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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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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -168,7 +168,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">30 December 2022</h4>
<h4 data-toc-skip class="date">05 January 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="d-none name"><code>AMR.Rmd</code></div>
@ -180,7 +180,7 @@ Berends</h4>
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 30 December 2022.</p>
generated on 05 January 2023.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -236,21 +236,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-12-30</td>
<td align="center">2023-01-05</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2022-12-30</td>
<td align="center">2023-01-05</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2022-12-30</td>
<td align="center">2023-01-05</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -400,42 +400,31 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-10-07</td>
<td align="center">H2</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">2017-08-08</td>
<td align="center">G10</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-01-23</td>
<td align="center">S1</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">2013-01-20</td>
<td align="center">Y2</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2011-06-02</td>
<td align="center">B5</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-09-18</td>
<td align="center">S10</td>
<td align="center">Hospital D</td>
<td align="center">2010-03-18</td>
<td align="center">T1</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
@ -443,28 +432,39 @@ data set:</p>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-07-30</td>
<td align="center">K5</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-07-25</td>
<td align="center">U6</td>
<td align="center">2015-01-19</td>
<td align="center">A2</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2017-11-10</td>
<td align="center">S3</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2015-08-08</td>
<td align="center">N3</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>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -499,16 +499,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,393</td>
<td align="right">51.97%</td>
<td align="right">10,393</td>
<td align="right">51.97%</td>
<td align="right">10,351</td>
<td align="right">51.76%</td>
<td align="right">10,351</td>
<td align="right">51.76%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,607</td>
<td align="right">48.04%</td>
<td align="right">9,649</td>
<td align="right">48.25%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -621,9 +621,9 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,583 'phenotype-based' first isolates (52.9% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,772 'phenotype-based' first isolates (53.9% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 52.9% is suitable for resistance analysis! We can now filter
<p>So only 53.9% 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">
@ -634,7 +634,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<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 10,583 isolates for analysis. Now our data looks
<p>So we end up with 10,772 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>
@ -674,28 +674,60 @@ like:</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2014-10-07</td>
<td align="center">H2</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">2017-08-08</td>
<td align="center">G10</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2013-01-20</td>
<td align="center">Y2</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">2011-06-02</td>
<td align="center">B5</td>
<td align="center">Hospital C</td>
<td align="center">2010-03-18</td>
<td align="center">T1</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">2015-01-19</td>
<td align="center">A2</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</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>
@ -706,25 +738,25 @@ like:</p>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="center">2016-07-30</td>
<td align="center">K5</td>
<td align="center">Hospital A</td>
<td align="center">2017-11-10</td>
<td align="center">S3</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="center">2015-07-25</td>
<td align="center">U6</td>
<td align="center">Hospital B</td>
<td align="left">7</td>
<td align="center">2017-03-22</td>
<td align="center">P2</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
@ -736,38 +768,6 @@ like:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2012-02-07</td>
<td align="center">E10</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2016-06-14</td>
<td align="center">Y3</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -801,8 +801,8 @@ readable:</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,583<br>
Available: 10,583 (100%, NA: 0 = 0%)<br>
Length: 10,772<br>
Available: 10,772 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -827,33 +827,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,619</td>
<td align="right">43.65%</td>
<td align="right">4,619</td>
<td align="right">43.65%</td>
<td align="right">4,699</td>
<td align="right">43.62%</td>
<td align="right">4,699</td>
<td align="right">43.62%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,672</td>
<td align="right">25.25%</td>
<td align="right">7,291</td>
<td align="right">68.89%</td>
<td align="right">2,732</td>
<td align="right">25.36%</td>
<td align="right">7,431</td>
<td align="right">68.98%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,144</td>
<td align="right">20.26%</td>
<td align="right">9,435</td>
<td align="right">89.15%</td>
<td align="right">2,159</td>
<td align="right">20.04%</td>
<td align="right">9,590</td>
<td align="right">89.03%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,148</td>
<td align="right">10.85%</td>
<td align="right">10,583</td>
<td align="right">1,182</td>
<td align="right">10.97%</td>
<td align="right">10,772</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -902,58 +902,73 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-06-02</td>
<td align="center">B5</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">2017-08-08</td>
<td align="center">G10</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-07-25</td>
<td align="center">U6</td>
<td align="center">2015-01-19</td>
<td align="center">A2</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">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">2015-07-05</td>
<td align="center">C5</td>
<td align="center">Hospital A</td>
<td align="center">2017-11-10</td>
<td align="center">S3</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-09-15</td>
<td align="center">E4</td>
<td align="center">2017-03-22</td>
<td align="center">P2</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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-09-11</td>
<td align="center">L10</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -961,34 +976,19 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2013-10-10</td>
<td align="center">V1</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-01-02</td>
<td align="center">R4</td>
<td align="center">2010-02-02</td>
<td align="center">P10</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</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">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -1013,50 +1013,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2200</td>
<td align="center">131</td>
<td align="center">2288</td>
<td align="center">4619</td>
<td align="center">2231</td>
<td align="center">147</td>
<td align="center">2321</td>
<td align="center">4699</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3389</td>
<td align="center">145</td>
<td align="center">1085</td>
<td align="center">4619</td>
<td align="center">3449</td>
<td align="center">182</td>
<td align="center">1068</td>
<td align="center">4699</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3401</td>
<td align="center">3429</td>
<td align="center">0</td>
<td align="center">1218</td>
<td align="center">4619</td>
<td align="center">1270</td>
<td align="center">4699</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4069</td>
<td align="center">4090</td>
<td align="center">0</td>
<td align="center">550</td>
<td align="center">4619</td>
<td align="center">609</td>
<td align="center">4699</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">1148</td>
<td align="center">1148</td>
<td align="center">1182</td>
<td align="center">1182</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">901</td>
<td align="center">44</td>
<td align="center">203</td>
<td align="center">1148</td>
<td align="center">935</td>
<td align="center">39</td>
<td align="center">208</td>
<td align="center">1182</td>
</tr>
</tbody>
</table>
@ -1078,34 +1078,34 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4069</td>
<td align="center">4090</td>
<td align="center">0</td>
<td align="center">550</td>
<td align="center">4619</td>
<td align="center">609</td>
<td align="center">4699</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1048</td>
<td align="center">1071</td>
<td align="center">0</td>
<td align="center">100</td>
<td align="center">1148</td>
<td align="center">111</td>
<td align="center">1182</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2381</td>
