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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="">1.8.2.9061</small>
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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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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">
@ -380,12 +380,12 @@ data set:</p>
<col width="13%">
<col width="13%">
<col width="13%">
<col width="28%">
<col width="26%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="8%">
<col width="9%">
</colgroup>
<thead><tr class="header">
<th align="center">date</th>
@ -400,66 +400,66 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-06-10</td>
<td align="center">K4</td>
<td align="center">Hospital A</td>
<td align="center">2017-09-13</td>
<td align="center">T10</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-10-31</td>
<td align="center">G8</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2011-07-13</td>
<td align="center">Q7</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-05-04</td>
<td align="center">F6</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R3</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2010-05-15</td>
<td align="center">N5</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-12-18</td>
<td align="center">O8</td>
<td align="center">Hospital D</td>
<td align="center">2013-09-12</td>
<td align="center">A3</td>
<td align="center">Hospital C</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-12-01</td>
<td align="center">T2</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-05-10</td>
<td align="center">W4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">2011-12-19</td>
<td align="center">R10</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -499,16 +499,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,335</td>
<td align="right">51.68%</td>
<td align="right">10,335</td>
<td align="right">51.68%</td>
<td align="right">10,363</td>
<td align="right">51.82%</td>
<td align="right">10,363</td>
<td align="right">51.82%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,665</td>
<td align="right">48.33%</td>
<td align="right">9,637</td>
<td align="right">48.19%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -621,10 +621,10 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,609 'phenotype-based' first isolates (53.0% of total where a</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"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53% 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
<p>So only 53.1% is suitable for resistance analysis! We can now filter
on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
<code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<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>
@ -634,11 +634,11 @@ it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" cl
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,609 isolates for analysis. Now our data looks
<p>So we end up with 10,615 isolates for analysis. Now our data looks
like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<table style="width:100%;" class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -651,7 +651,7 @@ like:</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@ -673,99 +673,99 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">2</td>
<td align="center">2016-05-04</td>
<td align="center">F6</td>
<td align="left">8</td>
<td align="center">2014-11-28</td>
<td align="center">R9</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">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">3</td>
<td align="center">2010-05-15</td>
<td align="center">N5</td>
<td align="left">10</td>
<td align="center">2011-11-04</td>
<td align="center">U10</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">S</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2015-12-18</td>
<td align="center">O8</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">2016-12-01</td>
<td align="center">T2</td>
<td align="center">Hospital B</td>
<td align="left">11</td>
<td align="center">2011-05-17</td>
<td align="center">F5</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2012-12-26</td>
<td align="center">U7</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<tr class="even">
<td align="left">12</td>
<td align="center">2016-12-09</td>
<td align="center">A9</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">13</td>
<td align="center">2011-06-24</td>
<td align="center">M5</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">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">9</td>
<td align="center">2010-11-22</td>
<td align="center">R6</td>
<td align="left">16</td>
<td align="center">2010-11-26</td>
<td align="center">F5</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">B_STPHY_AURS</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">F</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -801,8 +801,8 @@ readable:</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,609<br>
Available: 10,609 (100%, NA: 0 = 0%)<br>
Length: 10,615<br>
Available: 10,615 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -827,33 +827,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,637</td>
<td align="right">43.71%</td>
<td align="right">4,637</td>
<td align="right">43.71%</td>
<td align="right">4,550</td>
<td align="right">42.86%</td>
<td align="right">4,550</td>
<td align="right">42.86%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,731</td>
<td align="right">25.74%</td>
<td align="right">7,368</td>
<td align="right">69.45%</td>
<td align="right">2,715</td>
<td align="right">25.58%</td>
<td align="right">7,265</td>
<td align="right">68.44%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,078</td>
<td align="right">19.59%</td>
<td align="right">9,446</td>
<td align="right">89.04%</td>
<td align="right">2,147</td>
<td align="right">20.23%</td>
<td align="right">9,412</td>
<td align="right">88.67%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,163</td>
<td align="right">10.96%</td>
<td align="right">10,609</td>
<td align="right">1,203</td>
<td align="right">11.33%</td>
<td align="right">10,615</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -874,14 +874,14 @@ antibiotic class they are in:</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="11%">
<col width="10%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@ -902,42 +902,12 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-05-04</td>
<td align="center">F6</td>
<td align="center">2014-11-28</td>
<td align="center">R9</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">2010-05-15</td>
<td align="center">N5</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-12-26</td>
<td align="center">U7</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
@ -947,43 +917,73 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2010-11-22</td>
<td align="center">R6</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">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-02-05</td>
<td align="center">U1</td>
<td align="center">2016-12-17</td>
<td align="center">M1</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-05-10</td>
<td align="center">T3</td>
<td align="center">Hospital A</td>
<tr class="odd">
<td align="center">2016-09-19</td>
<td align="center">B9</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">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">2016-12-18</td>
<td align="center">N3</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">2010-04-19</td>
<td align="center">N5</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">2016-09-02</td>
<td align="center">W3</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@ -1013,50 +1013,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2169</td>
<td align="center">134</td>
<td align="center">2334</td>
<td align="center">4637</td>
<td align="center">2178</td>
<td align="center">98</td>
<td align="center">2274</td>
<td align="center">4550</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3403</td>
<td align="center">162</td>
<td align="center">1072</td>
