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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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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="">1.8.2.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9011</small>
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@ -325,69 +325,69 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-08-15</td>
<td align="center">V8</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-01-31</td>
<td align="center">L3</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-03-22</td>
<td align="center">Y6</td>
<td align="center">2012-05-04</td>
<td align="center">P4</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-02-11</td>
<td align="center">I1</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2014-03-03</td>
<td align="center">N3</td>
<td align="center">Hospital A</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">2016-09-06</td>
<td align="center">M1</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-09-29</td>
<td align="center">F5</td>
<tr class="even">
<td align="center">2014-01-03</td>
<td align="center">T9</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2013-12-05</td>
<td align="center">T7</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-03-01</td>
<td align="center">H10</td>
<td align="center">2017-01-24</td>
<td align="center">A5</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">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
</tbody>
@ -422,16 +422,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,361</td>
<td align="right">51.81%</td>
<td align="right">10,361</td>
<td align="right">51.81%</td>
<td align="right">10,425</td>
<td align="right">52.13%</td>
<td align="right">10,425</td>
<td align="right">52.13%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,639</td>
<td align="right">48.20%</td>
<td align="right">9,575</td>
<td align="right">47.88%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -488,9 +488,9 @@ Longest: 1</p>
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,672 'phenotype-based' first isolates (53.4% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,700 'phenotype-based' first isolates (53.5% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.4% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<p>So only 53.5% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
@ -499,7 +499,7 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,672 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,700 isolates for analysis. Now our data looks like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
<table style="width:100%;" class="table">
@ -537,26 +537,10 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2017-08-15</td>
<td align="center">V8</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>
<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">2012-03-22</td>
<td align="center">Y6</td>
<td align="center">Hospital D</td>
<td align="left">5</td>
<td align="center">2013-12-05</td>
<td align="center">T7</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -568,11 +552,59 @@ Longest: 1</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="center">2017-01-24</td>
<td align="center">A5</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2011-12-23</td>
<td align="center">B5</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="left">8</td>
<td align="center">2012-06-13</td>
<td align="center">C3</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">9</td>
<td align="center">2013-06-02</td>
<td align="center">G6</td>
<td align="center">Hospital B</td>
<td align="center">2017-04-10</td>
<td align="center">C3</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
@ -586,43 +618,11 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2014-03-13</td>
<td align="center">C9</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">11</td>
<td align="center">2016-12-02</td>
<td align="center">S9</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">13</td>
<td align="center">2017-06-05</td>
<td align="center">U8</td>
<td align="center">2013-09-19</td>
<td align="center">R2</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -653,8 +653,8 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,672<br>
Available: 10,672 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,700<br>
Available: 10,700 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -671,33 +671,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,684</td>
<td align="right">43.89%</td>
<td align="right">4,684</td>
<td align="right">43.89%</td>
<td align="right">4,656</td>
<td align="right">43.51%</td>
<td align="right">4,656</td>
<td align="right">43.51%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,763</td>
<td align="right">25.89%</td>
<td align="right">7,447</td>
<td align="right">69.78%</td>
<td align="right">2,775</td>
<td align="right">25.93%</td>
<td align="right">7,431</td>
<td align="right">69.45%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,092</td>
<td align="right">2,097</td>
<td align="right">19.60%</td>
<td align="right">9,539</td>
<td align="right">89.38%</td>
<td align="right">9,528</td>
<td align="right">89.05%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,133</td>
<td align="right">10.62%</td>
<td align="right">10,672</td>
<td align="right">1,172</td>
<td align="right">10.95%</td>
<td align="right">10,700</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -744,72 +744,12 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-08-15</td>
<td align="center">V8</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>
<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">2010-05-16</td>
<td align="center">G10</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-11-18</td>
<td align="center">Z3</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2010-06-25</td>
<td align="center">W9</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">2014-12-03</td>
<td align="center">A1</td>
<td align="center">2017-01-24</td>
<td align="center">A5</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
@ -819,18 +759,78 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-11-26</td>
<td align="center">A3</td>
<td align="center">2011-12-23</td>
<td align="center">B5</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-03-01</td>
<td align="center">W9</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-10-21</td>
<td align="center">M6</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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">2017-09-13</td>
<td align="center">D7</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-06-26</td>
<td align="center">L7</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -854,50 +854,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2201</td>
<td align="center">138</td>
<td align="center">2345</td>
<td align="center">4684</td>
<td align="center">2196</td>
<td align="center">122</td>
<td align="center">2338</td>
<td align="center">4656</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3471</td>
<td align="center">156</td>
<td align="center">1057</td>
<td align="center">4684</td>
<td align="center">3393</td>
<td align="center">163</td>
<td align="center">1100</td>
<td align="center">4656</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3422</td>
<td align="center">3421</td>
<td align="center">0</td>
<td align="center">1262</td>
<td align="center">4684</td>
<td align="center">1235</td>
<td align="center">4656</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4073</td>
<td align="center">4068</td>
<td align="center">0</td>
<td align="center">611</td>
<td align="center">4684</td>
<td align="center">588</td>
<td align="center">4656</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">1133</td>
<td align="center">1133</td>
<td align="center">1172</td>
<td align="center">1172</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">898</td>
<td align="center">43</td>
<td align="center">192</td>
<td align="center">1133</td>
<td align="center">905</td>
<td align="center">39</td>
<td align="center">228</td>
<td align="center">1172</td>
</tr>
</tbody>
</table>
@ -920,34 +920,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4073</td>
<td align="center">4068</td>
<td align="center">0</td>
<td align="center">611</td>
<td align="center">4684</td>
<td align="center">588</td>
<td align="center">4656</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1009</td>
<td align="center">1068</td>
<td align="center">0</td>
<td align="center">124</td>
<td align="center">1133</td>
<td align="center">104</td>
<td align="center">1172</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2462</td>
