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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9146</small>
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@ -408,70 +408,70 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-10-24</td>
<td align="center">V3</td>
<td align="center">Hospital C</td>
<td align="center">2015-09-16</td>
<td align="center">Z5</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-01-11</td>
<td align="center">K4</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">2017-09-08</td>
<td align="center">V1</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-08-05</td>
<td align="center">B1</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-08-24</td>
<td align="center">E10</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2014-07-11</td>
<td align="center">W3</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-04-14</td>
<td align="center">X5</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">2011-06-19</td>
<td align="center">R10</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2013-07-12</td>
<td align="center">V7</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-09-22</td>
<td align="center">Y4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">2013-07-14</td>
<td align="center">L4</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
@ -507,16 +507,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,503</td>
<td align="right">52.52%</td>
<td align="right">10,503</td>
<td align="right">52.52%</td>
<td align="right">10,355</td>
<td align="right">51.78%</td>
<td align="right">10,355</td>
<td align="right">51.78%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,497</td>
<td align="right">47.49%</td>
<td align="right">9,645</td>
<td align="right">48.23%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -629,9 +629,9 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co">#&gt; Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co">#&gt; 2</span></span>
<span><span class="co">#&gt; Including isolates from ICU.</span></span>
<span><span class="co">#&gt; =&gt; Found 12,333 'phenotype-based' first isolates (61.7% of total where a</span></span>
<span><span class="co">#&gt; =&gt; Found 12,372 'phenotype-based' first isolates (61.9% of total where a</span></span>
<span><span class="co">#&gt; microbial ID was available)</span></span></code></pre></div>
<p>So only 61.7% is suitable for resistance analysis! We can now filter
<p>So only 61.9% 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">
@ -641,7 +641,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>So we end up with 12 333 isolates for analysis. Now our data looks
<p>So we end up with 12 372 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>
@ -658,8 +658,8 @@ like:</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="7%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
<thead><tr class="header">
@ -681,77 +681,13 @@ like:</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2011-10-24</td>
<td align="center">V3</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">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">3</td>
<td align="center">2014-07-11</td>
<td align="center">W3</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">2011-09-22</td>
<td align="center">Y4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2010-12-17</td>
<td align="center">G6</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</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="odd">
<td align="left">8</td>
<td align="center">2010-01-14</td>
<td align="center">S8</td>
<td align="center">2015-09-16</td>
<td align="center">Z5</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
@ -760,19 +696,83 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2015-08-01</td>
<td align="center">G9</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="left">2</td>
<td align="center">2017-09-08</td>
<td align="center">V1</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">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">2016-08-05</td>
<td align="center">B1</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">2010-08-24</td>
<td align="center">E10</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2011-06-03</td>
<td align="center">D1</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2016-04-15</td>
<td align="center">T10</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -808,8 +808,8 @@ 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: 12,333<br>
Available: 12,333 (100%, NA: 0 = 0%)<br>
Length: 12,372<br>
Available: 12,372 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -834,33 +834,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">5,838</td>
<td align="right">47.34%</td>
<td align="right">5,838</td>
<td align="right">47.34%</td>
<td align="right">5,982</td>
<td align="right">48.35%</td>
<td align="right">5,982</td>
<td align="right">48.35%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,318</td>
<td align="right">26.90%</td>
<td align="right">9,156</td>