<td align="center">4637</td>
<td align="center">3344</td>
<td align="center">135</td>
<td align="center">1071</td>
<td align="center">4550</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3398</td>
<td align="center">3331</td>
<td align="center">0</td>
<td align="center">1239</td>
<td align="center">4637</td>
<td align="center">1219</td>
<td align="center">4550</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4041</td>
<td align="center">3996</td>
<td align="center">0</td>
<td align="center">596</td>
<td align="center">4637</td>
<td align="center">554</td>
<td align="center">4550</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">1163</td>
<td align="center">1163</td>
<td align="center">1203</td>
<td align="center">1203</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">906</td>
<td align="center">45</td>
<td align="center">212</td>
<td align="center">1163</td>
<td align="center">947</td>
<td align="center">52</td>
<td align="center">204</td>
<td align="center">1203</td>
</tr>
</tbody>
</table>
@ -1078,34 +1078,34 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4041</td>
<td align="center">3996</td>
<td align="center">0</td>
<td align="center">596</td>
<td align="center">4637</td>
<td align="center">554</td>
<td align="center">4550</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1041</td>
<td align="center">1097</td>
<td align="center">0</td>
<td align="center">122</td>
<td align="center">1163</td>
<td align="center">106</td>
<td align="center">1203</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2436</td>
<td align="center">2393</td>
<td align="center">0</td>
<td align="center">295</td>
<td align="center">2731</td>
<td align="center">322</td>
<td align="center">2715</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">2078</td>
<td align="center">2078</td>
<td align="center">2147</td>
<td align="center">2147</td>
</tr>
</tbody>
</table>
@ -1137,7 +1137,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&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] 0.5435951</span></span></code></pre></div>
<span><span class="co"># [1] 0.5501649</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
@ -1152,19 +1152,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5376442</td>
<td align="center">0.5511084</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5473011</td>
<td align="center">0.5511442</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5522855</td>
<td align="center">0.5606154</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5400188</td>
<td align="center">0.5390071</td>
</tr>
</tbody>
</table>
@ -1189,23 +1189,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5376442</td>
<td align="center">3294</td>
<td align="center">0.5511084</td>
<td align="center">3248</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5473011</td>
<td align="center">3594</td>
<td align="center">0.5511442</td>
<td align="center">3627</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5522855</td>
<td align="center">1597</td>
<td align="center">0.5606154</td>
<td align="center">1625</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5400188</td>
<td align="center">2124</td>
<td align="center">0.5390071</td>
<td align="center">2115</td>
</tr>
</tbody>
</table>
@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7688160</td>
<td align="center">0.8714686</td>
<td align="center">0.9775717</td>
<td align="center">0.7646154</td>
<td align="center">0.8782418</td>
<td align="center">0.9764835</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8177128</td>
<td align="center">0.8950989</td>
<td align="center">0.9819433</td>
<td align="center">0.8304239</td>
<td align="center">0.9118869</td>
<td align="center">0.9825436</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8033687</td>
<td align="center">0.8919810</td>
<td align="center">0.9794947</td>
<td align="center">0.8040516</td>
<td align="center">0.8813996</td>
<td align="center">0.9793738</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5413859</td>
<td align="center">0.5365626</td>
<td align="center">0.0000000</td>
<td align="center">0.5413859</td>
<td align="center">0.5365626</td>
</tr>
</tbody>
</table>
@ -1278,23 +1278,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">53.8%</td>
<td align="right">26.2%</td>
<td align="right">55.1%</td>
<td align="right">26.8%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.7%</td>
<td align="right">26.7%</td>
<td align="right">55.1%</td>
<td align="right">26.1%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">55.2%</td>
<td align="right">25.7%</td>
<td align="right">56.1%</td>
<td align="right">26.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">54.0%</td>
<td align="right">25.4%</td>
<td align="right">53.9%</td>
<td align="right">26.5%</td>
</tr>
</tbody>
</table>
@ -1410,18 +1410,18 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</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 'mic'</span></span>
<span><span class="co"># [1] 0.005 0.0625 &lt;=0.001 8 0.025 0.01 8 0.0625 128 </span></span>
<span><span class="co"># [10] 2 0.025 32 1 128 32 2 0.002 &lt;=0.001</span></span>
<span><span class="co"># [19] 8 8 64 64 0.25 0.005 0.0625 8 0.5 </span></span>
<span><span class="co"># [28] 0.0625 0.25 1 64 1 32 16 16 1 </span></span>
<span><span class="co"># [37] 16 0.005 0.25 64 &gt;=256 0.01 2 0.025 0.01 </span></span>
<span><span class="co"># [46] 64 0.5 16 0.01 &gt;=256 0.025 32 0.025 0.5 </span></span>
<span><span class="co"># [55] 0.025 16 &gt;=256 0.01 32 0.125 4 1 8 </span></span>
<span><span class="co"># [64] 128 128 0.0625 2 &gt;=256 64 0.005 0.0625 0.25 </span></span>
<span><span class="co"># [73] 0.002 0.025 2 32 0.005 0.25 64 0.5 4 </span></span>
<span><span class="co"># [82] 128 4 1 16 0.01 8 2 64 0.0625 </span></span>
<span><span class="co"># [91] 64 32 1 4 16 &gt;=256 32 0.25 2 </span></span>
<span><span class="co"># [100] 0.005</span></span></code></pre></div>
<span><span class="co"># [1] 64 2 0.01 128 1 8 16 &lt;=0.001 256 </span></span>
<span><span class="co"># [10] 0.025 0.005 0.002 256 2 &lt;=0.001 0.5 256 128 </span></span>
<span><span class="co"># [19] 16 0.025 0.25 0.002 0.5 8 32 0.125 1 </span></span>
<span><span class="co"># [28] 1 0.002 0.125 0.025 32 0.005 0.25 0.0625 0.002 </span></span>
<span><span class="co"># [37] 0.01 0.002 32 &lt;=0.001 16 &lt;=0.001 0.125 1 128 </span></span>
<span><span class="co"># [46] 0.005 2 0.01 8 0.0625 16 32 0.01 8 </span></span>
<span><span class="co"># [55] 256 0.002 0.0625 0.0625 0.005 2 256 4 0.0625 </span></span>
<span><span class="co"># [64] 256 4 16 &lt;=0.001 256 0.125 0.002 256 64 </span></span>
<span><span class="co"># [73] 4 64 0.0625 0.125 0.25 16 8 1 16 </span></span>
<span><span class="co"># [82] 0.125 0.005 128 0.25 16 0.005 256 8 0.01 </span></span>
<span><span class="co"># [91] 0.0625 64 4 8 0.01 0.01 128 2 8 </span></span>
<span><span class="co"># [100] 8</span></span></code></pre></div>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1455,10 +1455,10 @@ plotting:</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 21 23 25 27 17 22 21 27 27 22 29 31 31 29 17 18 20 26 27 29 24 26 30 25 23</span></span>
<span><span class="co"># [26] 22 22 19 29 21 31 29 22 29 21 17 26 21 20 28 26 24 21 25 23 25 28 28 29 21</span></span>
<span><span class="co"># [51] 28 20 17 18 27 25 30 28 30 18 22 23 26 31 26 28 27 18 19 22 22 27 28 28 30</span></span>
<span><span class="co"># [76] 29 26 20 20 26 28 19 27 23 20 21 17 30 24 26 25 30 26 28 20 20 27 31 31 18</span></span></code></pre></div>
<span><span class="co"># [1] 20 22 20 20 22 17 24 28 30 26 26 27 18 26 22 21 23 29 27 21 24 29 19 28 30</span></span>
<span><span class="co"># [26] 21 31 29 27 20 23 18 20 19 19 23 27 29 24 17 29 17 17 22 31 19 25 20 25 19</span></span>
<span><span class="co"># [51] 24 25 21 23 26 28 26 24 17 21 26 23 30 28 19 26 18 28 17 17 27 26 22 26 23</span></span>
<span><span class="co"># [76] 21 18 30 23 25 24 25 31 21 31 20 30 17 23 29 27 17 21 30 19 17 17 21 30 23</span></span></code></pre></div>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>