<td align="center">2464</td>
<td align="center">0</td>
<td align="center">301</td>
<td align="center">2763</td>
<td align="center">311</td>
<td align="center">2775</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">2092</td>
<td align="center">2092</td>
<td align="center">2097</td>
<td align="center">2097</td>
</tr>
</tbody>
</table>
@ -961,7 +961,7 @@ Longest: 24</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5403861</span></span></code></pre></div>
<span><span class="co"># [1] 0.5437383</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@ -975,19 +975,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5367144</td>
<td align="center">0.5490758</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5420436</td>
<td align="center">0.5407427</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5339252</td>
<td align="center">0.5584975</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5478097</td>
<td align="center">0.5302961</td>
</tr>
</tbody>
</table>
@ -1008,23 +1008,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5367144</td>
<td align="center">3214</td>
<td align="center">0.5490758</td>
<td align="center">3138</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5420436</td>
<td align="center">3758</td>
<td align="center">0.5407427</td>
<td align="center">3743</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5339252</td>
<td align="center">1577</td>
<td align="center">0.5584975</td>
<td align="center">1624</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5478097</td>
<td align="center">2123</td>
<td align="center">0.5302961</td>
<td align="center">2195</td>
</tr>
</tbody>
</table>
@ -1047,27 +1047,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7743382</td>
<td align="center">0.8695559</td>
<td align="center">0.9739539</td>
<td align="center">0.7637457</td>
<td align="center">0.8737113</td>
<td align="center">0.9755155</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8305384</td>
<td align="center">0.8905560</td>
<td align="center">0.9841130</td>
<td align="center">0.8054608</td>
<td align="center">0.9112628</td>
<td align="center">0.9778157</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7853782</td>
<td align="center">0.8910604</td>
<td align="center">0.9768368</td>
<td align="center">0.7895495</td>
<td align="center">0.8879279</td>
<td align="center">0.9819820</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5363289</td>
<td align="center">0.5398188</td>
<td align="center">0.0000000</td>
<td align="center">0.5363289</td>
<td align="center">0.5398188</td>
</tr>
</tbody>
</table>
@ -1092,23 +1092,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">53.7%</td>
<td align="right">26.5%</td>
<td align="right">54.9%</td>
<td align="right">26.7%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.2%</td>
<td align="right">26.3%</td>
<td align="right">54.1%</td>
<td align="right">27.4%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">53.4%</td>
<td align="right">25.1%</td>
<td align="right">55.8%</td>
<td align="right">27.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">54.8%</td>
<td align="right">27.1%</td>
<td align="right">53.0%</td>
<td align="right">26.1%</td>
</tr>
</tbody>
</table>
@ -1206,16 +1206,16 @@ Longest: 24</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class &lt;mic&gt;</span></span>
<span><span class="co"># [1] 0.125 64 256 0.005 0.001 0.025 2 256 16 256 </span></span>
<span><span class="co"># [11] 0.002 0.25 0.002 4 64 256 16 0.01 0.025 0.025 </span></span>
<span><span class="co"># [21] 8 8 4 0.005 32 1 0.0625 0.125 0.125 0.025 </span></span>
<span><span class="co"># [31] 4 0.025 0.005 16 0.001 256 8 0.002 0.0625 0.0625</span></span>
<span><span class="co"># [41] 256 0.25 4 0.005 0.5 16 64 0.002 0.125 4 </span></span>
<span><span class="co"># [51] 128 32 8 0.125 0.005 128 0.01 0.5 128 0.025 </span></span>
<span><span class="co"># [61] 0.125 0.002 64 0.005 0.001 0.01 64 0.01 0.01 16 </span></span>
<span><span class="co"># [71] 32 64 16 1 64 0.002 8 0.0625 0.125 0.01 </span></span>
<span><span class="co"># [81] 32 2 0.125 8 128 0.005 0.01 0.002 0.5 0.25 </span></span>
<span><span class="co"># [91] 0.01 1 64 0.025 0.25 2 256 0.0625 0.001 0.002</span></span></code></pre></div>
<span><span class="co"># [1] 8 0.001 0.0625 0.025 128 0.005 16 64 &gt;=256 128 </span></span>
<span><span class="co"># [11] 128 0.5 0.005 0.005 &gt;=256 16 0.025 0.01 16 16 </span></span>
<span><span class="co"># [21] 2 32 0.01 &gt;=256 16 4 0.0625 8 128 1 </span></span>
<span><span class="co"># [31] 0.25 &gt;=256 8 64 0.01 32 0.25 32 0.25 8 </span></span>
<span><span class="co"># [41] 0.25 128 16 1 0.5 0.5 0.01 2 64 0.002 </span></span>
<span><span class="co"># [51] &gt;=256 2 0.001 8 0.0625 16 0.025 64 16 0.5 </span></span>
<span><span class="co"># [61] 128 16 0.025 16 8 128 0.001 &gt;=256 2 0.001 </span></span>
<span><span class="co"># [71] 16 1 32 16 16 0.25 0.025 32 0.0625 0.125 </span></span>
<span><span class="co"># [81] 0.25 16 128 0.001 1 0.25 0.001 0.01 8 4 </span></span>
<span><span class="co"># [91] 128 0.025 2 0.005 4 16 16 0.001 0.5 0.001</span></span></code></pre></div>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1242,10 +1242,10 @@ Longest: 24</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 &lt;disk&gt;</span></span>
<span><span class="co"># [1] 26 20 31 29 17 23 21 22 28 21 30 24 28 29 31 26 21 29 27 18 18 24 18 20 26</span></span>
<span><span class="co"># [26] 19 23 21 29 25 25 18 21 22 28 29 30 20 20 23 23 30 23 26 23 30 31 30 29 25</span></span>
<span><span class="co"># [51] 19 25 31 18 30 31 25 27 28 29 27 22 26 29 23 18 24 20 20 17 21 19 21 23 28</span></span>
<span><span class="co"># [76] 21 30 23 31 17 19 17 31 17 29 17 26 17 23 26 27 18 21 24 19 22 20 22 31 18</span></span></code></pre></div>
<span><span class="co"># [1] 30 18 18 30 21 28 31 27 24 20 27 20 27 21 27 17 22 19 28 23 19 25 21 17 21</span></span>
<span><span class="co"># [26] 24 22 27 26 18 22 17 18 21 26 17 17 22 31 24 30 20 28 23 17 29 19 30 22 24</span></span>
<span><span class="co"># [51] 25 22 18 19 30 24 19 26 17 18 17 21 26 18 31 21 24 24 19 30 30 18 27 18 18</span></span>
<span><span class="co"># [76] 25 26 22 31 26 19 17 24 24 22 28 17 26 17 19 30 18 20 18 18 18 27 23 25 30</span></span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>

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articles/EUCAST.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9011</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="">1.8.2.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9011</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -314,18 +314,18 @@ Unique: 2</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 R R R I R R</span></span>
<span><span class="co"># 2 R R S R I R</span></span>
<span><span class="co"># 3 I R S S R S</span></span>
<span><span class="co"># 4 I I S R R S</span></span>
<span><span class="co"># 5 I R I I R I</span></span>
<span><span class="co"># 6 S R I R R R</span></span>
<span><span class="co"># 1 I S S S S S</span></span>
<span><span class="co"># 2 I S S I S I</span></span>
<span><span class="co"># 3 R R S S S S</span></span>
<span><span class="co"># 4 S S S R R R</span></span>
<span><span class="co"># 5 R R R R R S</span></span>
<span><span class="co"># 6 I R I R I R</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 R</span></span>
<span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -357,40 +357,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3199</td>
<td align="right">63.98%</td>
<td align="right">3199</td>
<td align="right">63.98%</td>
<td align="right">3214</td>
<td align="right">64.28%</td>
<td align="right">3214</td>
<td align="right">64.28%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1012</td>
<td align="right">20.24%</td>
<td align="right">4211</td>
<td align="right">84.22%</td>
<td align="right">967</td>
<td align="right">19.34%</td>
<td align="right">4181</td>
<td align="right">83.62%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">428</td>
<td align="right">8.56%</td>
<td align="right">4639</td>
<td align="right">92.78%</td>
<td align="right">480</td>
<td align="right">9.60%</td>
<td align="right">4661</td>
<td align="right">93.22%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">252</td>
<td align="right">5.04%</td>
<td align="right">4891</td>
<td align="right">97.82%</td>
<td align="right">224</td>
<td align="right">4.48%</td>
<td align="right">4885</td>
<td align="right">97.70%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">109</td>
<td align="right">2.18%</td>
<td align="right">115</td>