<td align="center">2423</td>
<td align="center">0</td>
<td align="center">291</td>
<td align="center">2672</td>
<td align="center">309</td>
<td align="center">2732</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">2144</td>
<td align="center">2144</td>
<td align="center">2159</td>
<td align="center">2159</td>
</tr>
</tbody>
</table>
@ -1137,7 +1137,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5408674</span></span></code></pre></div>
<span><span class="co"># [1] 0.5386186</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
@ -1152,19 +1152,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5445669</td>
<td align="center">0.5404491</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5366764</td>
<td align="center">0.5344360</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5427167</td>
<td align="center">0.5435294</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5413386</td>
<td align="center">0.5391467</td>
</tr>
</tbody>
</table>
@ -1189,23 +1189,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5445669</td>
<td align="center">3175</td>
<td align="center">0.5404491</td>
<td align="center">3251</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5366764</td>
<td align="center">3749</td>
<td align="center">0.5344360</td>
<td align="center">3688</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5427167</td>
<td align="center">1627</td>
<td align="center">0.5435294</td>
<td align="center">1700</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5413386</td>
<td align="center">2032</td>
<td align="center">0.5391467</td>
<td align="center">2133</td>
</tr>
</tbody>
</table>
@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7651007</td>
<td align="center">0.8809266</td>
<td align="center">0.9742368</td>
<td align="center">0.7727176</td>
<td align="center">0.8703980</td>
<td align="center">0.9765908</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8231707</td>
<td align="center">0.9128920</td>
<td align="center">0.9799652</td>
<td align="center">0.8240271</td>
<td align="center">0.9060914</td>
<td align="center">0.9780034</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7911677</td>
<td align="center">0.8910928</td>
<td align="center">0.9805389</td>
<td align="center">0.7986823</td>
<td align="center">0.8868960</td>
<td align="center">0.9795022</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5270522</td>
<td align="center">0.5368226</td>
<td align="center">0.0000000</td>
<td align="center">0.5270522</td>
<td align="center">0.5368226</td>
</tr>
</tbody>
</table>
@ -1278,23 +1278,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.5%</td>
<td align="right">27.0%</td>
<td align="right">54.0%</td>
<td align="right">25.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">53.7%</td>
<td align="right">26.7%</td>
<td align="right">53.4%</td>
<td align="right">25.6%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">54.3%</td>
<td align="right">27.8%</td>
<td align="right">54.4%</td>
<td align="right">28.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">54.1%</td>
<td align="right">27.0%</td>
<td align="right">53.9%</td>
<td align="right">26.0%</td>
</tr>
</tbody>
</table>
@ -1410,18 +1410,16 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 32 8 128 256 0.5 32 0.025 0.005 0.005 </span></span>
<span><span class="co"># [10] 64 0.002 16 0.5 0.002 1 &lt;=0.001 256 0.125 </span></span>
<span><span class="co"># [19] 0.25 256 0.025 0.0625 8 0.0625 256 0.125 128 </span></span>
<span><span class="co"># [28] 0.005 256 64 0.025 4 8 2 0.0625 8 </span></span>
<span><span class="co"># [37] 32 1 16 0.5 0.01 16 8 0.025 16 </span></span>
<span><span class="co"># [46] 0.005 &lt;=0.001 1 1 64 0.25 16 &lt;=0.001 0.025 </span></span>
<span><span class="co"># [55] 256 0.002 0.25 0.01 2 1 0.5 0.5 4 </span></span>
<span><span class="co"># [64] 0.01 0.5 2 0.5 0.0625 16 16 0.025 64 </span></span>
<span><span class="co"># [73] 256 0.5 0.5 0.125 16 16 0.125 0.002 128 </span></span>
<span><span class="co"># [82] &lt;=0.001 64 64 64 0.005 0.25 64 0.5 256 </span></span>
<span><span class="co"># [91] 0.025 16 4 0.025 0.0625 &lt;=0.001 64 128 128 </span></span>
<span><span class="co"># [100] 8</span></span></code></pre></div>
<span><span class="co"># [1] 1 0.5 16 0.5 0.01 0.25 128 0.025 0.005 0.005 </span></span>
<span><span class="co"># [11] 64 0.01 0.002 0.0625 1 4 0.002 0.025 0.125 0.5 </span></span>
<span><span class="co"># [21] 32 0.25 0.125 4 0.002 8 32 0.002 1 1 </span></span>
<span><span class="co"># [31] 0.01 128 1 1 0.25 0.5 0.125 4 4 64 </span></span>
<span><span class="co"># [41] &gt;=256 64 0.5 0.025 32 2 16 128 1 0.005 </span></span>
<span><span class="co"># [51] 64 &gt;=256 8 0.002 64 0.005 0.125 0.0625 8 128 </span></span>
<span><span class="co"># [61] 4 128 2 &gt;=256 64 0.005 0.01 8 0.002 0.5 </span></span>
<span><span class="co"># [71] 0.0625 64 1 0.001 8 0.0625 8 0.002 8 &gt;=256 </span></span>
<span><span class="co"># [81] 1 0.01 &gt;=256 0.01 0.0625 0.0625 0.0625 0.0625 8 0.25 </span></span>
<span><span class="co"># [91] 4 1 0.0625 8 2 1 0.25 0.5 0.25 4</span></span></code></pre></div>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1455,10 +1453,10 @@ plotting:</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 24 19 26 26 21 31 28 19 25 29 20 26 22 18 20 29 18 18 20 18 26 20 17 19 25</span></span>
<span><span class="co"># [26] 25 24 23 28 22 21 23 21 29 19 22 31 30 25 26 31 20 21 21 27 26 20 30 22 20</span></span>
<span><span class="co"># [51] 25 17 23 24 17 19 26 25 30 20 20 20 26 26 29 17 29 24 22 18 26 25 28 23 20</span></span>
<span><span class="co"># [76] 23 31 17 17 18 24 19 27 30 22 17 23 22 17 21 18 29 19 26 31 27 26 22 22 25</span></span></code></pre></div>
<span><span class="co"># [1] 25 23 29 18 18 18 18 19 27 19 28 23 26 20 17 22 30 31 31 31 21 20 31 17 27</span></span>
<span><span class="co"># [26] 25 19 26 23 18 19 26 23 26 18 24 21 25 28 27 23 24 17 21 30 23 19 20 20 27</span></span>
<span><span class="co"># [51] 24 23 18 25 31 30 24 23 17 30 18 27 20 21 30 31 17 25 24 27 25 28 26 25 18</span></span>
<span><span class="co"># [76] 18 29 26 28 21 18 24 27 29 17 26 20 17 23 22 29 23 24 19 31 30 20 29 25 31</span></span></code></pre></div>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>

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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="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

62
articles/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="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -375,19 +375,19 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 S S R S S S</span></span>
<span><span class="co"># 2 R I S S R I</span></span>
<span><span class="co"># 3 S S R S S R</span></span>
<span><span class="co"># 4 R R I S S I</span></span>
<span><span class="co"># 5 I S I I I S</span></span>
<span><span class="co"># 6 R R S R I I</span></span>
<span><span class="co"># 1 I S S R I R</span></span>
<span><span class="co"># 2 R S S R R R</span></span>
<span><span class="co"># 3 R S I S S S</span></span>
<span><span class="co"># 4 I S I I R R</span></span>
<span><span class="co"># 5 I S S I S S</span></span>
<span><span class="co"># 6 S I R I R S</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 R</span></span>
<span><span class="co"># 6 I</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -428,40 +428,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3144</td>
<td align="right">62.88%</td>
<td align="right">3144</td>
<td align="right">62.88%</td>
<td align="right">3261</td>
<td align="right">65.22%</td>
<td align="right">3261</td>
<td align="right">65.22%</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">4156</td>
<td align="right">83.12%</td>
<td align="right">959</td>
<td align="right">19.18%</td>
<td align="right">4220</td>
<td align="right">84.40%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">482</td>
<td align="right">9.64%</td>
<td align="right">4638</td>
<td align="right">92.76%</td>
<td align="right">434</td>
<td align="right">8.68%</td>
<td align="right">4654</td>
<td align="right">93.08%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">261</td>
<td align="right">5.22%</td>
<td align="right">4899</td>
<td align="right">97.98%</td>
<td align="right">243</td>
<td align="right">4.86%</td>
<td align="right">4897</td>
<td align="right">97.94%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">101</td>
<td align="right">2.02%</td>
<td align="right">103</td>
<td align="right">2.06%</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="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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@ -168,7 +168,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">30 December 2022</h4>
<h4 data-toc-skip class="date">05 January 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="d-none name"><code>SPSS.Rmd</code></div>
@ -247,7 +247,7 @@ data using a custom made website. The webdesign knowledge needed
<li>
<p><strong>R has a huge community.</strong></p>
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">475,704
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">476,194
R-related questions</a> have already been asked on this platform (that
covers questions and answers for any programming language). In my own
experience, most questions are answered within a couple of
@ -306,7 +306,7 @@ didn’t even had a professional user interface until the last decade