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@ -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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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">

56
articles/MDR.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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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">
@ -375,18 +375,18 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 S S I R R S</span></span>
<span><span class="co"># 2 I R I S S R</span></span>
<span><span class="co"># 3 S I R S S S</span></span>
<span><span class="co"># 4 R S R I I R</span></span>
<span><span class="co"># 5 I I R I S I</span></span>
<span><span class="co"># 6 S I I S S S</span></span>
<span><span class="co"># 1 S S I R I S</span></span>
<span><span class="co"># 2 I S I R R R</span></span>
<span><span class="co"># 3 R I I R S I</span></span>
<span><span class="co"># 4 S S R S S S</span></span>
<span><span class="co"># 5 I S S I R I</span></span>
<span><span class="co"># 6 I R S R S S</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 I</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 I</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
@ -428,40 +428,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3201</td>
<td align="right">64.02%</td>
<td align="right">3201</td>
<td align="right">64.02%</td>
<td align="right">3173</td>
<td align="right">63.46%</td>
<td align="right">3173</td>
<td align="right">63.46%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">985</td>
<td align="right">19.70%</td>
<td align="right">4186</td>
<td align="right">83.72%</td>
<td align="right">1011</td>
<td align="right">20.22%</td>
<td align="right">4184</td>
<td align="right">83.68%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">470</td>
<td align="right">9.40%</td>
<td align="right">4656</td>
<td align="right">93.12%</td>
<td align="right">481</td>
<td align="right">9.62%</td>
<td align="right">4665</td>
<td align="right">93.30%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">240</td>
<td align="right">4.80%</td>
<td align="right">4896</td>
<td align="right">97.92%</td>
<td align="right">236</td>
<td align="right">4.72%</td>
<td align="right">4901</td>
<td align="right">98.02%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">104</td>
<td align="right">2.08%</td>
<td align="right">99</td>
<td align="right">1.98%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
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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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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
articles/SPSS.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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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">
@ -247,7 +247,7 @@ data using a custom made website. The webdesign knowledge needed
<li>
<p><strong>R has a huge community.</strong></p>
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">473,435
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">474,212
R-related questions</a> have already been asked on this platform (that
covers questions and answers for any programming language). In my own
experience, most questions are answered within a couple of

2
articles/WHONET.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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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">

62
articles/datasets.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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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">
@ -187,7 +187,7 @@ of the data sets look like.</p>
<h2 id="microorganisms-full-microbial-taxonomy">
<code>microorganisms</code>: Full Microbial Taxonomy<a class="anchor" aria-label="anchor" href="#microorganisms-full-microbial-taxonomy"></a>
</h2>
<p>A data set with 48,883 rows and 22 columns, containing the following
<p>A data set with 48,050 rows and 22 columns, containing the following
column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>,
<em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>,
<em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>,
@ -196,7 +196,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
<em>gbif_renamed_to</em>, <em>prevalence</em> and <em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 9 December 2022 12:37:08 UTC. Find more info
<p>It was last updated on 11 December 2022 23:14:56 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>
@ -204,25 +204,25 @@ about the structure of this data set <a href="https://msberends.github.io/AMR/re
R Data Structure (RDS) file</a> (1.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">tab-separated
text file</a> (10.6 MB)<br>
text file</a> (10.4 MB)<br>
</li>
<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> (4.8 MB)<br>
Excel workbook</a> (4.7 MB)<br>
</li>
<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> (5.1 MB)<br>
Feather file</a> (5 MB)<br>
</li>
<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> (2.5 MB)<br>
Parquet file</a> (2.4 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
data file</a> (47.8 MB)<br>
data file</a> (46.9 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> (15.8 MB)<br>
SPSS Statistics data file</a> (15.5 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> (43.8 MB)</li>
DTA file</a> (43.4 MB)</li>
</ul>
<p><strong>NOTE: The exported files for SAS, SPSS and Stata contain only
the first 50 SNOMED codes per record, as their file size would otherwise
@ -240,9 +240,9 @@ and the Global Biodiversity Information Facility (GBIF):</p>
<li>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names
with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong>
International Journal of Systematic and Evolutionary Microbiology, 70,
5607-5612; . Accessed from <a href="https://lpsn.dsmz.de" class="external-link uri">https://lpsn.dsmz.de</a> on 12 September, 2022.</li>
<li>GBIF Secretariat (November 26, 2021). GBIF Backbone Taxonomy.
Checklist dataset . Accessed from <a href="https://www.gbif.org" class="external-link uri">https://www.gbif.org</a> on 12 September, 2022.</li>
5607-5612; . Accessed from <a href="https://lpsn.dsmz.de" class="external-link uri">https://lpsn.dsmz.de</a> on 11 December, 2022.</li>
<li>GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset .
Accessed from <a href="https://www.gbif.org" class="external-link uri">https://www.gbif.org</a> on 11 December, 2022.</li>
<li>Public Health Information Network Vocabulary Access and Distribution
System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value
Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link uri">https://phinvads.cdc.gov</a>
@ -261,27 +261,27 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
<tbody>
<tr class="odd">
<td align="center">(unknown kingdom)</td>
<td align="center">5</td>
<td align="center">1</td>
</tr>
<tr class="even">
<td align="center">Animalia</td>
<td align="center">1,524</td>
<td align="center">1,061</td>
</tr>
<tr class="odd">
<td align="center">Archaea</td>
<td align="center">1,237</td>
<td align="center">1,291</td>
</tr>
<tr class="even">
<td align="center">Bacteria</td>
<td align="center">33,716</td>
<td align="center">34,398</td>
</tr>
<tr class="odd">
<td align="center">Fungi</td>
<td align="center">7,450</td>
<td align="center">6,852</td>
</tr>
<tr class="even">
<td align="center">Protozoa</td>
<td align="center">4,951</td>
<td align="center">4,447</td>
</tr>
</tbody>
</table>
@ -355,7 +355,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
<td align="center">482</td>
<td align="center"></td>
<td align="center">3221780</td>
<td align="center">4899</td>
<td align="center">11158430</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">407310004, 407251000, 407281008, …</td>
@ -450,7 +450,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
<td align="center">776057</td>
<td align="center">515602</td>
<td align="center"></td>
<td align="center">6110934</td>
<td align="center">11286021</td>
<td align="center">3221780</td>
<td align="center"></td>
<td align="center">1</td>
@ -1042,37 +1042,37 @@ diffusion diameters. Included guidelines are CLSI (2013-2022) and EUCAST
<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 134,659 rows and 2 columns, containing the following
<p>A data set with 206,832 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 31 October 2022 10:19:06 UTC. Find more info
<p>It was last updated on 11 December 2022 23:14:56 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">original
R Data Structure (RDS) file</a> (78 kB)<br>
R Data Structure (RDS) file</a> (0.1 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">tab-separated
text file</a> (5.1 MB)<br>
text file</a> (7.9 MB)<br>
</li>
<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>
Excel workbook</a> (1.9 MB)<br>
</li>
<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>
Feather file</a> (1.8 MB)<br>
</li>
<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>
Parquet file</a> (0.3 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
data file</a> (9.8 MB)<br>
data file</a> (17.6 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>
SPSS Statistics data file</a> (11.4 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> (9.5 MB)</li>
DTA file</a> (17.2 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>