<td align="right">2.30%</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="">1.8.2.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9011</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/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="">1.8.2.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9011</small>
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2
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@ -177,7 +177,7 @@
</h2>
<p>A data set with 48,787 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>, <em>ref</em>, <em>source</em>, <em>lpsn</em>, <em>lpsn_parent</em>, <em>lpsn_renamed_to</em>, <em>gbif</em>, <em>gbif_parent</em>, <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 10 October 2022 08:13:13 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p>It was last updated on 10 October 2022 18:22:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">original R Data Structure (RDS) file</a> (1.1 MB)<br>
@ -449,7 +449,7 @@
</h2>
<p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 10 October 2022 08:13:13 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 10 October 2022 18:22:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">original R Data Structure (RDS) file</a> (36 kB)<br>
@ -622,7 +622,7 @@
</h2>
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 10 October 2022 08:13:13 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 10 October 2022 18:22:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">original R Data Structure (RDS) file</a> (4 kB)<br>
@ -754,7 +754,7 @@
</h2>
<p>A data set with 20,369 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 10 October 2022 08:13:13 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p>It was last updated on 10 October 2022 18:22:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">original R Data Structure (RDS) file</a> (49 kB)<br>
@ -913,7 +913,7 @@
</h2>
<p>A data set with 134,659 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 10 October 2022 08:13:13 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p>It was last updated on 10 October 2022 18:22:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><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>
@ -1185,7 +1185,7 @@
</h2>
<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 10 October 2022 08:13:13 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p>It was last updated on 10 October 2022 18:22:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">original R Data Structure (RDS) file</a> (3 kB)<br>
@ -1302,7 +1302,7 @@
</h2>
<p>A data set with 2,000 rows and 46 columns, containing the following column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>, <em>ward</em>, <em>mo</em>, <em>PEN</em>, <em>OXA</em>, <em>FLC</em>, <em>AMX</em>, <em>AMC</em>, <em>AMP</em>, <em>TZP</em>, <em>CZO</em>, <em>FEP</em>, <em>CXM</em>, <em>FOX</em>, <em>CTX</em>, <em>CAZ</em>, <em>CRO</em>, <em>GEN</em>, <em>TOB</em>, <em>AMK</em>, <em>KAN</em>, <em>TMP</em>, <em>SXT</em>, <em>NIT</em>, <em>FOS</em>, <em>LNZ</em>, <em>CIP</em>, <em>MFX</em>, <em>VAN</em>, <em>TEC</em>, <em>TCY</em>, <em>TGC</em>, <em>DOX</em>, <em>ERY</em>, <em>CLI</em>, <em>AZM</em>, <em>IPM</em>, <em>MEM</em>, <em>MTR</em>, <em>CHL</em>, <em>COL</em>, <em>MUP</em> and <em>RIF</em>.</p>
<p>This data set is in R available as <code>example_isolates</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 10 October 2022 08:13:13 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
<p>It was last updated on 10 October 2022 18:22:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
<div class="section level3">
<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
</h3>
@ -1707,7 +1707,7 @@
</h2>
<p>A data set with 3,000 rows and 8 columns, containing the following column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>, <em>bacteria</em>, <em>AMX</em>, <em>AMC</em>, <em>CIP</em> and <em>GEN</em>.</p>
<p>This data set is in R available as <code>example_isolates_unclean</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 10 October 2022 08:13:13 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
<p>It was last updated on 10 October 2022 18:22:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
<div class="section level3">
<h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>
</h3>

2
articles/index.html
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articles/welcome_to_AMR.html
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authors.html
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index.html
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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="">1.8.2.9008</small>
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news/index.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
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@ -127,10 +127,10 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="1.8.2.9008" id="amr-1829008">AMR 1.8.2.9008<a class="anchor" aria-label="anchor" href="#amr-1829008"></a></h2>
<h2 class="pkg-version" data-toc-text="1.8.2.9011" id="amr-1829011">AMR 1.8.2.9011<a class="anchor" aria-label="anchor" href="#amr-1829011"></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-1-8-2-9008">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9008"></a></h4>
<h4 id="breaking-1-8-2-9011">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9011"></a></h4>
<ul><li>Removed all species of the taxonomic kingdom Chromista 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>
<li>Chromista are not relevant when it comes to antimicrobial resistance, thus lacking the primary scope of this package</li>
<li>Chromista are almost never clinically relevant, thus lacking the secondary scope of this package</li>
@ -140,7 +140,7 @@
<li>The <code><a href="../reference/mo_matching_score.html">mo_matching_score()</a></code> now count deletions and substitutions as 2 instead of 1, which impacts the outcome of <code><a href="../reference/as.mo.html">as.mo()</a></code> and any <code>mo_*()</code> function</li>
</ul></div>
<div class="section level4">
<h4 id="new-1-8-2-9008">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9008"></a></h4>
<h4 id="new-1-8-2-9011">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9011"></a></h4>
<ul><li>EUCAST 2022 and CLSI 2022 guidelines have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.</li>
<li>All new algorithm for <code><a href="../reference/as.mo.html">as.mo()</a></code> (and thus internally all <code>mo_*()</code> functions) while still following our original set-up as described in our paper (DOI 10.18637/jss.v104.i03).<ul><li>A new argument <code>keep_synonyms</code> allows to <em>not</em> correct for updated taxonomy, in favour of the now deleted argument <code>allow_uncertain</code>
</li>
@ -150,13 +150,14 @@
<li>Function <code><a href="../reference/mean_amr_distance.html">mean_amr_distance()</a></code> to calculate the mean AMR distance. The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand.</li>
<li>Function <code><a href="../reference/as.rsi.html">rsi_interpretation_history()</a></code> to view the history of previous runs of <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. This returns a ‘logbook’ with the selected guideline, reference table and specific interpretation of each row in a data set on which <code><a href="../reference/as.rsi.html">as.rsi()</a></code> was run.</li>
<li>Function <code><a href="../reference/mo_property.html">mo_current()</a></code> to get the currently valid taxonomic name of a microorganism</li>
<li>Function <code><a href="../reference/add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code> to add custom antimicrobial codes and names to the <code>AMR</code> package</li>
<li>Support for <code>data.frame</code>-enhancing R packages, more specifically: <code><a href="https://Rdatatable.gitlab.io/data.table/reference/data.table.html" class="external-link">data.table::data.table</a></code>, <code><a href="https://rdrr.io/pkg/janitor/man/tabyl.html" class="external-link">janitor::tabyl</a></code>, <code><a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a></code>, and <code>tsibble::tsibble</code>. AMR package functions that have a data set as output (such as <code><a href="../reference/proportion.html">rsi_df()</a></code> and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code>), will now return the same data type as the input.</li>
<li>All data sets in this package are now exported as <code>tibble</code>, instead of base R <code>data.frame</code>s. Older R versions are still supported.</li>
<li>Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. We are very grateful for the valuable input by our colleagues from other countries. The <code>AMR</code> package is now available in 16 languages.</li>