language itself <a href="https://www.tidyverse.org/packages/" class="external-link">has been
restyled completely</a> by volunteers who are dedicated professionals in
the field of data science. SPSS was great when there was nothing else
that could compete. But now in 2022, I don’t see any reason why SPSS
that could compete. But now in 2023, I don’t see any reason why SPSS
would be of any better use than R.</p>
</li>
</ul>

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@ -166,7 +166,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">30 December 2022</h4>
<h4 data-toc-skip class="date">05 January 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
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@ -228,7 +228,7 @@ number of observations, the actual observed resistance, the estimated
resistance and the standard error below and above the estimation:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">predict_TZP</span></span>
<span><span class="co"># <span style="color: #949494;"># A tibble: 31 × 7</span></span></span>
<span><span class="co"># <span style="color: #949494;"># A tibble: 32 × 7</span></span></span>
<span><span class="co"># year value se_min se_max observations observed estimated</span></span>
<span><span class="co"># <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span></span>
<span><span class="co"># <span style="color: #BCBCBC;"> 1</span> <span style="text-decoration: underline;">2</span>002 0.2 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 15 0.2 0.056<span style="text-decoration: underline;">2</span></span></span>
@ -241,7 +241,7 @@ resistance and the standard error below and above the estimation:</p>
<span><span class="co"># <span style="color: #BCBCBC;"> 8</span> <span style="text-decoration: underline;">2</span>009 0.016<span style="text-decoration: underline;">4</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 61 0.016<span style="text-decoration: underline;">4</span> 0.106 </span></span>
<span><span class="co"># <span style="color: #BCBCBC;"> 9</span> <span style="text-decoration: underline;">2</span>010 0.056<span style="text-decoration: underline;">6</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 53 0.056<span style="text-decoration: underline;">6</span> 0.116 </span></span>
<span><span class="co"># <span style="color: #BCBCBC;">10</span> <span style="text-decoration: underline;">2</span>011 0.183 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 93 0.183 0.127 </span></span>
<span><span class="co"># <span style="color: #949494;"># … with 21 more rows</span></span></span></code></pre></div>
<span><span class="co"># <span style="color: #949494;"># … with 22 more rows</span></span></span></code></pre></div>
<p>The function <code>plot</code> is available in base R, and can be
extended by other packages to depend the output based on the type of
input. We extended its function to cope with resistance predictions:</p>

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@ -131,7 +131,134 @@
<small>Source: <a href="https://github.com/msberends/AMR/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
</div>
</main></div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="1.8.2.9078" id="amr-1829078">AMR 1.8.2.9078<a class="anchor" aria-label="anchor" href="#amr-1829078"></a></h2>
<p><em>(this beta version will eventually become v2.0! We’re happy to reach a new major milestone soon!)</em></p>
<p>This is a new major release of the AMR package, with great new additions but also some breaking changes for current users. These are all listed below.</p>
<p><strong><a href="https://en.wikipedia.org/wiki/TL;DR" class="external-link">TL;DR</a></strong></p>
<ul><li>Microbiological taxonomy (<code>microorganisms</code> data set) updated to 2022 and now based on LPSN and GBIF</li>
<li>Much increased algorithms to translate user input to valid taxonomy, e.g. by using <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">recent scientific work</a> about per-species human pathogenicity</li>
<li>Clinical breakpoints added for EUCAST 2022 and CLSI 2022</li>
<li>20 new antibiotics added and updated all DDDs and ATC codes</li>
<li>Extended support for antiviral agents (<code>antivirals</code> data set), with many new functions</li>
<li>Now available in 16 languages</li>
<li>Many new interesting functions, such as <code><a href="../reference/proportion.html">rsi_confidence_interval()</a></code> and <code><a href="../reference/mean_amr_distance.html">mean_amr_distance()</a></code>, and <code><a href="../reference/add_custom_microorganisms.html">add_custom_microorganisms()</a></code> to add custom microorganisms to this package</li>
<li>Many small bug fixes</li>
</ul><div class="section level3">
<h3 id="new-1-8-2-9078">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9078"></a></h3>
<div class="section level4">
<h4 id="interpretation-of-mic-and-disk-diffusion-values-1-8-2-9078">Interpretation of MIC and disk diffusion values<a class="anchor" aria-label="anchor" href="#interpretation-of-mic-and-disk-diffusion-values-1-8-2-9078"></a></h4>
<p>The clinical breakpoints and intrinsic resistance of EUCAST 2022 and CLSI 2022 have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 (v12.0) is now the new default guideline for all MIC and disks diffusion interpretations, and for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> to apply EUCAST Expert Rules. The default guideline (EUCAST) can now be changed with the new <code>AMR_guideline</code> option, such as: <code>options(AMR_guideline = "CLSI 2020")</code>.</p>
<p>Interpretation guidelines older than 10 years were removed, the oldest now included guidelines of EUCAST and CLSI are from 2013.</p>
</div>
<div class="section level4">
<h4 id="supported-languages-1-8-2-9078">Supported languages<a class="anchor" aria-label="anchor" href="#supported-languages-1-8-2-9078"></a></h4>
<p>We added support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. All antibiotic names are now available in these languages, and the AMR package will automatically determine a supported language based on the user system language.</p>
<p>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 and according to download stats used in almost all countries in the world!</p>
</div>
<div class="section level4">
<h4 id="microbiological-taxonomy-1-8-2-9078">Microbiological taxonomy<a class="anchor" aria-label="anchor" href="#microbiological-taxonomy-1-8-2-9078"></a></h4>
<p>The <code>microorganisms</code> data set no longer relies on the Catalogue of Life, but on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and is supplemented with the ‘backbone taxonomy’ from the Global Biodiversity Information Facility (GBIF). The structure of this data set has changed to include separate LPSN and GBIF identifiers. Almost all previous MO codes were retained. It contains over 1,400 taxonomic names from 2022.</p>
<p>We previously relied on our own experience to categorise species into pathogenic groups, but we were very happy to encounter the very recent work of Bartlett <em>et al.</em> (2022, DOI <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">10.1099/mic.0.001269</a>) who extensively studied medical-scientific literature to categorise all bacterial species into groups. See <code><a href="../reference/mo_matching_score.html">mo_matching_score()</a></code> on how their work was incorporated into the <code>prevalence</code> column of the <code>microorganisms</code> data set. Using their results, the <code><a href="../reference/as.mo.html">as.mo()</a></code> and all <code>mo_*()</code> functions are now much better capable of converting user input to valid taxonomic records.</p>
<p>The new function <code><a href="../reference/add_custom_microorganisms.html">add_custom_microorganisms()</a></code> allows users to add custom microorganisms to the <code>AMR</code> package.</p>
<p>We also made the following changes regarding the included taxonomy or microorganisms functions:</p>
<ul><li>Updated full microbiological taxonomy according to the latest daily LPSN data set (December 2022) and latest yearly GBIF taxonomy backbone (November 2022)</li>
<li>Support for all 1,516 city-like serovars of <em>Salmonella</em>, such as <em>Salmonella</em> Goldcoast. Formally, these are serovars belonging to the <em>S. enterica</em> species, but they are reported with only the name of the genus and the city. For this reason, the serovars are in the <code>subspecies</code> column of the <code>microorganisms</code> data set and “enterica” is in the <code>species</code> column, but the full name does not contain the species name (<em>enterica</em>).</li>
<li>All new algorithm for <code><a href="../reference/as.mo.html">as.mo()</a></code> (and thus all <code>mo_*()</code> functions) while still following our original set-up as described in our recently published JSS paper (DOI <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">10.18637/jss.v104.i03</a>).
<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>
<li>It has increased tremendously in speed and returns generally more consequent results</li>
<li>Sequential coercion is now extremely fast as results are stored to the package environment, although coercion of unknown values must be run once per session. Previous results can be reset/removed with the new <code><a href="../reference/as.mo.html">mo_reset_session()</a></code> function.</li>