2
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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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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
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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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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">
@ -192,7 +192,7 @@ treatment evaluation in any setting.</p>
10.18637/jss.v104.i03</a>) and 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>).</p>
<p>After installing this package, R knows ~49,000 distinct microbial
<p>After installing this package, R knows ~48,000 distinct microbial
species and all ~600 antibiotic, antimycotic and antiviral drugs by name
and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED
CT), and knows all about valid R/SI and MIC values. The integral

2
authors.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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">

12
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@ -29,6 +29,18 @@
# ==================================================================== #
*/
/* fix some footer issues with the logos */
@media (min-width: 576px) {
footer .pkgdown-footer-right {
width: 300px;
}
}
@media (max-width: 575.98px) {
footer .pkgdown-footer-right {
text-align: center;
}
}
/* replace 'Developers' with 'Maintainers' */
.developers h2 {
display: none;

4
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@ -42,7 +42,7 @@
<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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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">
@ -194,7 +194,7 @@
</h3>
<p>The <code>AMR</code> package is a <a href="#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>This work was published in the Journal of Statistical Software (Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">DOI 10.18637/jss.v104.i03</a>) and 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>).</p>
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~49,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~600 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. The integral breakpoint guidelines from CLSI and EUCAST are included from the last 10 years. It supports and can read any data format, including WHONET data. This package 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>. It 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>, and is being <a href="./news">actively and durably maintained</a> by two public healthcare organisations in the Netherlands.</p>
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~48,000 distinct microbial species</strong></a> (updated December 2022) and all <a href="./reference/antibiotics.html"><strong>~600 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. The integral breakpoint guidelines from CLSI and EUCAST are included from the last 10 years. It supports and can read any data format, including WHONET data. This package 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>. It 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>, and is being <a href="./news">actively and durably maintained</a> by two public healthcare organisations in the Netherlands.</p>
<div class="section level5">
<h5 id="used-in-175-countries-translated-to-16-languages">Used in 175 countries, translated to 16 languages<a class="anchor" aria-label="anchor" href="#used-in-175-countries-translated-to-16-languages"></a>
</h5>

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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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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">
@ -132,10 +132,10 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="1.8.2.9061" id="amr-1829061">AMR 1.8.2.9061<a class="anchor" aria-label="anchor" href="#amr-1829061"></a></h2>
<h2 class="pkg-version" data-toc-text="1.8.2.9062" id="amr-1829062">AMR 1.8.2.9062<a class="anchor" aria-label="anchor" href="#amr-1829062"></a></h2>
<p>This version will eventually become v2.0! We’re happy to reach a new major milestone soon!</p>
<div class="section level4">
<h4 id="breaking-1-8-2-9061">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9061"></a></h4>
<h4 id="breaking-1-8-2-9062">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9062"></a></h4>
<ul><li>
<strong>Removed all species of the taxonomic kingdom Chromista</strong> from the package. This was done for multiple reasons:
<ul><li>CRAN allows packages to be around 5 MB maximum, some packages are exempted but this package is not one of them</li>
@ -152,7 +152,7 @@
<li>Using <code>units</code> in <code>ab_ddd(..., units = "...")</code> had been deprecated and is now not supported anymore. Use <code><a href="../reference/ab_property.html">ab_ddd_units()</a></code> instead.</li>
</ul></div>
<div class="section level4">
<h4 id="new-1-8-2-9061">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9061"></a></h4>
<h4 id="new-1-8-2-9062">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9062"></a></h4>
<ul><li>
<strong>EUCAST 2022 and CLSI 2022 guidelines</strong> have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 (v12.0) is now the new default guideline for all MIC and disks diffusion interpretations, and for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> to apply EUCAST Expert Rules.</li>
<li>Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. We are very grateful for the valuable input by our colleagues from other countries. The <code>AMR</code> package is now available in 16 languages. The automatic language determination will give a note on systems in supported languages.</li>
@ -194,8 +194,9 @@
</li>
</ul></div>
<div class="section level4">
<h4 id="changes-1-8-2-9061">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9061"></a></h4>
<ul><li>For <code><a href="../reference/as.rsi.html">as.rsi()</a></code>:
<h4 id="changes-1-8-2-9062">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9062"></a></h4>
<ul><li>Updated the microbiological taxonomy using the latest GBIF backbone (November 2022) and latest LPSN records (11 December 2022)</li>
<li>For <code><a href="../reference/as.rsi.html">as.rsi()</a></code>:
<ul><li>Fixed certain EUCAST breakpoints for MIC values</li>
<li>Allow <code>NA</code> values (e.g. <code>as.rsi(as.disk(NA), ...)</code>)</li>
<li>Fix for bug-drug combinations with multiple breakpoints for different body sites</li>
@ -233,7 +234,7 @@
<li>Cleaning columns with <code><a href="../reference/as.rsi.html">as.rsi()</a></code>, <code><a href="../reference/as.mic.html">as.mic()</a></code>, or <code><a href="../reference/as.disk.html">as.disk()</a></code> will now show the column name in the warning for invalid results</li>
</ul></div>
<div class="section level4">
<h4 id="other-1-8-2-9061">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9061"></a></h4>
<h4 id="other-1-8-2-9062">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9062"></a></h4>
<ul><li>New website to make use of the new Bootstrap 5 and pkgdown 2.0. 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, Dmytro Mykhailenko, Anton Mymrikov, and Jonas Salm as contributors, to thank them for their valuable input</li>
<li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>

2
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@ -11,7 +11,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2022-12-11T10:47Z
last_built: 2022-12-11T23:19Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