<li>Our data sets are now also continually exported to Apache Feather and Apache Parquet formats. You can find more info <a href="https://msberends.github.io/AMR/articles/datasets.html">in this article on our website</a>.</li>
</ul></div>
<div class="section level4">
<h4 id="changed-1-8-2-9008">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9008"></a></h4>
<h4 id="changed-1-8-2-9011">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9011"></a></h4>
<ul><li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</li>
<li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on <code>NA</code> values (e.g. <code>as.rsi(as.disk(NA), ...)</code>)</li>
<li>Removed <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> for MIC values, since MIC are not integer values and running <code><a href="https://rdrr.io/r/base/table.html" class="external-link">table()</a></code> on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on <code>factor</code>s work)</li>
@ -179,9 +180,10 @@
<li>Black and white message texts are now reversed in colour if using an RStudio dark theme</li>
<li>
<code><a href="../reference/mo_property.html">mo_snomed()</a></code> now returns class <code>character</code>, not <code>numeric</code> anymore (to make long SNOMED codes readable)</li>
<li>Fix for using <code><a href="../reference/as.ab.html">as.ab()</a></code> on <code>NA</code> values</li>
</ul></div>
<div class="section level4">
<h4 id="other-1-8-2-9008">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9008"></a></h4>
<h4 id="other-1-8-2-9011">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9011"></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 and Anton Mymrikov 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>

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datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2022-10-10T08:15Z
last_built: 2022-10-10T18:24Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<img src="../logo.svg" class="logo" alt=""><h1>Add Manual Antimicrobials to This Package</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/add_custom_antimicrobials.R" class="external-link"><code>R/add_custom_antimicrobials.R</code></a></small>
<div class="d-none name"><code>add_custom_antimicrobials.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>With <code>add_custom_antimicrobials()</code> you can add your own manual antimicrobial codes to the <code>AMR</code> package.</p>
</div>
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">add_custom_antimicrobials</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">clear_custom_antimicrobials</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> resembling the <a href="antibiotics.html">antibiotics</a> data set, at least containing columns "ab" and "name"</p></dd>
</dl></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>Due to how <span style="R">R</span> works, the <code>add_custom_antimicrobials()</code> function has to be run in every <span style="R">R</span> session - added antimicrobials are not stored between sessions and are thus lost when <span style="R">R</span> is exited. It is possible to save the antimicrobial additions to your <code>.Rprofile</code> file to circumvent this, for example:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span></span>
<span><span class="fu"><a href="../reference/add_custom_antimicrobials.html">add_custom_antimicrobials</a></span><span class="op">(</span></span>
<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>ab <span class="op">=</span> <span class="st">"TEST"</span>,</span>
<span> name <span class="op">=</span> <span class="st">"Test Antibiotic"</span>,</span>
<span> group <span class="op">=</span> <span class="st">"Test Group"</span><span class="op">)</span></span>
<span><span class="op">)</span></span></code></pre><p></p></div>
<p>Use <code>clear_custom_antimicrobials()</code> to clear the previously added antimicrobials.</p>
</div>
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
</div>
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<p></p><p><code>AMR</code> (for R). Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><a target="_blank" href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
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22
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -190,16 +190,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1943-01-25 79 79.70685 56</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1995-08-08 27 27.17260 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1984-05-25 38 38.37808 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1961-04-13 61 61.49315 38</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1975-12-08 46 46.83836 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1994-09-30 28 28.02740 5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1998-12-17 23 23.81370 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1977-02-03 45 45.68219 22</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1951-12-10 70 70.83288 48</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1949-05-23 73 73.38356 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-05-19 23 23.39452 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1950-08-05 72 72.18082 49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1979-11-26 42 42.87123 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1991-10-28 30 30.95068 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1938-03-15 84 84.57260 61</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1986-05-15 36 36.40548 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1986-02-23 36 36.62740 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1965-11-25 56 56.87397 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1949-10-01 73 73.02466 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1959-07-24 63 63.21370 40</span>
</code></pre></div>
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@ -10,7 +10,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
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3
reference/as.ab.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="">1.8.2.9008</small>
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@ -175,6 +175,7 @@
<li><p>Digitalised paper records, leaving artefacts like 0/o/O (zero and O's), B/8, n/r, etc.</p></li>
</ul><p>Use the <code><a href="ab_property.html">ab_*</a></code> functions to get properties based on the returned antibiotic ID, see <em>Examples</em>.</p>
<p>Note: the <code>as.ab()</code> and <code><a href="ab_property.html">ab_*</a></code> functions may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems.</p>
<p>You can add your own manual codes to be considered by <code>as.ab()</code> and all <code><a href="ab_property.html">ab_*</a></code> functions, see <code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code>.</p>
</div>
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>

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@ -484,16 +484,16 @@ 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 × 13</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_consid…¹ mo_in…² mo_conside…³ guide…⁴</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> 2022-10-10 <span style="color: #949494;">08:15:37</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> 2022-10-10 <span style="color: #949494;">08:15:37</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-10-10 <span style="color: #949494;">08:15:37</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-10-10 <span style="color: #949494;">08:15:37</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-10-10 <span style="color: #949494;">08:15:37</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-10-10 <span style="color: #949494;">08:15:38</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> 2022-10-10 <span style="color: #949494;">08:15:38</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> 2022-10-10 <span style="color: #949494;">08:15:38</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> 2022-10-10 <span style="color: #949494;">08:15:38</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> 2022-10-10 <span style="color: #949494;">08:15:38</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> 2022-10-10 <span style="color: #949494;">18:24:54</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> 2022-10-10 <span style="color: #949494;">18:24:54</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-10-10 <span style="color: #949494;">18:24:54</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-10-10 <span style="color: #949494;">18:24:54</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-10-10 <span style="color: #949494;">18:24:55</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-10-10 <span style="color: #949494;">18:24:55</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> 2022-10-10 <span style="color: #949494;">18:24:55</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> 2022-10-10 <span style="color: #949494;">18:24:55</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> 2022-10-10 <span style="color: #949494;">18:24:55</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> 2022-10-10 <span style="color: #949494;">18:24:55</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, 6 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;"># breakpoint_S &lt;dbl&gt;, breakpoint_R &lt;dbl&gt;, input &lt;dbl&gt;, interpretation &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># and abbreviated variable names ¹​ab_considered, ²​mo_input, ³​mo_considered,</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>