<li>Support for microorganism codes of the ASIan Antimicrobial Resistance Surveillance Network (ASIARS-Net)</li>
<li>The MO matching score algorithm (<code><a href="../reference/mo_matching_score.html">mo_matching_score()</a></code>) now counts 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></li>
<li>
<strong>Removed all species of the taxonomic kingdom Chromista</strong> from the package. This was done for multiple reasons:
<ul><li>CRAN allows packages to be around 5 MB maximum, some packages are exempted but this package is not one of them</li>
<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>
</ul></li>
<li>The <code>microorganisms.old</code> data set was removed, and all previously accepted names are now included in the <code>microorganisms</code> data set. A new column <code>status</code> contains <code>"accepted"</code> for currently accepted names and <code>"synonym"</code> for taxonomic synonyms; currently invalid names. All previously accepted names now have a microorganisms ID and - if available - an LPSN, GBIF and SNOMED CT identifier.</li>
</ul></div>
<div class="section level4">
<h4 id="antibiotic-agents-and-selectors-1-8-2-9078">Antibiotic agents and selectors<a class="anchor" aria-label="anchor" href="#antibiotic-agents-and-selectors-1-8-2-9078"></a></h4>
<p>The new function <code><a href="../reference/add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code> allows users to add custom antimicrobial codes and names to the <code>AMR</code> package.</p>
<p>The <code>antibiotics</code> data set was greatly updated:</p>
<ul><li>The following 20 antibiotics have been added (also includes the <a href="https://www.whocc.no/atc_ddd_index/?code=J01RA&amp;showdescription=no" class="external-link">new J01RA ATC group</a>): azithromycin/fluconazole/secnidazole (AFC), cefepime/amikacin (CFA), cefixime/ornidazole (CEO), ceftriaxone/beta-lactamase inhibitor (CEB), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), furazidin (FUR), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), lascufloxacin (LSC), levofloxacin/ornidazole (LEO), nemonoxacin (NEM), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin/ornidazole (OOR), oteseconazole (OTE), rifampicin/ethambutol/isoniazid (REI), sarecycline (SRC), tetracycline/oleandomycin (TOL), and thioacetazone (TAT)</li>
<li>Added some missing ATC codes</li>
<li>Updated DDDs and PubChem Compound IDs</li>
<li>Updated some antibiotic name spelling, now used by WHOCC (such as cephalexin -&gt; cefalexin, and phenethicillin -&gt; pheneticillin)</li>
<li>Antibiotic code “CEI” for ceftolozane/tazobactam has been replaced with “CZT” to comply with EARS-Net and WHONET 2022. The old code will still work in all cases when using <code><a href="../reference/as.ab.html">as.ab()</a></code> or any of the <code>ab_*()</code> functions.</li>
<li>Support for antimicrobial interpretation of anaerobic bacteria, by adding a ‘placeholder’ code <code>B_ANAER</code> to the <code>microorganisms</code> data set and adding the breakpoints of anaerobics to the <code>rsi_interpretation</code> data set, which is used by <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for interpretion of MIC and disk diffusion values</li>
</ul><p>Also, we added support for using antibiotic selectors in scoped <code>dplyr</code> verbs (with or without using <code><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars()</a></code>), such as in: <code>... %&gt;% summarise_at(aminoglycosides(), resistance)</code>, please see <code><a href="../reference/proportion.html">resistance()</a></code> for examples.</p>
</div>
<div class="section level4">
<h4 id="antiviral-agents-1-8-2-9078">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents-1-8-2-9078"></a></h4>
<p>We now added extensive support for antiviral agents! For the first time, the <code>AMR</code> package has extensive support for antiviral drugs and to work with their names, codes and other data in any way.</p>
<ul><li>The <code>antivirals</code> data set has been extended with 18 new drugs (also from the <a href="https://www.whocc.no/atc_ddd_index/?code=J05AJ&amp;showdescription=no" class="external-link">new J05AJ ATC group</a>) and now also contains antiviral identifiers and LOINC codes</li>
<li>A new data type <code>av</code> (<em>antivirals</em>) has been added, which is functionally similar to <code>ab</code> for antibiotics</li>
<li>Functions <code><a href="../reference/as.av.html">as.av()</a></code>, <code><a href="../reference/av_property.html">av_name()</a></code>, <code><a href="../reference/av_property.html">av_atc()</a></code>, <code><a href="../reference/av_property.html">av_synonyms()</a></code>, <code><a href="../reference/av_from_text.html">av_from_text()</a></code> have all been added as siblings to their <code>ab_*()</code> equivalents</li>
</ul></div>
<div class="section level4">
<h4 id="other-new-functions-1-8-2-9078">Other new functions<a class="anchor" aria-label="anchor" href="#other-new-functions-1-8-2-9078"></a></h4>
<ul><li>Function <code><a href="../reference/proportion.html">rsi_confidence_interval()</a></code> to add confidence intervals in AMR calculation. This is now also included in <code><a href="../reference/proportion.html">rsi_df()</a></code> and <code><a href="../reference/proportion.html">proportion_df()</a></code>.</li>
<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>
</ul></div>
</div>
<div class="section level3">
<h3 id="changes-1-8-2-9078">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9078"></a></h3>
<ul><li>Argument <code>combine_IR</code> has been removed from this package (affecting functions <code><a href="../reference/count.html">count_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code>, and <code><a href="../reference/proportion.html">rsi_df()</a></code> and some plotting functions), since it was replaced with <code>combine_SI</code> three years ago</li>
<li>Using <code>units</code> in <code>ab_ddd(..., units = "...")</code> had been deprecated for some time and is now not supported anymore. Use <code><a href="../reference/ab_property.html">ab_ddd_units()</a></code> instead.</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><a href="https://tsibble.tidyverts.org/reference/tsibble.html" class="external-link">tsibble::tsibble</a></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 a <code>tibble</code>, instead of base R <code>data.frame</code>s. Older R versions are still supported, even if they do not support <code>tibble</code>s.</li>
<li>Our data sets are now also continually exported to <strong>Apache Feather and Apache Parquet formats</strong>. You can find more info <a href="https://msberends.github.io/AMR/articles/datasets.html">in this article on our website</a>.</li>
<li>For <code><a href="../reference/as.rsi.html">as.rsi()</a></code>:
<ul><li>Fixed certain EUCAST breakpoints for MIC values</li>
<li>Allow <code>NA</code> values (e.g. <code>as.rsi(as.disk(NA), ...)</code>)</li>
<li>Fix for bug-drug combinations with multiple breakpoints for different body sites</li>
<li>Interpretation from MIC and disk zones is now more informative about availability of breakpoints and more robust</li>
</ul></li>
<li>Removed the <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> method for MIC values, since MIC are not integer values and running <code><a href="https://rdrr.io/r/base/table.html" class="external-link">table()</a></code> on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on <code>factor</code>s work)</li>
<li>Fixed determination of Gram stains (<code><a href="../reference/mo_property.html">mo_gramstain()</a></code>), since the taxonomic phyla Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes have been renamed to respectively Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota in 2021</li>
<li>
<code><a href="https://rdrr.io/r/base/droplevels.html" class="external-link">droplevels()</a></code> on MIC will now return a common <code>factor</code> at default and will lose the <code>mic</code> class. Use <code>droplevels(..., as.mic = TRUE)</code> to keep the <code>mic</code> class.</li>
<li>Small fix for using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>
</li>
<li>Fixes for reading in text files using <code><a href="../reference/mo_source.html">set_mo_source()</a></code>, which now also allows the source file to contain valid taxonomic names instead of only valid microorganism ID of this package</li>
<li>Fixed a bug for <code><a href="../reference/mdro.html">mdro()</a></code> when using similar column names with the Magiorakos guideline</li>
<li>Using any <code>random_*()</code> function (such as <code><a href="../reference/random.html">random_mic()</a></code>) is now possible by directly calling the package without loading it first: <code>AMR::random_mic(10)</code>
</li>
<li>Extended support for the <code>vctrs</code> package, used internally by the tidyverse. This allows to change values of class <code>mic</code>, <code>disk</code>, <code>rsi</code>, <code>mo</code> and <code>ab</code> in tibbles, and to use antibiotic selectors for selecting/filtering, e.g. <code>df[carbapenems() == "R", ]</code>
</li>
<li>Fix for using <code>info = FALSE</code> in <code><a href="../reference/mdro.html">mdro()</a></code>
</li>
<li>For all interpretation guidelines using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on amoxicillin, the rules for ampicillin will be used if amoxicillin rules are not available</li>