2
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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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
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8
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@ -5,7 +5,7 @@ This work was published in the Journal of Statistical Software (Volume 104(3); d
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
and doi:10.33612/diss.192486375
).
After installing this package, R knows ~49,000 distinct microbial species and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
After installing this package, R knows ~48,000 distinct microbial species and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.
This package can be used for:
Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF)
@ -31,7 +31,7 @@ This work was published in the Journal of Statistical Software (Volume 104(3); d
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
and doi:10.33612/diss.192486375
).
After installing this package, R knows ~49,000 distinct microbial species and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
After installing this package, R knows ~48,000 distinct microbial species and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.
This package can be used for:
Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF)
@ -62,7 +62,7 @@ Principal component analysis for AMR
<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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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">
@ -191,7 +191,7 @@ Principal component analysis for AMR
) and 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>
).</p>
<p>After installing this package, <span style="R">R</span> knows ~49,000 distinct microbial species and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, 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>After installing this package, <span style="R">R</span> knows ~48,000 distinct microbial species and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, 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>This package is fully independent of any other <span style="R">R</span> package and works on Windows, macOS and Linux with all versions of <span style="R">R</span> since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This <span style="R">R</span> package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.</p>
<p>This package can be used for:</p><ul><li><p>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF)</p></li>
<li><p>Interpreting raw MIC and disk diffusion values, based on any CLSI or EUCAST guideline from the last 10 years</p></li>

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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -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="">1.8.2.9061</small>
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2
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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
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2
reference/ab_property.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9061</small>
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2
reference/add_custom_antimicrobials.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="">1.8.2.9061</small>
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22
reference/age.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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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">
@ -195,16 +195,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1989-09-25 33 33.21096 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1941-12-25 80 80.96164 58</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1987-05-25 35 35.54795 12</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1957-06-15 65 65.49041 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1984-05-25 38 38.54795 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1937-04-16 85 85.65479 62</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1949-06-01 73 73.52877 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1961-04-18 61 61.64932 38</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1965-05-20 57 57.56164 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1982-06-09 40 40.50685 17</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1987-02-24 35 35.79452 12</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1960-01-10 62 62.91781 39</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1981-09-28 41 41.20274 18</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1979-02-26 43 43.78904 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1970-04-15 52 52.65753 29</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1953-06-21 69 69.47397 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1961-04-15 61 61.65753 38</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1993-03-18 29 29.73425 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1936-11-22 86 86.05205 63</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1941-07-31 81 81.36438 58</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -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="">1.8.2.9061</small>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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8
reference/as.mo.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -270,9 +270,9 @@
<li><p>Lancefield RC (1933). <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. <em>J Exp Med.</em> 57(4): 571-95; <a href="https://doi.org/10.1084/jem.57.4.571" class="external-link">doi:10.1084/jem.57.4.571</a></p></li>
<li><p>Berends MS <em>et al.</em> (2022). <strong>Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019</strong> <em>Microorganisms</em> 10(9), 1801; <a href="https://doi.org/10.3390/microorganisms10091801" class="external-link">doi:10.3390/microorganisms10091801</a></p></li>
<li><p>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong> International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a>
. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on 12 September, 2022.</p></li>
<li><p>GBIF Secretariat (November 26, 2021). GBIF Backbone Taxonomy. Checklist dataset <a href="https://doi.org/10.15468/39omei" class="external-link">doi:10.15468/39omei</a>
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on 12 September, 2022.</p></li>
. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on 11 December, 2022.</p></li>
<li><p>GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset <a href="https://doi.org/10.15468/39omei" class="external-link">doi:10.15468/39omei</a>
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on 11 December, 2022.</p></li>
<li><p>Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link">https://phinvads.cdc.gov</a></p></li>
</ol></div>
<div class="section level2">

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@ -10,7 +10,7 @@
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@ -506,16 +506,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 12</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_gu…¹ mo_in…² mo_guideline guide…³</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-12-11 <span style="color: #949494;">10:47:56</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-12-11 <span style="color: #949494;">10:47:56</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-12-11 <span style="color: #949494;">10:47:57</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-12-11 <span style="color: #949494;">10:47:57</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-12-11 <span style="color: #949494;">10:47:57</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-12-11 <span style="color: #949494;">10:47:58</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-12-11 <span style="color: #949494;">10:47:58</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-12-11 <span style="color: #949494;">10:47:58</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-12-11 <span style="color: #949494;">10:47:58</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-12-11 <span style="color: #949494;">10:47:58</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-12-11 <span style="color: #949494;">23:19:53</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-12-11 <span style="color: #949494;">23:19:53</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-12-11 <span style="color: #949494;">23:19:54</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-12-11 <span style="color: #949494;">23:19:54</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-12-11 <span style="color: #949494;">23:19:54</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-12-11 <span style="color: #949494;">23:19:55</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-12-11 <span style="color: #949494;">23:19:55</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-12-11 <span style="color: #949494;">23:19:55</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-12-11 <span style="color: #949494;">23:19:55</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-12-11 <span style="color: #949494;">23:19:55</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 5 more variables: ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># input &lt;dbl&gt;, outcome &lt;rsi&gt;, breakpoint_S_R &lt;chr&gt;, and abbreviated variable</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># names ¹​ab_guideline, ²​mo_input, ³​guideline</span></span>

2
reference/atc_online.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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/av_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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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/av_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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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
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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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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
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@ -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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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
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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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
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2
reference/dosage.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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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/eucast_rules.html
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@ -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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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">
@ -234,7 +234,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p><strong>Note:</strong> This function does not translate MIC values to RSI values. Use <code><a href="as.rsi.html">as.rsi()</a></code> for that. <br><strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. <br></p>
<p>The file containing all EUCAST rules is located here: <a href="https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv</a>. <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The <code>AMR</code> package contains the full microbial taxonomy updated until 12 September, 2022, see <a href="microorganisms.html">microorganisms</a>.</p><div class="section">
<p>The file containing all EUCAST rules is located here: <a href="https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv</a>. <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The <code>AMR</code> package contains the full microbial taxonomy updated until 11 December, 2022, see <a href="microorganisms.html">microorganisms</a>.</p><div class="section">
<h3 id="custom-rules">Custom Rules<a class="anchor" aria-label="anchor" href="#custom-rules"></a></h3>