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reference/availability.html
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@ -10,7 +10,7 @@
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reference/bug_drug_combinations.html
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@ -10,7 +10,7 @@
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reference/count.html
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@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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2
reference/custom_eucast_rules.html
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@ -10,7 +10,7 @@
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2
reference/dosage.html
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@ -10,7 +10,7 @@
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2
reference/eucast_rules.html
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@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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2
reference/example_isolates.html
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@ -10,7 +10,7 @@
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2
reference/example_isolates_unclean.html
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@ -10,7 +10,7 @@
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17
reference/first_isolate.html
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@ -12,7 +12,7 @@
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@ -274,22 +274,24 @@
<p>According to Hindler <em>et al.</em> (2007, <a href="https://doi.org/10.1086/511864" class="external-link">doi:10.1086/511864</a>
), there are different methods (algorithms) to select first isolates with increasing reliability: isolate-based, patient-based, episode-based and phenotype-based. All methods select on a combination of the taxonomic genus and species (not subspecies).</p>
<p>All mentioned methods are covered in the <code>first_isolate()</code> function:</p><table class="table table"><tr><td><strong>Method</strong></td><td><strong>Function to apply</strong></td></tr><tr><td><strong>Isolate-based</strong></td><td><code>first_isolate(x, method = "isolate-based")</code></td></tr><tr><td><em>(= all isolates)</em></td><td></td></tr><tr><td></td><td></td></tr><tr><td></td><td></td></tr><tr><td><strong>Patient-based</strong></td><td><code>first_isolate(x, method = "patient-based")</code></td></tr><tr><td><em>(= first isolate per patient)</em></td><td></td></tr><tr><td></td><td></td></tr><tr><td></td><td></td></tr><tr><td><strong>Episode-based</strong></td><td><code>first_isolate(x, method = "episode-based")</code>, or:</td></tr><tr><td><em>(= first isolate per episode)</em></td><td></td></tr><tr><td>- 7-Day interval from initial isolate</td><td>- <code>first_isolate(x, method = "e", episode_days = 7)</code></td></tr><tr><td>- 30-Day interval from initial isolate</td><td>- <code>first_isolate(x, method = "e", episode_days = 30)</code></td></tr><tr><td></td><td></td></tr><tr><td></td><td></td></tr><tr><td><strong>Phenotype-based</strong></td><td><code>first_isolate(x, method = "phenotype-based")</code>, or:</td></tr><tr><td><em>(= first isolate per phenotype)</em></td><td></td></tr><tr><td>- Major difference in any antimicrobial result</td><td>- <code>first_isolate(x, type = "points")</code></td></tr><tr><td>- Any difference in key antimicrobial results</td><td>- <code>first_isolate(x, type = "keyantimicrobials")</code></td></tr></table><div class="section">
<h4 id="isolate-based">Isolate-based<a class="anchor" aria-label="anchor" href="#isolate-based"></a></h4>
<p>All mentioned methods are covered in the <code>first_isolate()</code> function:</p><table class="table table"><tr><td><strong>Method</strong></td><td><strong>Function to apply</strong></td></tr><tr><td><strong>Isolate-based</strong></td><td><code>first_isolate(x, method = "isolate-based")</code></td></tr><tr><td><em>(= all isolates)</em></td><td></td></tr><tr><td></td><td></td></tr><tr><td></td><td></td></tr><tr><td><strong>Patient-based</strong></td><td><code>first_isolate(x, method = "patient-based")</code></td></tr><tr><td><em>(= first isolate per patient)</em></td><td></td></tr><tr><td></td><td></td></tr><tr><td></td><td></td></tr><tr><td><strong>Episode-based</strong></td><td><code>first_isolate(x, method = "episode-based")</code>, or:</td></tr><tr><td><em>(= first isolate per episode)</em></td><td></td></tr><tr><td>- 7-Day interval from initial isolate</td><td>- <code>first_isolate(x, method = "e", episode_days = 7)</code></td></tr><tr><td>- 30-Day interval from initial isolate</td><td>- <code>first_isolate(x, method = "e", episode_days = 30)</code></td></tr><tr><td></td><td></td></tr><tr><td></td><td></td></tr><tr><td><strong>Phenotype-based</strong></td><td><code>first_isolate(x, method = "phenotype-based")</code>, or:</td></tr><tr><td><em>(= first isolate per phenotype)</em></td><td></td></tr><tr><td>- Major difference in any antimicrobial result</td><td>- <code>first_isolate(x, type = "points")</code></td></tr><tr><td>- Any difference in key antimicrobial results</td><td>- <code>first_isolate(x, type = "keyantimicrobials")</code></td></tr></table></div>
<div class="section">
<h3 id="isolate-based">Isolate-based<a class="anchor" aria-label="anchor" href="#isolate-based"></a></h3>
<p>This method does not require any selection, as all isolates should be included. It does, however, respect all arguments set in the <code>first_isolate()</code> function. For example, the default setting for <code>include_unknown</code> (<code>FALSE</code>) will omit selection of rows without a microbial ID.</p>
</div>
<div class="section">
<h4 id="patient-based">Patient-based<a class="anchor" aria-label="anchor" href="#patient-based"></a></h4>
<h3 id="patient-based">Patient-based<a class="anchor" aria-label="anchor" href="#patient-based"></a></h3>
<p>To include every genus-species combination per patient once, set the <code>episode_days</code> to <code>Inf</code>. Although often inappropriate, this method makes sure that no duplicate isolates are selected from the same patient. In a large longitudinal data set, this could mean that isolates are <em>excluded</em> that were found years after the initial isolate.</p>
</div>
<div class="section">
<h4 id="episode-based">Episode-based<a class="anchor" aria-label="anchor" href="#episode-based"></a></h4>
<h3 id="episode-based">Episode-based<a class="anchor" aria-label="anchor" href="#episode-based"></a></h3>
<p>To include every genus-species combination per patient episode once, set the <code>episode_days</code> to a sensible number of days. Depending on the type of analysis, this could be 14, 30, 60 or 365. Short episodes are common for analysing specific hospital or ward data, long episodes are common for analysing regional and national data.</p>
@ -297,7 +299,7 @@
</div>
<div class="section">
<h4 id="phenotype-based">Phenotype-based<a class="anchor" aria-label="anchor" href="#phenotype-based"></a></h4>
<h3 id="phenotype-based">Phenotype-based<a class="anchor" aria-label="anchor" href="#phenotype-based"></a></h3>
<p>This is a more reliable method, since it also <em>weighs</em> the antibiogram (antimicrobial test results) yielding so-called 'first weighted isolates'. There are two different methods to weigh the antibiogram:</p><ol><li><p>Using <code>type = "points"</code> and argument <code>points_threshold</code> (default)</p>
@ -307,9 +309,6 @@
<p>This method only weighs specific antimicrobial agents, called <em>key antimicrobials</em>. Any difference from S to R (or vice versa) in these key antimicrobials will select an isolate as a first weighted isolate. With <code>ignore_I = FALSE</code>, also differences from I to S or R (or vice versa) will lead to this.</p>