<li>Fix for using <code><a href="../reference/ab_property.html">ab_atc()</a></code> on non-existing ATC codes</li>
<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>
<li>Updated support for all WHONET 2022 microorganism codes</li>
<li>Antimicrobial interpretation ‘SDD’ (susceptible dose-dependent, coined by CLSI) will be interpreted as ‘I’ to comply with EUCAST’s ‘I’ in <code><a href="../reference/as.rsi.html">as.rsi()</a></code>
</li>
<li>Fix for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> in case of higher taxonomic ranks (order, class, phylum)</li>
<li>Cleaning columns with <code><a href="../reference/as.rsi.html">as.rsi()</a></code>, <code><a href="../reference/as.mic.html">as.mic()</a></code>, or <code><a href="../reference/as.disk.html">as.disk()</a></code> will now show the column name in the warning for invalid results</li>
</ul></div>
<div class="section level3">
<h3 id="other-1-8-2-9078">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9078"></a></h3>
<ul><li>New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions</li>
<li>Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, and Jonas Salm as contributors, to thank them for their valuable input</li>
<li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>
<li>Set scalar conditional expressions (<code>&amp;&amp;</code> and <code>||</code>) where possible to comply with the upcoming R 4.3</li>
<li>An enormous lot of code cleaning, fixing some small bugs on the way</li>
</ul><hr><p>This changelog only contains changes from AMR v2.0 and later. For prior versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our archive</a>.</p>
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@ -11,7 +11,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2022-12-30T12:06Z
last_built: 2023-01-05T13:50Z
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
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reference/ab_property.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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@ -190,7 +190,7 @@
<dt>...</dt>
<dd><p>in case of <code>set_ab_names()</code> and <code>data</code> is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: variables to select (supports tidy selection such as <code>column1:column4</code>), otherwise other arguments passed on to <code><a href="as.ab.html">as.ab()</a></code></p></dd>
<dd><p>in case of <code>set_ab_names()</code> and <code>data</code> is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: columns to select (supports tidy selection such as <code>column1:column4</code>), otherwise other arguments passed on to <code><a href="as.ab.html">as.ab()</a></code></p></dd>
<dt>only_first</dt>

2
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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reference/age.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
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@ -195,16 +195,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1981-01-25 41 41.92877 18</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-07-25 42 42.43288 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1991-10-10 31 31.22192 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1967-05-14 55 55.63014 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1999-10-10 23 23.22192 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1970-08-21 52 52.35890 29</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1967-02-25 55 55.84384 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1963-10-06 59 59.23288 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1964-12-12 58 58.04932 35</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1958-12-04 64 64.07123 41</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1968-01-10 54 54.98630 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1991-02-27 31 31.85479 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1948-01-05 75 75.00000 51</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1985-02-05 37 37.91507 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-08-26 90 90.36164 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-08-28 73 73.35616 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1985-11-10 37 37.15342 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1947-09-21 75 75.29041 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1992-05-26 30 30.61370 7</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1955-09-09 67 67.32329 44</span>
</code></pre></div>
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18
reference/antibiotic_class_selectors.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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@ -918,7 +918,21 @@
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="fu">ab_class</span><span class="op">(</span><span class="st">"mycobact"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in select(., mo, ab_class("mycobact")):</span> Problem while evaluating `ab_class("mycobact")`.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For ab_class("mycobact") using column 'RIF' (rifampicin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo RIF </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> B_ESCHR_COLI R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> B_ESCHR_COLI R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B_STPHY_EPDR NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> B_STPHY_EPDR NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> B_STPHY_EPDR NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B_STPHY_EPDR NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B_STPHY_AURS NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B_STPHY_AURS NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B_STPHY_EPDR NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B_STPHY_EPDR NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
<span class="r-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"># get bug/drug combinations for only glycopeptides in Gram-positives:</span></span></span>

2
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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2
reference/as.ab.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
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2
reference/as.av.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="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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2
reference/as.disk.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
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2
reference/as.mic.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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2
reference/as.mo.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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22
reference/as.rsi.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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@ -506,16 +506,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 12</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_gu…¹ mo_in…² mo_guideline guide…³</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-12-30 <span style="color: #949494;">12:07:24</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-12-30 <span style="color: #949494;">12:07:25</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-12-30 <span style="color: #949494;">12:07:25</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-12-30 <span style="color: #949494;">12:07:26</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-12-30 <span style="color: #949494;">12:07:26</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-12-30 <span style="color: #949494;">12:07:27</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-12-30 <span style="color: #949494;">12:07:28</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-12-30 <span style="color: #949494;">12:07:28</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-12-30 <span style="color: #949494;">12:07:28</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-12-30 <span style="color: #949494;">12:07:28</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> 2023-01-05 <span style="color: #949494;">13:50:52</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> 2023-01-05 <span style="color: #949494;">13:50:53</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-01-05 <span style="color: #949494;">13:50:53</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-01-05 <span style="color: #949494;">13:50:53</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-01-05 <span style="color: #949494;">13:50:54</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-01-05 <span style="color: #949494;">13:50:55</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> 2023-01-05 <span style="color: #949494;">13:50:55</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> 2023-01-05 <span style="color: #949494;">13:50:55</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> 2023-01-05 <span style="color: #949494;">13:50:55</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> 2023-01-05 <span style="color: #949494;">13:50:55</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 5 more variables: ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># input &lt;dbl&gt;, outcome &lt;rsi&gt;, breakpoint_S_R &lt;chr&gt;, and abbreviated variable</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># names ¹​ab_guideline, ²​mo_input, ³​guideline</span></span>

