11 60 37 62 24 18 50 9 5 29</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 63 50 32 51 5 3 44 4 43 63 62 33 54 9 7 4 54 48 40 19 37 53 12 49 24</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE FALSE TRUE FALSE TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE TRUE FALSE TRUE TRUE TRUE TRUE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] TRUE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] TRUE TRUE FALSE FALSE TRUE TRUE 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: 2 × 49</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> 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> 2002-11-12 B TRUE FALSE FALSE 29 M CF9318 B_STPHY_CONS</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-09-24 B TRUE FALSE FALSE 29 M CF9318 B_CMPYL_JEJN</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-07-30 A TRUE TRUE FALSE 76 F 218912 B_ESCHR_COLI</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-07-30 A TRUE TRUE FALSE 76 F 218912 B_ESCHR_COLI</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-07-16 D FALSE FALSE TRUE 78 M 241328 B_STPHY_CONS</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>

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@ -167,9 +167,9 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.955404</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.964037</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] -0.04293402</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.06905028</span>
</code></pre></div>
</div>
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@ -178,43 +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] 4 0.01 &lt;=0.001 0.0625 0.002 0.002 2 32 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &lt;=0.001 0.002 0.125 16 8 &lt;=0.001 0.002 &gt;=64 0.0625 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 8 0.005 0.005 0.25 0.125 2 &lt;=0.001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.0625 0.5 4 16 4 0.0625 8 0.002 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.25 64 64 0.5 &lt;=0.001 0.5 &lt;=0.001 8 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 2 0.01 0.5 0.0625 0.125 &gt;=256 0.025 </span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 25 38 46 47 12 49 31 7 28 47 28 22 49 26 50 7 18 48 32 35 20 41 47 49 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 39 16 46 31 49 28 18 41 45 40 42 49 22 47 40 6 49 25 12 43 43 36 7 16 10</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 R S I I S R R R I R S S I R R S R I R S R R S S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S I S S R S S I S R R S S S S R S R I R R R R S R</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] 0.025 4 1 64 0.125 8 1 32 0.002 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.002 32 2 0.0625 2 0.125 &lt;=0.001 0.25 0.002 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 128 32 0.005 8 16 64 0.025 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 0.002 &lt;=0.001 0.005 0.125 256 4 32 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &lt;=0.001 0.25 1 0.025 0.125 32 32 16 0.005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.5 &lt;=0.001 0.0625 0.5 256 2 64 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 1 8 1 &gt;=32 &gt;=32 &lt;=0.5 2 16 2 4 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 16 4 &gt;=32 16 4 8 8 4 &gt;=32 2 16 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 32 &lt;=0.25 16 0.5 8 &lt;=0.25 8 16 8 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 32 0.5 &lt;=0.25 32 32 32 0.5 4 8 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] &lt;=0.25 32 16 16 2 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"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] &gt;=16 &gt;=16 &gt;=16 0.5 4 1 1 1 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &lt;=0.125 1 8 &lt;=0.125 0.25 &gt;=16 4 0.25 &gt;=16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.5 4 2 0.25 8 2 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.25 0.25 &lt;=0.025 &gt;=16 0.0625 0.5 8 0.25 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 4 0.125 1 0.5 0.125 8 &gt;=16 0.0625 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.25 &gt;=16 2 &gt;=16 1 1 4 </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 50 11 47 9 25 21 25 20 11 21 22 48 23 24 37 32 17 9 48 36 20 26 29 31 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 47 15 40 39 45 10 36 40 47 22 12 11 44 14 45 21 17 49 24 14 11 22 44 45 11</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] 13 13 11 11 11 12 15 16 11 14 11 16 15 17 12 11 15 15 13 17 16 15 14 13 17</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 14 13 11 11 14 12 14 15 14 14 16 15 11 14 12 13 17 11 17 13 11 15 11 16</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 21 15 21 21 27 25 24 26 20 22 26 15 24 23 26 24 18 23 18 23 25 24 23 19 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 25 23 21 19 21 15 15 25 22 22 16 16 18 16 25 23 24 17 23 15 25 22 23 16</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>

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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="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
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reference/skewness.html
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@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9027</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -166,7 +166,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.04432341</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.06729828</span>
</code></pre></div>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9027</small>
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