<p>Key antimicrobials are internally selected using the <code><a href="key_antimicrobials.html">key_antimicrobials()</a></code> function, but can also be added manually as a variable to the data and set in the <code>col_keyantimicrobials</code> argument. Another option is to pass the output of the <code><a href="key_antimicrobials.html">key_antimicrobials()</a></code> function directly to the <code>col_keyantimicrobials</code> argument.</p></li>
</ol><p>The default method is phenotype-based (using <code>type = "points"</code>) and episode-based (using <code>episode_days = 365</code>). This makes sure that every genus-species combination is selected per patient once per year, while taking into account all antimicrobial test results. If no antimicrobial test results are available in the data set, only the episode-based method is applied at default.</p>
</div>
</div>
</div>

2
reference/g.test.html
View File

@ -10,7 +10,7 @@
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128
reference/get_episode.html
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@ -10,7 +10,7 @@
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@ -177,40 +177,40 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">200</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 49 45 39 34 32 25 14 10 65 5 28 63 26 42 9 56 25 35 9 5 24 67 19 40 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 53 31 61 38 67 8 42 28 40 45 33 4 1 50 5 44 49 26 40 22 64 29 51 58 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 57 31 7 44 53 13 5 64 10 7 11 23 30 59 20 11 5 37 67 60 32 60 59 10 7</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 44 61 49 55 20 3 12 62 20 27 41 46 24 56 13 19 34 47 52 12 11 59 5 54 12</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 17 30 26 43 25 25 56 17 47 18 67 40 27 25 45 23 64 43 8 46 60 8 15 25 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 67 11 2 9 50 4 46 60 59 46 49 14 7 28 9 36 36 50 60 2 12 11 66 48 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 31 65 66 12 54 42 62 3 64 42 61 2 7 9 25 1 16 41 63 37 38 39 51 60 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 59 17 62 41 55 62 59 45 25 33 21 50 62 35 57 57 15 52 40 13 48 33 67 63 33</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 63 26 20 5 31 26 3 19 11 9 24 53 40 62 43 19 12 22 12 52 62 27 5 40 23</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 22 39 56 13 5 58 32 59 38 23 57 51 17 15 24 35 34 37 11 4 64 62 45 32 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 41 50 60 54 61 15 43 63 16 1 39 23 20 14 55 33 20 53 42 37 64 42 46 32 35</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 49 59 13 50 62 32 19 3 31 27 31 1 18 44 12 39 51 1 7 24 61 13 31 21 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 1 4 18 10 31 39 13 33 39 9 10 45 7 58 56 20 32 37 62 61 9 43 52 38 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 57 62 23 29 38 25 54 40 63 46 52 33 45 29 58 37 48 28 48 12 50 29 59 23 18</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 44 22 2 57 36 61 59 49 32 24 34 12 9 4 46 23 20 61 22 13 29 24 19 20 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 28 29 24 5 30 21 6 52 39 21 25 7 16 45 1 44 36 1 64 23 47 10 55 2 55</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 TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE FALSE TRUE TRUE FALSE TRUE TRUE FALSE TRUE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE TRUE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE FALSE FALSE TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE TRUE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE FALSE TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE 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 FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 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> 2002-06-23 798871 82 M Clinical B_ENTRC_FCLS NA NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-07-21 955940 82 F Clinical B_PSDMN_AERG R NA NA R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-06-06 24D393 20 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;">2</span> 2002-07-23 F35553 51 M ICU B_STPHY_AURS R NA S R </span>
<span class="r-out co"><span class="r-pr">#&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>
@ -246,16 +246,16 @@
<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> 545388 2013-07-29 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 107DD1 2012-09-03 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 829641 2011-01-03 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> B54813 2009-10-15 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 942999 2009-02-17 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 0E2483 2007-08-10 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 871360 2004-12-13 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> C58921 2004-01-01 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 468282 2017-05-31 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 762305 2002-11-16 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 622358 2017-09-02 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 401043 2007-12-15 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E19253 2006-08-22 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> E26415 2002-12-28 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 0DBB93 2009-05-08 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 9C1B92 2008-01-25 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 24D393 2002-06-06 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> F81262 2006-05-29 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 189363 2004-06-22 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 118928 2004-02-01 C 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>
@ -267,19 +267,19 @@
<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 [178]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [180]</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 2013-07-29 545388 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2012-09-03 107DD1 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2011-01-03 829641 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU 2009-10-15 B54813 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2009-02-17 942999 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU 2007-08-10 0E2483 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2004-12-13 871360 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2004-01-01 C58921 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2017-05-31 468282 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2002-11-16 762305 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> ICU 2017-09-02 622358 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2007-12-15 401043 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2006-08-22 E19253 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU 2002-12-28 E26415 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2009-05-08 0DBB93 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2008-01-25 9C1B92 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2002-06-06 24D393 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2006-05-29 F81262 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2004-06-22 189363 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2004-02-01 118928 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>
@ -294,9 +294,9 @@
<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 111 15 55 72</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 55 13 37 44</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 12 8 12 12</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 115 14 55 75</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 53 13 36 44</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 12 7 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>
@ -315,7 +315,7 @@
<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] TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE</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>
@ -326,19 +326,19 @@