2
reference/atc_online.html
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="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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2
reference/av_from_text.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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2
reference/av_property.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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2
reference/availability.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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2
reference/bug_drug_combinations.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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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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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
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4
reference/custom_eucast_rules.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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@ -197,7 +197,7 @@
<h3 id="using-taxonomic-properties-in-rules">Using taxonomic properties in rules<a class="anchor" aria-label="anchor" href="#using-taxonomic-properties-in-rules"></a></h3>
<p>There is one exception in variables used for the rules: all column names of the <a href="microorganisms.html">microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence" and "snomed". Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p>
<p>There is one exception in columns used for the rules: all column names of the <a href="microorganisms.html">microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence" and "snomed". Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_eucast_rules.html">custom_eucast_rules</a></span><span class="op">(</span><span class="va">TZP</span> <span class="op">==</span> <span class="st">"S"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"S"</span>,</span>
<span> <span class="va">TZP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></span>
<span></span>

2
reference/dosage.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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2
reference/eucast_rules.html
View File

@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
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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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2
reference/first_isolate.html
View File

@ -12,7 +12,7 @@
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2
reference/g.test.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
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135
reference/get_episode.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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@ -182,42 +182,39 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">200</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 67 8 32 43 12 22 22 31 7 57 67 15 29 40 20 1 43 49 7 45 64 1 31 67 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 65 20 55 41 2 9 20 31 60 61 36 24 41 34 41 62 34 20 5 11 63 49 41 61 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 16 33 28 29 51 50 29 61 14 7 18 10 60 18 47 59 22 16 55 33 64 33 48 3 58</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 57 6 31 40 21 36 24 61 14 57 26 2 24 27 12 12 22 17 9 18 66 34 14 3 5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 53 67 38 1 18 65 33 46 46 51 4 17 5 1 55 40 44 20 51 38 50 38 18 47 62</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 12 14 18 51 25 31 35 30 40 14 61 54 47 16 67 36 14 39 23 55 7 56 39 13 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 12 44 25 35 50 27 51 2 1 58 49 20 60 52 66 63 17 31 19 47 15 52 64 31 17</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 25 30 8 54 36 39 21 51 23 64 3 66 19 38 3 27 26 44 6 48 11 42 61 5 37</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 60 59 40 62 19 23 22 5 49 47 2 53 35 32 20 62 40 56 17 42 59 57 38 15 61</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 14 26 13 6 9 27 28 59 34 36 44 9 7 47 17 5 16 5 14 13 24 48 9 62 5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 56 1 57 6 26 52 22 13 16 51 42 19 30 13 15 2 38 63 4 9 13 34 13 1 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 29 44 19 11 58 1 61 21 37 61 64 41 26 39 40 19 31 21 1 43 1 23 52 27 5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 31 31 23 43 57 3 6 59 55 22 58 29 33 12 32 63 25 11 61 29 37 62 26 21 57</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 61 25 26 34 54 7 10 13 11 18 56 33 23 2 34 45 24 20 64 24 30 57 50 39 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 60 8 56 62 45 43 61 53 8 4 9 51 56 15 49 11 10 10 41 26 49 36 63 13 26</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 46 13 13 38 54 14 27 10 58 55 29 25 39 27 22 60 32 8 59 25 8 23 56 57 24</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE TRUE FALSE TRUE FALSE TRUE FALSE 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 TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE TRUE TRUE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] TRUE TRUE TRUE TRUE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE FALSE TRUE TRUE TRUE TRUE TRUE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE TRUE FALSE TRUE TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] TRUE FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-07-21 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;">2</span> 2002-07-15 426426 67 F ICU B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</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;">4</span> 2002-07-15 C42193 84 M ICU B_STPHY_HMNS R NA R 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>
@ -253,16 +250,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: condition [3]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 5DB1C8 2017-12-28 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 4DD722 2003-06-02 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> C7C641 2008-12-27 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 704554 2012-01-01 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 304508 2004-05-09 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> E27874 2006-12-19 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 418311 2006-11-10 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 501361 2008-11-01 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 6BC362 2003-04-02 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> D40405 2015-06-03 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 671620 2016-12-04 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> BF4515 2016-09-25 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 116866 2011-11-07 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 422833 2017-05-26 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 344184 2006-08-01 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 92F410 2007-09-03 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 534816 2007-04-16 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 088256 2003-01-25 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 959835 2013-11-16 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 255339 2013-07-22 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@ -274,19 +271,19 @@
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [177]</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 2017-12-28 5DB1C8 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU 2003-06-02 4DD722 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Outpatient 2008-12-27 C7C641 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU 2012-01-01 704554 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2004-05-09 304508 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2006-12-19 E27874 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2006-11-10 418311 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2008-11-01 501361 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU 2003-04-02 6BC362 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> ICU 2015-06-03 D40405 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [182]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2016-12-04 671620 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2016-09-25 BF4515 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2011-11-07 116866 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2017-05-26 422833 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2006-08-01 344184 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2007-09-03 92F410 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2007-04-16 534816 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ICU 2003-01-25 088256 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2013-11-16 959835 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2013-07-22 255339 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@ -301,9 +298,9 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 115 14 50 71</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 56 13 37 43</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 6 4 5 5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 127 15 55 79</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 44 11 31 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 11 6 9 10</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>