2
reference/example_isolates.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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
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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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
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139
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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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">
@ -182,42 +182,39 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">200</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 56 21 10 22 60 49 59 8 10 10 65 26 58 62 39 39 50 7 41 9 63 25 46 11 56</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 66 44 3 13 54 23 25 3 50 5 41 48 33 28 51 54 1 14 37 6 27 62 11 52 7</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 21 61 44 19 54 47 57 12 28 62 48 60 12 59 64 19 16 5 46 66 46 13 67 6 65</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 11 7 8 26 39 66 51 1 8 3 49 49 32 14 27 28 67 34 39 11 58 53 22 5 23</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 38 44 16 31 45 5 14 56 28 16 31 58 14 13 49 44 46 42 2 58 49 2 61 5 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 17 67 19 38 55 4 53 66 1 19 60 23 27 30 62 38 8 36 13 46 58 45 47 25 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 20 35 14 46 57 3 17 57 40 32 38 19 67 57 24 61 13 10 11 5 24 40 42 61 28</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 37 39 54 34 20 30 14 18 29 15 48 41 19 29 63 44 62 27 26 12 43 61 17 30 63</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 31 15 35 59 42 8 19 11 59 56 46 26 40 55 57 31 38 1 61 14 29 39 19 38 55</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 49 37 55 3 6 58 60 26 49 51 59 12 19 47 1 33 18 40 21 51 11 30 26 6 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 35 16 19 52 4 4 43 14 8 58 13 23 10 15 31 29 33 38 50 57 22 49 59 43 29</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 5 34 9 12 60 46 49 36 57 4 57 31 50 30 60 10 24 45 32 26 54 46 13 48 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 33 54 26 51 18 34 14 53 18 14 25 37 47 8 4 57 14 14 27 48 6 50 14 48 7</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 37 4 44 41 1 38 21 51 20 11 24 37 59 15 61 8 34 49 49 40 36 25 20 56 53</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 55 35 25 58 37 21 21 28 27 49 17 17 52 58 32 4 14 52 56 4 41 16 14 21 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 28 52 10 17 32 30 23 16 11 19 52 7 52 14 33 13 6 47 1 54 36 12 24 4 59</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] TRUE TRUE FALSE TRUE TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-12-13 285137 78 F ICU B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-10-20 F35553 51 M ICU B_STPHY_AURS S NA S NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-11-18 956065 89 F Clinical B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2002-11-04 304347 62 M Clinical B_STRPT_PNMN S NA NA S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-08-19 A49852 70 M Clinical B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 36 more variables: AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;, CZO &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FEP &lt;rsi&gt;, CXM &lt;rsi&gt;, FOX &lt;rsi&gt;, CTX &lt;rsi&gt;, CAZ &lt;rsi&gt;, CRO &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># GEN &lt;rsi&gt;, TOB &lt;rsi&gt;, AMK &lt;rsi&gt;, KAN &lt;rsi&gt;, TMP &lt;rsi&gt;, SXT &lt;rsi&gt;,</span></span>
@ -253,16 +250,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: condition [3]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 523893 2015-04-13 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 89F578 2007-03-17 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E9C268 2004-06-11 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> EF6234 2007-04-30 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 960787 2016-03-27 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 835073 2013-09-27 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 559068 2016-01-03 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> D27318 2003-12-18 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 984417 2004-06-09 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 389884 2004-06-07 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 6D2377 2009-12-30 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> A92398 2005-05-14 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B26873 2011-01-09 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> D80438 2017-07-03 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 74D480 2012-10-09 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 1B0933 2003-09-28 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 092034 2006-06-12 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B32F57 2004-04-17 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 422833 2017-05-26 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 620753 2016-10-15 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@ -274,19 +271,19 @@
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [186]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2015-04-13 523893 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2007-03-17 89F578 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ICU 2004-06-11 E9C268 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2007-04-30 EF6234 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2016-03-27 960787 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2013-09-27 835073 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2016-01-03 559068 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ICU 2003-12-18 D27318 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2004-06-09 984417 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2004-06-07 389884 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [178]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2009-12-30 6D2377 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2005-05-14 A92398 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2011-01-09 B26873 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2017-07-03 D80438 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2012-10-09 74D480 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2003-09-28 1B0933 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2006-06-12 092034 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Outpatient 2004-04-17 B32F57 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2017-05-26 422833 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2016-10-15 620753 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@ -301,9 +298,9 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 123 15 59 79</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 50 11 33 43</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 13 6 10 12</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 102 15 48 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 63 13 40 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 13 8 10 12</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
@ -322,7 +319,7 @@
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Including isolates from ICU.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="co"># but is_new_episode() has a lot more flexibility than first_isolate(),</span></span></span>
@ -333,19 +330,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [195]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 523893 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 89F578 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E9C268 B_STPHY_EPDR ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> EF6234 B_STRPT_PYGN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 960787 B_KLBSL_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 835073 B_STPHY_HMNS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 559068 B_STPHY_CPTS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> D27318 B_STPHY_AURS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 984417 UNKNOWN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 389884 B_STPHY_EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [190]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 6D2377 B_FSBCT Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> A92398 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B26873 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> D80438 B_CRYNB_STRT Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 74D480 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 1B0933 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 092034 B_STPHY_AURS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B32F57 B_STPHY_CONS Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 422833 B_ENTRC_FCLS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 620753 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>

2
reference/ggplot_pca.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9061</small>
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reference/guess_ab_col.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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
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4
reference/index.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
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@ -355,7 +355,7 @@
<code><a href="microorganisms.html">microorganisms</a></code>
</dt>
<dd>Data Set with 48,883 Microorganisms</dd>
<dd>Data Set with 48,050 Microorganisms</dd>
</dl><dl><dt>
<code><a href="microorganisms.codes.html">microorganisms.codes</a></code>