<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 [191]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [189]</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> 545388 B_KLBSL_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 107DD1 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 829641 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> B54813 B_ENTRC ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 942999 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 0E2483 B_ENTRC_FACM ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 871360 B_KLBSL_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> C58921 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 468282 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 762305 B_PROTS_MRBL Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 622358 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 401043 B_ENTRC_FACM Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E19253 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> E26415 B_STPHY_CONS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 0DBB93 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 9C1B92 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 24D393 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> F81262 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 189363 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 118928 B_STPHY_AURS 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
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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="">1.8.2.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9011</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/ggplot_rsi.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9011</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/guess_ab_col.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9011</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">

7
reference/index.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9011</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">
@ -182,6 +182,11 @@
<code><a href="atc_online.html">atc_online_property()</a></code> <code><a href="atc_online.html">atc_online_groups()</a></code> <code><a href="atc_online.html">atc_online_ddd()</a></code> <code><a href="atc_online.html">atc_online_ddd_units()</a></code>
</dt>
<dd>Get ATC Properties from WHOCC Website</dd>
</dl><dl><dt>
<code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code> <code><a href="add_custom_antimicrobials.html">clear_custom_antimicrobials()</a></code>
</dt>
<dd>Add Manual Antimicrobials to This Package</dd>
</dl></div><div class="section level2">
<h2 id="preparing-data-antimicrobial-resistance">Preparing data: antimicrobial resistance<a class="anchor" aria-label="anchor" href="#preparing-data-antimicrobial-resistance"></a></h2>

2
reference/intrinsic_resistant.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9011</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/italicise_taxonomy.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9011</small>
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2
reference/join.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9011</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/key_antimicrobials.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9011</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">

6
reference/kurtosis.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9011</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">
@ -167,9 +167,9 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.029181</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.977264</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] -0.01584586</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.05527123</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

2
reference/like.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
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2
reference/mdro.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
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78
reference/mean_amr_distance.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="">1.8.2.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9011</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">
@ -195,10 +195,10 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.001 0.125 1 &gt;=128 0.005 &gt;=128 0.001 0.0625 0.005 0.005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 32 0.25 0.005 0.002 &gt;=256 0.125 &gt;=256 1 32 0.025</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.99724839 0.09165344 0.56061793 1.65486841 -0.63428112 1.65486841</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.99724839 -0.06466806 -0.63428112 -0.63428112</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.80748877 -0.30231828 -1.19711705 -1.40670064 1.28312036 -0.46086214</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 1.28312036 0.01476945 0.80748877 -0.82898960</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>
@ -208,38 +208,38 @@
<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 8 0.5 &lt;=0.5 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 1 &lt;=0.0625 2 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 16 0.25 4 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 &lt;=0.0625 &lt;=0.5 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 &lt;=0.0625 4 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 2 0.25 4 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 4 1 1 &lt;=2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 1 4 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 4 &lt;=0.0625 2 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 1 1 1 &lt;=2</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 0.25 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 8 0.125 4 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 2 &gt;=2 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 4 0.25 &lt;=0.25 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 16 0.025 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 2 0.0625 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 4 0.125 0.5 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 1 0.5 2 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 1 0.5 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 8 0.5 &lt;=0.25 1</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "id" and "tobr"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.14820813 -0.44647774 0.81311070 -0.56450282 0.14549038 0.23021697</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.29155363 0.70353938 -0.05788192 -0.68014945</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.10394761 0.66349051 0.01965569 -0.28215761 0.23498276 -0.67838327</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.01166250 0.27821650 -0.10451638 -0.24689831</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> 10 J 1 1 1 &lt;=2 -0.68014945</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 &lt;=0.0625 &lt;=0.5 4 -0.56450282</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 1 &lt;=0.0625 2 &gt;=8 -0.44647774</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 4 1 1 &lt;=2 -0.29155363</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 4 &lt;=0.0625 2 &gt;=8 -0.05788192</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 &lt;=0.0625 4 &gt;=8 0.14549038</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 8 0.5 &lt;=0.5 &gt;=8 0.14820813</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 2 0.25 4 &gt;=8 0.23021697</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 1 4 &gt;=8 0.70353938</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 16 0.25 4 &gt;=8 0.81311070</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 0.0625 1 1 -0.67838327</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 4 0.25 &lt;=0.25 4 -0.28215761</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 8 0.5 &lt;=0.25 1 -0.24689831</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 1 0.5 4 1 -0.10451638</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 4 0.125 0.5 16 0.01166250</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 2 &gt;=2 1 1 0.01965569</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 16 0.25 1 1 0.10394761</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 16 0.025 4 4 0.23498276</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 1 0.5 2 16 0.27821650</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 8 0.125 4 16 0.66349051</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>
@ -251,17 +251,17 @@