<td align="right">74.24%</td>
<td align="right">3,218</td>
<td align="right">26.01%</td>
<td align="right">9,200</td>
<td align="right">74.36%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,871</td>
<td align="right">15.17%</td>
<td align="right">11,027</td>
<td align="right">89.41%</td>
<td align="right">1,867</td>
<td align="right">15.09%</td>
<td align="right">11,067</td>
<td align="right">89.45%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,306</td>
<td align="right">10.59%</td>
<td align="right">12,333</td>
<td align="right">1,305</td>
<td align="right">10.55%</td>
<td align="right">12,372</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -909,43 +909,13 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-10-24</td>
<td align="center">V3</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">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-07-11</td>
<td align="center">W3</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2010-01-14</td>
<td align="center">S8</td>
<td align="center">2015-09-16</td>
<td align="center">Z5</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
@ -954,27 +924,12 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-11-09</td>
<td align="center">P5</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-05-08</td>
<td align="center">Z4</td>
<td align="center">2017-09-08</td>
<td align="center">V1</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">R</td>
<td align="center">R</td>
<td align="center">F</td>
@ -983,14 +938,14 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-09-09</td>
<td align="center">I7</td>
<td align="center">Hospital A</td>
<tr class="odd">
<td align="center">2016-08-05</td>
<td align="center">B1</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">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -998,6 +953,51 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-06-03</td>
<td align="center">D1</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-04-15</td>
<td align="center">T10</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-03-09</td>
<td align="center">X8</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in
@ -1020,50 +1020,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">2657</td>
<td align="center">1244</td>
<td align="center">1937</td>
<td align="center">5838</td>
<td align="center">2826</td>
<td align="center">1184</td>
<td align="center">1972</td>
<td align="center">5982</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">1415</td>
<td align="center">1280</td>
<td align="center">3143</td>
<td align="center">5838</td>
<td align="center">1517</td>
<td align="center">1305</td>
<td align="center">3160</td>
<td align="center">5982</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">1998</td>
<td align="center">1817</td>
<td align="center">2023</td>
<td align="center">5838</td>
<td align="center">2041</td>
<td align="center">1879</td>
<td align="center">2062</td>
<td align="center">5982</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">1984</td>
<td align="center">1767</td>
<td align="center">2087</td>
<td align="center">5838</td>
<td align="center">2065</td>
<td align="center">1813</td>
<td align="center">2104</td>
<td align="center">5982</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">561</td>
<td align="center">285</td>
<td align="center">460</td>
<td align="center">1306</td>
<td align="center">587</td>
<td align="center">263</td>
<td align="center">455</td>
<td align="center">1305</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1306</td>
<td align="center">1306</td>
<td align="center">1305</td>
<td align="center">1305</td>
</tr>
</tbody>
</table>
@ -1085,34 +1085,34 @@ 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">1984</td>
<td align="center">1767</td>
<td align="center">2087</td>
<td align="center">5838</td>
<td align="center">2065</td>
<td align="center">1813</td>
<td align="center">2104</td>
<td align="center">5982</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">435</td>
<td align="center">423</td>
<td align="center">448</td>
<td align="center">1306</td>
<td align="center">440</td>
<td align="center">426</td>
<td align="center">439</td>
<td align="center">1305</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1143</td>
<td align="center">1003</td>
<td align="center">1172</td>
<td align="center">3318</td>
<td align="center">1124</td>
<td align="center">1044</td>
<td align="center">1050</td>
<td align="center">3218</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">1871</td>
<td align="center">1871</td>
<td align="center">1867</td>
<td align="center">1867</td>
</tr>
</tbody>
</table>
@ -1144,7 +1144,7 @@ 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">#&gt; [1] 0.5837996</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 0.5813935</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">
@ -1159,19 +1159,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5860452</td>
<td align="center">0.5902375</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5836969</td>