32
reference/intrinsic_resistant.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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
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@ -143,7 +143,7 @@
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 134,659 observations and 2 variables:</p><ul><li><p><code>mo</code><br> Microorganism ID</p></li>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 206,832 observations and 2 variables:</p><ul><li><p><code>mo</code><br> Microorganism ID</p></li>
<li><p><code>ab</code><br> Antibiotic ID</p></li>
</ul></div>
<div class="section level2">
@ -161,20 +161,20 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">intrinsic_resistant</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 134,659 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> B_GRAMP ATM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> B_GRAMP COL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B_GRAMP NAL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> B_GRAMP PLB </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> B_GRAMP TEM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B_ABTRP ATM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B_ABTRP COL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B_ABTRP NAL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B_ABTRP PLB </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B_ABTRP TEM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 134,649 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 206,832 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> B_GRAMP ATM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> B_GRAMP COL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B_GRAMP NAL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> B_GRAMP PLB </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> B_GRAMP TEM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B_ABTRP ATM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B_ABTRP COL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B_ABTRP NAL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B_ABTRP PLB </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B_ABTRP TEM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 206,822 more rows</span></span>
</code></pre></div>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
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6
reference/kurtosis.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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
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@ -172,9 +172,9 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.984464</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.972835</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] 0.07405619</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.07797644</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="">1.8.2.9061</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="">1.8.2.9061</small>
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80
reference/mean_amr_distance.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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
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@ -200,11 +200,11 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 0.25 8 0.025 128 4 0.0625 0.0625 &lt;=0.002</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.025 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.125 4 0.025 32 &lt;=0.001 128 0.002 16 &lt;=0.001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 1 </span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.0547374 -0.1257265 0.8579935 -0.7792959 1.6449694 0.6612495</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.5192145 -0.5192145 -1.4962027 -0.7792959</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.1673708 0.6088797 -0.5278503 1.0746300 -1.2488094 1.3851301</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.0935593 0.9193799 -1.2488094 0.2983795</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@ -214,38 +214,38 @@
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 16 0.5 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B &gt;=32 0.5 1 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 4 0.25 2 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 16 0.5 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 8 &gt;=1 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 2 0.125 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 1 0.5 &gt;=8 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 2 &gt;=1 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 16 &gt;=1 &gt;=8 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 0.125 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A &gt;=64 4 1 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 4 1 &gt;=4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 16 &lt;=0.125 &gt;=4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 2 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 32 1 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 8 0.25 &gt;=4 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &gt;=64 0.5 2 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 0.5 &gt;=4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &gt;=64 2 1 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 &lt;=0.125 2 0.5</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "id" and "tobr"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.036743946 0.196829201 -0.376851467 0.425339766 0.497315583</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [6] -0.848366515 -0.464960905 0.006554142 0.542471648 -0.015075399</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.12023536 0.33318132 0.20872945 0.16343985 -0.14151184 -0.36277928</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.52860021 -0.18662082 -0.02573319 -0.63754106</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 2 0.125 4 1 -0.848366515</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 1 0.5 &gt;=8 0.5 -0.464960905</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 4 0.25 2 4 -0.376851467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 0.125 4 4 -0.015075399</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 2 &gt;=1 4 2 0.006554142</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 16 0.5 4 1 0.036743946</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B &gt;=32 0.5 1 8 0.196829201</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 16 0.5 4 4 0.425339766</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 8 &gt;=1 4 4 0.497315583</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 16 &gt;=1 &gt;=8 1 0.542471648</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 &lt;=0.125 2 0.5 -0.63754106</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 8 0.25 &gt;=4 0.5 -0.36277928</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 0.5 &gt;=4 1 -0.18662082</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 32 1 1 1 -0.14151184</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &gt;=64 2 1 0.5 -0.02573319</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A &gt;=64 4 1 0.5 0.12023536</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 2 2 2 0.16343985</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 16 &lt;=0.125 &gt;=4 4 0.20872945</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 4 1 &gt;=4 4 0.33318132</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &gt;=64 0.5 2 4 0.52860021</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@ -257,17 +257,17 @@
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C 4 0.25 2 4 -0.376851467 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 G 1 0.5 &gt;=8 0.5 -0.464960905 0.08810944</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 J 16 0.125 4 4 -0.015075399 0.36177607</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 H 2 &gt;=1 4 2 0.006554142 0.38340561</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 A 16 0.5 4 1 0.036743946 0.41359541</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 2 0.125 4 1 -0.848366515 0.47151505</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 B &gt;=32 0.5 1 8 0.196829201 0.57368067</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 D 16 0.5 4 4 0.425339766 0.80219123</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 E 8 &gt;=1 4 4 0.497315583 0.87416705</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 I 16 &gt;=1 &gt;=8 1 0.542471648 0.91932312</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C 16 &lt;=0.125 &gt;=4 4 0.20872945 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 D 8 2 2 2 0.16343985 0.04528960</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 A &gt;=64 4 1 0.5 0.12023536 0.08849408</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 B 4 1 &gt;=4 4 0.33318132 0.12445187</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 I &gt;=64 2 1 0.5 -0.02573319 0.23446263</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 G &gt;=64 0.5 2 4 0.52860021 0.31987077</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 E 32 1 1 1 -0.14151184 0.35024128</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 0.5 &gt;=4 1 -0.18662082 0.39535027</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 F 8 0.25 &gt;=4 0.5 -0.36277928 0.57150872</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 &lt;=0.125 2 0.5 -0.63754106 0.84627050</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>

2
reference/microorganisms.codes.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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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">

48
reference/microorganisms.html
View File

@ -1,5 +1,5 @@
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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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
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@ -127,13 +127,13 @@
</nav><div class="container template-reference-topic">
<div class="row">
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 48,883 Microorganisms</h1>
<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 48,050 Microorganisms</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
<div class="d-none name"><code>microorganisms.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>A data set containing the full microbial taxonomy (<strong>last updated: 12 September, 2022</strong>) of five kingdoms from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF). This data set is the backbone of this <code>AMR</code> package. MO codes can be looked up using <code><a href="as.mo.html">as.mo()</a></code>.</p>
<p>A data set containing the full microbial taxonomy (<strong>last updated: 11 December, 2022</strong>) of five kingdoms from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF). This data set is the backbone of this <code>AMR</code> package. MO codes can be looked up using <code><a href="as.mo.html">as.mo()</a></code>.</p>
</div>
<div class="section level2">
@ -143,7 +143,7 @@
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 48,883 observations and 22 variables:</p><ul><li><p><code>mo</code><br> ID of microorganism as used by this package</p></li>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 48,050 observations and 22 variables:</p><ul><li><p><code>mo</code><br> ID of microorganism as used by this package</p></li>
<li><p><code>fullname</code><br> Full name, like <code>"Escherichia coli"</code>. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon.</p></li>
<li><p><code>status</code> <br> Status of the taxon, either "accepted" or "synonym"</p></li>
<li><p><code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br> Taxonomic rank of the microorganism</p></li>
@ -163,9 +163,9 @@
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
<ul><li><p>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong> International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a>
. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on 12 September, 2022.</p></li>
<li><p>GBIF Secretariat (November 26, 2021). GBIF Backbone Taxonomy. Checklist dataset <a href="https://doi.org/10.15468/39omei" class="external-link">doi:10.15468/39omei</a>
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on 12 September, 2022.</p></li>
. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on 11 December, 2022.</p></li>
<li><p>GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset <a href="https://doi.org/10.15468/39omei" class="external-link">doi:10.15468/39omei</a>
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on 11 December, 2022.</p></li>
<li><p>Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link">https://phinvads.cdc.gov</a></p></li>
</ul></div>
<div class="section level2">
@ -180,10 +180,10 @@
<p>Included taxonomic data are:</p><ul><li><p>All ~34,000 (sub)species from the kingdoms of Archaea and Bacteria</p></li>
<li><p>~7,400 (sub)species from the kingdom of Fungi. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package. Only relevant fungi are covered (such as all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Cryptococcus</em>, <em>Histoplasma</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>~5,000 (sub)species from the kingdom of Protozoa</p></li>
<li><p>~1,500 (sub)species from ~50 other relevant genera from the kingdom of Animalia (such as <em>Strongyloides</em> and <em>Taenia</em>)</p></li>
<li><p>All ~9,400 previously accepted names of all included (sub)species (these were taxonomically renamed)</p></li>
<li><p>~6,900 (sub)species from the kingdom of Fungi. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package. Only relevant fungi are covered (such as all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Cryptococcus</em>, <em>Histoplasma</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>~4,400 (sub)species from the kingdom of Protozoa</p></li>
<li><p>~1,100 (sub)species from ~40 other relevant genera from the kingdom of Animalia (such as <em>Strongyloides</em> and <em>Taenia</em>)</p></li>
<li><p>All ~9,100 previously accepted names of all included (sub)species (these were taxonomically renamed)</p></li>
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
<li><p>The identifier of the parent taxons</p></li>
<li><p>The year and first author of the related scientific publication</p></li>
@ -222,20 +222,20 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">microorganisms</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 48,883 × 22</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 48,050 × 22</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo fullname status kingdom phylum class order family genus</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&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;chr&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> B_ANAER (unknown ana… accep… Bacter… (unkn… (unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> F_FUNGUS (unknown fun… accep… Fungi (unkn… (unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B_GRAMN (unknown Gra… accep… Bacter… (unkn… (unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> B_GRAMP (unknown Gra… accep… Bacter… (unkn… (unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> UNKNOWN (unknown nam… accep… (unkno… (unkn… (unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> F_YEAST (unknown yea… accep… Fungi (unkn… (unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B_[CLS]_ABDTBCTR Abditibacter… accep… Bacter… Armat… Abdi… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B_[FAM]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… Abdi… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">"</span>Abdi… <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B_[ORD]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… Abdi… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B_[CLS]_ADTBCTRA Abditibacter… accep… Bacter… Abdit… Abdi… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 48,873 more rows, and 13 more variables: species &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> B_ANAER (unknown ana… accep… Bacter… (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> F_FUNGUS (unknown fun… accep… Fungi (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B_GRAMN (unknown Gra… accep… Bacter… (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> B_GRAMP (unknown Gra… accep… Bacter… (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> UNKNOWN (unknown nam… accep… (unkno… (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> F_YEAST (unknown yea… accep… Fungi (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B_[FAM]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">"</span>Abdi… <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B_[ORD]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B_[CLS]_ADTBCTRA Abditibacter… accep… Bacter… Abdit… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B_[PHL]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 48,040 more rows, and 13 more variables: species &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># subspecies &lt;chr&gt;, rank &lt;chr&gt;, ref &lt;chr&gt;, source &lt;chr&gt;, lpsn &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># lpsn_parent &lt;chr&gt;, lpsn_renamed_to &lt;chr&gt;, gbif &lt;chr&gt;, gbif_parent &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># gbif_renamed_to &lt;chr&gt;, prevalence &lt;dbl&gt;, snomed &lt;list&gt;</span></span>