<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 16 0.25 4 &gt;=8 0.81311070 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 H 4 1 4 &gt;=8 0.70353938 0.1095713</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 F 2 0.25 4 &gt;=8 0.23021697 0.5828937</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 A 8 0.5 &lt;=0.5 &gt;=8 0.14820813 0.6649026</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 &lt;=0.0625 4 &gt;=8 0.14549038 0.6676203</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 I 4 &lt;=0.0625 2 &gt;=8 -0.05788192 0.8709926</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 4 1 1 &lt;=2 -0.29155363 1.1046643</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 B 1 &lt;=0.0625 2 &gt;=8 -0.44647774 1.2595884</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 D 8 &lt;=0.0625 &lt;=0.5 4 -0.56450282 1.3776135</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 1 1 1 &lt;=2 -0.68014945 1.4932602</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 2 &gt;=2 1 1 0.01965569 0.000000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 G 4 0.125 0.5 16 0.01166250 0.007993193</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 A 16 0.25 1 1 0.10394761 0.084291915</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 I 1 0.5 4 1 -0.10451638 0.124172073</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 16 0.025 4 4 0.23498276 0.215327070</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 H 1 0.5 2 16 0.27821650 0.258560809</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 J 8 0.5 &lt;=0.25 1 -0.24689831 0.266554002</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 D 4 0.25 &lt;=0.25 4 -0.28215761 0.301813300</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 B 8 0.125 4 16 0.66349051 0.643834823</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 F 2 0.0625 1 1 -0.67838327 0.698038966</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
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@ -10,7 +10,7 @@
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reference/microorganisms.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/mo_matching_score.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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2
reference/mo_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="">1.8.2.9008</small>
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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
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/plot.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
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2
reference/proportion.html
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@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</small>
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35
reference/random.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="">1.8.2.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9011</small>
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@ -178,43 +178,42 @@
<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 &lt;mic&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 2 0.5 32 0.01 1 0.5 &lt;=0.002 0.005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.01 32 &gt;=256 0.01 4 0.125 0.025 32 &gt;=256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 1 1 4 0.025 4 64 0.0625 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 32 &lt;=0.002 1 32 0.5 16 1 &gt;=256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 128 32 32 4 &gt;=256 0.005 0.0625 8 &gt;=256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.125 2 64 &lt;=0.002 64 0.5 0.005 </span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 46 43 39 46 43 42 23 46 47 47 49 43 50 47 45 32 40 43 37 43 40 48 21 12 49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 31 42 37 30 8 32 50 16 33 20 11 50 20 43 17 20 21 47 15 48 25 41 18 9 43</span>
<span class="r-in"><span><span class="fu">random_rsi</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;rsi&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R S S I S R I I I R S R R R S R R S R I I I S S I</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I I R S R S S I R I R S R I S S I I S I R R S I I</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 32 0.5 0.001 16 0.001 2 0.0625 0.0625 16 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.025 32 0.5 0.005 16 0.125 0.0625 0.125 0.002 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.01 32 8 16 0.0625</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.002 0.0625 4 0.025 4 0.01 128 0.01 0.25 &gt;=256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 8 0.5 0.002 4 0.005 0.5 16 0.0625 0.25 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] &gt;=256 0.025 &gt;=256 0.125 0.125 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 &gt;=32 16 4 4 16 2 16 4 2 &gt;=32 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 2 &lt;=0.5 &lt;=0.5 4 8 8 1 16 16 &gt;=32 8 &lt;=0.5</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 &lt;=1 2 &gt;=16 4 4 8 &lt;=1 &lt;=1 4 2 4 4 &lt;=1 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] &gt;=16 &lt;=1 &gt;=16 8 &lt;=1 2 &lt;=1 4 4 4 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 &gt;=16 2 0.25 0.125 8 0.25 &gt;=16 1 1 8 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 8 0.5 &gt;=16 0.25 1 0.5 &gt;=16 1 4 0.125 8 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.125 0.125 0.5 0.125 1 0.125 0.5 2 8 8 1 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 4 2 0.125 0.25 1 4 0.5 0.5 8 0.25 0.25 0.125</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 0.25 </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 28 44 33 10 35 18 23 48 50 33 44 27 41 19 40 45 44 42 18 42 38 29 47 47 48</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 44 35 15 34 22 8 39 24 20 46 37 46 19 49 28 29 48 50 15 35 26 8 50 33 30</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 12 17 15 17 14 16 17 13 14 16 16 16 12 13 12 12 14 12 16 17 17 12 15 13 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 14 14 15 13 11 17 15 12 14 16 14 15 15 12 14 14 11 15 12 14 17 14 11 12 16</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 24 22 25 27 24 26 18 22 17 20 24 18 17 20 23 26 15 22 22 21 19 17 16 17 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 15 25 23 22 24 22 16 20 22 17 24 22 27 18 19 27 20 24 15 25 24 24 20 25 23</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>

2
reference/resistance_predict.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="">1.8.2.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9011</small>
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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="">1.8.2.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9011</small>
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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="">1.8.2.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9011</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -166,7 +166,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.001386368</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.02114501</span>
</code></pre></div>
</div>
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9
reference/translate.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="">1.8.2.9008</small>
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@ -160,11 +160,8 @@
<span><span class="fu">utils</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/utils/file.edit.html" class="external-link">file.edit</a></span><span class="op">(</span><span class="st">"~/.Rprofile"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Add e.g. Italian support to that file using:</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>AMR_locale <span class="op">=</span> <span class="st">"Italian"</span><span class="op">)</span></span>
<span><span class="co"># or using:</span></span>
<span><span class="fu">AMR</span><span class="fu">::</span><span class="fu"><a href="../reference/translate.html">set_AMR_locale</a></span><span class="op">(</span><span class="st">"Italian"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># And save the file!</span></span></code></pre><p></p></div>
<span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>AMR_locale <span class="op">=</span> <span class="st">"Italian"</span><span class="op">)</span></span></code></pre><p></p></div>
<p>And then save the file.</p>
<p>Please read about adding or updating a language in <a href="https://github.com/msberends/AMR/wiki/" class="external-link">our Wiki</a>.</p><div class="section">
<h3 id="changing-the-default-language">Changing the Default Language<a class="anchor" aria-label="anchor" href="#changing-the-default-language"></a></h3>

2
search.json
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sitemap.xml
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@ -63,6 +63,9 @@
<url>
<loc>https://msberends.github.io/AMR/reference/ab_property.html</loc>
</url>
<url>
<loc>https://msberends.github.io/AMR/reference/add_custom_antimicrobials.html</loc>
</url>
<url>
<loc>https://msberends.github.io/AMR/reference/age.html</loc>
</url>