<td align="center">0.5636153</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5804851</td>
<td align="center">0.5920537</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5831363</td>
<td align="center">0.5911290</td>
</tr>
</tbody>
</table>
@ -1196,23 +1196,23 @@ 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">0.5860452</td>
<td align="center">3626</td>
<td align="center">0.5902375</td>
<td align="center">3790</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5836969</td>
<td align="center">4355</td>
<td align="center">0.5636153</td>
<td align="center">4315</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5804851</td>
<td align="center">1814</td>
<td align="center">0.5920537</td>
<td align="center">1787</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5831363</td>
<td align="center">2538</td>
<td align="center">0.5911290</td>
<td align="center">2480</td>
</tr>
</tbody>
</table>
@ -1237,27 +1237,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6682083</td>
<td align="center">0.6425146</td>
<td align="center">0.8795820</td>
<td align="center">0.6703444</td>
<td align="center">0.6482782</td>
<td align="center">0.8836510</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6477795</td>
<td align="center">0.6569678</td>
<td align="center">0.8843798</td>
<td align="center">0.6513410</td>
<td align="center">0.6636015</td>
<td align="center">0.8919540</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6564195</td>
<td align="center">0.6467752</td>
<td align="center">0.8758288</td>
<td align="center">0.6615911</td>
<td align="center">0.6737104</td>
<td align="center">0.8899938</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4820951</td>
<td align="center">0.4654526</td>
<td align="center">0.0000000</td>
<td align="center">0.4820951</td>
<td align="center">0.4654526</td>
</tr>
</tbody>
</table>
@ -1285,23 +1285,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">58.6%</td>
<td align="right">36.4%</td>
<td align="right">59.0%</td>
<td align="right">38.0%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">58.4%</td>
<td align="right">37.2%</td>
<td align="right">56.4%</td>
<td align="right">35.0%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">58.0%</td>
<td align="right">35.9%</td>
<td align="right">59.2%</td>
<td align="right">37.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">58.3%</td>
<td align="right">36.0%</td>
<td align="right">59.1%</td>
<td align="right">36.1%</td>
</tr>
</tbody>
</table>
@ -1417,16 +1417,16 @@ 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">#&gt; Class 'mic'</span></span>
<span><span class="co">#&gt; [1] 16 0.0625 0.0625 0.002 32 1 1 0.001 1 0.025 </span></span>
<span><span class="co">#&gt; [11] 32 2 256 0.25 64 0.25 4 0.025 256 0.25 </span></span>
<span><span class="co">#&gt; [21] 0.125 0.005 1 4 16 16 2 2 1 0.0625</span></span>
<span><span class="co">#&gt; [31] 0.125 0.025 8 0.002 16 0.0625 0.5 256 128 0.001 </span></span>
<span><span class="co">#&gt; [41] 8 1 0.01 0.001 0.01 64 16 32 128 64 </span></span>
<span><span class="co">#&gt; [51] 256 0.01 0.01 0.001 0.002 64 0.01 0.001 0.01 0.125 </span></span>
<span><span class="co">#&gt; [61] 0.01 0.125 128 0.01 64 8 32 64 2 1 </span></span>
<span><span class="co">#&gt; [71] 0.005 0.125 2 0.025 0.125 0.01 4 0.002 0.005 2 </span></span>
<span><span class="co">#&gt; [81] 4 64 8 0.002 0.125 256 16 1 2 0.5 </span></span>
<span><span class="co">#&gt; [91] 1 0.0625 32 0.001 2 0.025 0.002 0.002 0.25 1</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 16 128 0.01 0.002 4 16 0.01 0.01 128 0.5 </span></span>
<span><span class="co">#&gt; [11] 1 4 0.01 16 64 0.25 16 4 0.0625 0.002 </span></span>
<span><span class="co">#&gt; [21] 4 0.5 0.5 0.001 0.125 32 64 0.005 0.025 0.0625</span></span>
<span><span class="co">#&gt; [31] 0.125 32 0.25 0.25 0.5 0.001 32 0.01 8 256 </span></span>
<span><span class="co">#&gt; [41] 0.5 64 256 0.025 1 0.025 2 32 8 0.01 </span></span>
<span><span class="co">#&gt; [51] 0.025 0.01 0.001 0.0625 1 1 16 0.001 64 0.125 </span></span>
<span><span class="co">#&gt; [61] 0.0625 0.025 8 128 4 4 0.025 16 8 1 </span></span>
<span><span class="co">#&gt; [71] 4 2 0.5 0.5 1 0.002 128 256 0.025 0.005 </span></span>
<span><span class="co">#&gt; [81] 64 2 0.25 64 0.002 0.005 1 256 64 0.001 </span></span>
<span><span class="co">#&gt; [91] 8 64 0.25 4 1 32 16 2 32 8</span></span></code></pre></div>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1460,10 +1460,10 @@ 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">#&gt; Class 'disk'</span></span>
<span><span class="co">#&gt; [1] 29 27 23 23 27 24 27 29 26 18 17 28 21 27 22 20 17 18 21 23 19 25 30 22 18</span></span>
<span><span class="co">#&gt; [26] 21 25 27 17 27 22 28 18 27 21 29 19 28 24 29 27 26 18 29 30 25 24 25 22 17</span></span>
<span><span class="co">#&gt; [51] 30 30 29 21 29 19 21 26 17 31 23 25 27 29 19 18 18 30 18 24 18 26 27 21 25</span></span>