2
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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@ -446,9 +446,9 @@
<li><p>Lancefield RC (1933). <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. <em>J Exp Med.</em> 57(4): 571-95; <a href="https://doi.org/10.1084/jem.57.4.571" class="external-link">doi:10.1084/jem.57.4.571</a></p></li>
<li><p>Berends MS <em>et al.</em> (2022). <strong>Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019</strong> <em>Microorganisms</em> 10(9), 1801; <a href="https://doi.org/10.3390/microorganisms10091801" class="external-link">doi:10.3390/microorganisms10091801</a></p></li>
<li><p>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong> International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a>
. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on 12 September, 2022.</p></li>
<li><p>GBIF Secretariat (November 26, 2021). GBIF Backbone Taxonomy. Checklist dataset <a href="https://doi.org/10.15468/39omei" class="external-link">doi:10.15468/39omei</a>
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on 12 September, 2022.</p></li>
. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on 11 December, 2022.</p></li>
<li><p>GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset <a href="https://doi.org/10.15468/39omei" class="external-link">doi:10.15468/39omei</a>
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on 11 December, 2022.</p></li>
<li><p>Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link">https://phinvads.cdc.gov</a></p></li>
</ol></div>
<div class="section level2">

2
reference/mo_source.html
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@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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reference/random.html
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@ -183,43 +183,42 @@
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.001 0.0625 0.002 0.005 0.01 0.25 128 0.125 0.002 0.0625</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.025 0.25 &gt;=256 64 0.002 0.0625 1 0.25 0.01 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 4 1 0.5 0.002 0.025 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01 0.005 0.01 0.25 0.25 16 0.01 32 0.125 32 64 0.001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.002 16 1 0.002 32 32 0.5 0.001 128 128 0.001 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 0.001</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 43 6 16 49 45 14 26 43 40 22 38 32 15 38 8 47 17 22 50 50 37 32 36 18 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 21 32 24 30 24 6 44 26 46 8 27 18 45 44 42 39 24 34 8 37 34 15 17 48 17</span>
<span class="r-in"><span><span class="fu">random_rsi</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'rsi'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S R I S R S I S R R I I R S I S I R R I R S R S I</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I R S S S I S I R R R I R I R I R R R S I R I S I</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.0625 0.01 0.01 1 64 1 64 64 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.002 &lt;=0.001 4 2 1 &lt;=0.001 0.25 0.005 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.025 2 16 0.5 0.5 64 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4 0.005 0.025 32 8 0.025 8 16 64 0.125 4 0.005</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.5 2 0.025 4 0.001 0.5 2 1 0.001 32 4 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 1 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 8 &lt;=0.5 &gt;=16 &lt;=0.5 &lt;=0.5 8 &lt;=0.5 &lt;=0.5 8 1 &gt;=16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] &gt;=16 4 4 1 1 8 &gt;=16 8 4 4 &gt;=16 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 32 2 16 32 4 32 4 16 2 16 2 2 0.25 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] 4 2 16 2 16 2 0.5 0.5 2 32 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 0.25 1 2 2 1 1 1 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 2 2 8 1 0.25 2 0.5 0.25 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 2 0.25 0.25 0.0625 1 &lt;=0.025 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 0.125 4 0.125 1 0.0625 4 1 1 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 4 2 1 4 0.5 0.0625 0.125 1 0.0625 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 1 2 2 0.0625 2 </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 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 13 40 38 28 44 48 11 44 45 45 24 49 41 50 8 42 40 47 41 50 45 40 31 17 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 9 44 40 35 36 40 30 17 25 18 9 14 24 14 30 41 38 16 27 50 12 11 44 46 20</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 15 17 15 13 12 13 12 14 12 17 17 17 13 12 15 12 17 11 11 15 14 14 14 17 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 15 14 17 12 17 11 12 16 14 17 17 11 16 13 16 16 14 16 12 13 12 15 12 17 17</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 23 16 15 25 26 17 26 18 18 19 20 16 17 20 23 16 19 15 26 15 24 17 27 22 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 24 22 25 16 17 16 20 16 19 15 24 16 24 23 16 16 25 23 15 26 20 22 24 25 20</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>

2
reference/resistance_predict.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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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/rsi_translation.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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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/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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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">
@ -171,7 +171,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.0375987</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.05009634</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

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reference/translate.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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">

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