@ -333,19 +330,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [191]</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> 5DB1C8 B_STPHY_CPTS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 4DD722 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> C7C641 B_STPHY_CONS Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 704554 B_STPHY_CONS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 304508 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> E27874 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 418311 B_STPHY_EPDR ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 501361 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 6BC362 B_STRPT_PNMN ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> D40405 B_ENTRC_FCLS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [194]</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> 671620 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> BF4515 B_STPHY_EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 116866 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 422833 B_ENTRC_FCLS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 344184 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 92F410 B_ENTRBC_CLOC Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 534816 B_ENTRC_FCLS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 088256 B_STPHY_HMNS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 959835 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 255339 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>

2
reference/ggplot_pca.html
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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="">1.8.2.9076</small>
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2
reference/ggplot_rsi.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="">1.8.2.9076</small>
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reference/guess_ab_col.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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2
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="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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2
reference/intrinsic_resistant.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
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2
reference/join.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="">1.8.2.9076</small>
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2
reference/key_antimicrobials.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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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="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</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">
@ -172,9 +172,9 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.979693</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.923487</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] 0.0343079</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01643722</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

2
reference/like.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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155
reference/mean_amr_distance.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</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">
@ -152,7 +152,7 @@
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dd><p>a vector of class <a href="as.rsi.html">rsi</a>, <a href="as.rsi.html">rsi</a> or <a href="as.rsi.html">rsi</a>, or a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing columns of any of these classes</p></dd>
<dd><p>a vector of class <a href="as.rsi.html">rsi</a>, <a href="as.mic.html">mic</a> or <a href="as.disk.html">disk</a>, or a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing columns of any of these classes</p></dd>
<dt>...</dt>
@ -173,10 +173,10 @@
</dl></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand. For common numeric data this distance is equal to <a href="https://en.wikipedia.org/wiki/Standard_score" class="external-link">Z scores</a> (the number of standard deviations from the mean).</p>
<p>MIC values (see <code><a href="as.mic.html">as.mic()</a></code>) are transformed with <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2()</a></code> first; their distance is calculated as <code>(log2(x) - mean(log2(x))) / sd(log2(x))</code>.</p>
<p>The mean AMR distance is effectively <a href="https://en.wikipedia.org/wiki/Standard_score" class="external-link">the Z-score</a>; a normalised numeric value to compare AMR test results which can help to identify similar isolates, without comparing antibiograms by hand.</p>
<p>MIC values (see <code><a href="as.mic.html">as.mic()</a></code>) are transformed with <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2()</a></code> first; their distance is thus calculated as <code>(log2(x) - mean(log2(x))) / sd(log2(x))</code>.</p>
<p>R/SI values (see <code><a href="as.rsi.html">as.rsi()</a></code>) are transformed using <code>"S"</code> = 1, <code>"I"</code> = 2, and <code>"R"</code> = 3. If <code>combine_SI</code> is <code>TRUE</code> (default), the <code>"I"</code> will be considered to be 1.</p>
<p>For data sets, the mean AMR distance will be calculated per variable, after which the mean of all columns will returned per row (using <code><a href="https://rdrr.io/r/base/colSums.html" class="external-link">rowMeans()</a></code>), see <em>Examples</em>.</p>
<p>For data sets, the mean AMR distance will be calculated per column, after which the mean per row will be returned, see <em>Examples</em>.</p>
<p>Use <code>amr_distance_from_row()</code> to subtract distances from the distance of one row, see <em>Examples</em>.</p>
</div>
<div class="section level2">
@ -188,104 +188,121 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">x</span></span></span>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">rsi</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_rsi</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">rsi</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'rsi'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S I S S R S S S I R</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">rsi</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.4743416 -0.4743416 -0.4743416 -0.4743416 1.8973666 -0.4743416</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.4743416 -0.4743416 -0.4743416 1.8973666</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">mic</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">mic</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01 0.002 &gt;=256 1 &lt;=0.001 0.01 64 0.005 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &gt;=256 </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] -0.7233354 -1.0310806 1.2175417 0.1572324 -1.1636193 -0.7233354</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.9524644 -0.8558740 0.9524644 1.2175417</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &gt;=64 0.25 16 0.001 0.125 32 0.125 0.001 0.002 8 </span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.26281480 -0.01764874 0.94269891 -1.29263579 -0.17770669 1.10275686</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.17770669 -1.29263579 -1.13257785 0.78264097</span>
<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.26281480 -0.01764874 0.94269891 -1.29263579 -0.17770669 1.10275686</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.17770669 -1.29263579 -1.13257785 0.78264097</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">disk</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_disk</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">disk</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 29 32 37 48 40 28 37 40 49</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.9401430 -0.6951315 -0.3838786 0.1348763 1.2761369 0.4461291</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.7988824 0.1348763 0.4461291 1.3798878</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>
<span class="r-in"><span> amox <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"amox"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> cipr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"cipr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> amox <span class="op">=</span> <span class="fu"><a href="random.html">random_rsi</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"amox"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> cipr <span class="op">=</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"cipr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> gent <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"gent"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></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 1 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 32 &gt;=4 1 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 4 0.25 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 16 &gt;=4 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 &gt;=4 1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 16 1 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 4 0.5 1 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 0.25 1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 16 0.5 1 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 8 0.125 &gt;=8 0.5</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 R 23 &gt;=16 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B I 24 1 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C S 24 8 0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D R 18 2 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 17 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F S 22 8 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G R 29 2 0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H S 28 &gt;=16 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I I 31 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J S 20 &gt;=16 0.5</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "id" and "tobr"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.0410109 0.8951387 -0.4091718 0.5415853 -0.1399200 0.6721245</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.1964756 -0.6867320 -0.4492455 -0.2683146</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.76502575 -0.22559420 -0.39112580 0.14405101 -0.59747772 0.01884049</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.04569124 0.34391737 0.15560237 -0.25893050</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</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 "gent" and "tobr"</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 0.25 1 2 -0.6867320</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 16 0.5 1 0.5 -0.4492455</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 4 0.25 4 1 -0.4091718</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 8 0.125 &gt;=8 0.5 -0.2683146</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 4 0.5 1 &gt;=8 -0.1964756</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 &gt;=4 1 2 -0.1399200</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 8 1 2 2 0.0410109</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 16 &gt;=4 2 2 0.5415853</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 16 1 4 4 0.6721245</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 32 &gt;=4 1 &gt;=8 0.8951387</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> 7 G R 29 2 0.25 -1.2141339</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C S 24 8 0.25 -0.5147553</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B I 24 1 4 -0.1836920</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 17 4 1 -0.1743790</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I I 31 4 1 -0.1743790</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D R 18 2 4 0.1659973</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J S 20 &gt;=16 0.5 0.1799668</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F S 22 8 2 0.5203431</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H S 28 &gt;=16 1 0.5249996</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A R 23 &gt;=16 2 0.8700324</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> amr_distance <span class="op">=</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">.</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> amr_distance <span class="op">=</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-in"><span> check_id_C <span class="op">=</span> <span class="fu">amr_distance_from_row</span><span class="op">(</span><span class="va">amr_distance</span>, <span class="va">id</span> <span class="op">==</span> <span class="st">"C"</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">check_id_C</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C 4 0.25 4 1 -0.4091718 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 I 16 0.5 1 0.5 -0.4492455 0.0400737</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 J 8 0.125 &gt;=8 0.5 -0.2683146 0.1408572</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 G 4 0.5 1 &gt;=8 -0.1964756 0.2126962</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 &gt;=4 1 2 -0.1399200 0.2692518</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 H 4 0.25 1 2 -0.6867320 0.2775602</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 A 8 1 2 2 0.0410109 0.4501827</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 D 16 &gt;=4 2 2 0.5415853 0.9507571</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 F 16 1 4 4 0.6721245 1.0812963</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 B 32 &gt;=4 1 &gt;=8 0.8951387 1.3043105</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 S 24 8 0.25 -0.39112580 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 J S 20 &gt;=16 0.5 -0.25893050 0.1321953</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 B I 24 1 4 -0.22559420 0.1655316</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 E S 17 4 1 -0.59747772 0.2063519</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 F S 22 8 2 0.01884049 0.4099663</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 G R 29 2 0.25 0.04569124 0.4368170</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 D R 18 2 4 0.14405101 0.5351768</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 I I 31 4 1 0.15560237 0.5467282</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 H S 28 &gt;=16 1 0.34391737 0.7350432</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 A R 23 &gt;=16 2 0.76502575 1.1561516</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Enterococcus"</span> <span class="op">&amp;</span> <span class="fu"><a href="mo_property.html">mo_species</a></span><span class="op">(</span><span class="op">)</span> <span class="op">!=</span> <span class="st">""</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="va">TCY</span>, <span class="fu"><a href="antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>d <span class="op">=</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">.</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.rsi</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">mo</span>, <span class="va">d</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>dist <span class="op">=</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">.</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">mo</span>, <span class="va">dist</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for mo_genus()</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for mo_species()</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "IPM", "MEM" and "TCY"</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "TCY", "IPM" and "MEM"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 63 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: mo [4]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo TCY IPM MEM d</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> B_ENTRC_AVIM S S NA <span style="color: #BB0000;">NaN</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> B_ENTRC_AVIM S S NA <span style="color: #BB0000;">NaN</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B_ENTRC_CSSL NA S NA <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> B_ENTRC_FACM S S NA -<span style="color: #BB0000;">2.66</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> B_ENTRC_FACM S R R -<span style="color: #BB0000;">0.423</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B_ENTRC_FACM S R R -<span style="color: #BB0000;">0.423</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B_ENTRC_FACM NA R R 0.224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B_ENTRC_FACM NA R R 0.224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B_ENTRC_FACM NA R R 0.224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B_ENTRC_FACM NA R R 0.224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo TCY IPM MEM dist</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> B_ENTRC_AVIM S S NA 0 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> B_ENTRC_AVIM S S NA 0 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B_ENTRC_CSSL NA S NA <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> B_ENTRC_FACM S S NA -<span style="color: #BB0000;">2.66</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> B_ENTRC_FACM S R R -<span style="color: #BB0000;">0.423</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B_ENTRC_FACM S R R -<span style="color: #BB0000;">0.423</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B_ENTRC_FACM NA R R 0.224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B_ENTRC_FACM NA R R 0.224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B_ENTRC_FACM NA R R 0.224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B_ENTRC_FACM NA R R 0.224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 53 more rows</span></span>
</code></pre></div>
</div>

2
reference/microorganisms.codes.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</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/microorganisms.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
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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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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reference/mo_property.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
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reference/plot.html
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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="">1.8.2.9076</small>
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@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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