<span><span class="co">#&gt; [76] 30 26 19 17 19 27 31 19 19 23 29 30 22 19 30 17 24 31 26 29 19 20 23 25 30</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 23 30 22 17 17 18 24 30 24 17 19 28 19 31 28 17 28 18 20 31 27 25 22 22 18</span></span>
<span><span class="co">#&gt; [26] 30 29 25 26 25 20 18 26 26 28 21 22 25 19 27 22 31 19 18 25 30 24 28 30 19</span></span>
<span><span class="co">#&gt; [51] 22 18 26 19 20 20 31 26 30 22 17 17 27 23 19 30 27 28 25 28 20 23 28 27 19</span></span>
<span><span class="co">#&gt; [76] 25 30 25 27 28 24 24 21 22 22 31 21 21 27 17 19 29 29 29 26 28 21 28 29 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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@ -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="">1.8.2.9145</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9146</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">

60
articles/MDR.html
View File

@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9146</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">
@ -385,19 +385,19 @@ 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">#&gt; rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co">#&gt; 1 I I R R S S</span></span>
<span><span class="co">#&gt; 2 I R I I R S</span></span>
<span><span class="co">#&gt; 3 S S R S I I</span></span>
<span><span class="co">#&gt; 4 I S S S S R</span></span>
<span><span class="co">#&gt; 5 S S I I I I</span></span>
<span><span class="co">#&gt; 6 R S R R S S</span></span>
<span><span class="co">#&gt; 1 R R I S S R</span></span>
<span><span class="co">#&gt; 2 I R S R S R</span></span>
<span><span class="co">#&gt; 3 S R I S S R</span></span>
<span><span class="co">#&gt; 4 R R I S R S</span></span>
<span><span class="co">#&gt; 5 R R I I S I</span></span>
<span><span class="co">#&gt; 6 I R I R S R</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 R</span></span>
<span><span class="co">#&gt; 2 S</span></span>
<span><span class="co">#&gt; 3 I</span></span>
<span><span class="co">#&gt; 4 R</span></span>
<span><span class="co">#&gt; 5 R</span></span>
<span><span class="co">#&gt; 6 R</span></span></code></pre></div>
<span><span class="co">#&gt; 2 R</span></span>
<span><span class="co">#&gt; 3 S</span></span>
<span><span class="co">#&gt; 4 S</span></span>
<span><span class="co">#&gt; 5 S</span></span>
<span><span class="co">#&gt; 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">
@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3218</td>
<td align="right">64.36%</td>
<td align="right">3218</td>
<td align="right">64.36%</td>
<td align="right">3270</td>
<td align="right">65.40%</td>
<td align="right">3270</td>
<td align="right">65.40%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">991</td>
<td align="right">19.82%</td>
<td align="right">4209</td>
<td align="right">84.18%</td>
<td align="right">967</td>
<td align="right">19.34%</td>
<td align="right">4237</td>
<td align="right">84.74%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">442</td>
<td align="right">8.84%</td>
<td align="right">4651</td>
<td align="right">93.02%</td>
<td align="right">437</td>
<td align="right">8.74%</td>
<td align="right">4674</td>
<td align="right">93.48%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">241</td>
<td align="right">4.82%</td>
<td align="right">4892</td>
<td align="right">97.84%</td>
<td align="right">227</td>
<td align="right">4.54%</td>
<td align="right">4901</td>
<td align="right">98.02%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">108</td>
<td align="right">2.16%</td>
<td align="right">99</td>
<td align="right">1.98%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

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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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@ -142,7 +142,7 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="1.8.2.9145" id="amr-1829145">AMR 1.8.2.9145<a class="anchor" aria-label="anchor" href="#amr-1829145"></a></h2>
<h2 class="pkg-version" data-toc-text="1.8.2.9146" id="amr-1829146">AMR 1.8.2.9146<a class="anchor" aria-label="anchor" href="#amr-1829146"></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>
@ -156,32 +156,32 @@
<li>Now available in 20 languages</li>
<li>Many small bug fixes</li>
</ul><div class="section level3">
<h3 id="new-1-8-2-9145">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9145"></a></h3>
<h3 id="new-1-8-2-9146">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9146"></a></h3>
<div class="section level4">
<h4 id="sir-vs-rsi-1-8-2-9145">SIR vs. RSI<a class="anchor" aria-label="anchor" href="#sir-vs-rsi-1-8-2-9145"></a></h4>
<h4 id="sir-vs-rsi-1-8-2-9146">SIR vs. RSI<a class="anchor" aria-label="anchor" href="#sir-vs-rsi-1-8-2-9146"></a></h4>
<p>For this milestone version, we replaced all mentions of RSI with SIR, to comply with what is actually being commonly used in the field of clinical microbiology when it comes to this tri-form regarding AMR.</p>
<p>While existing functions such as <code><a href="../reference/AMR-deprecated.html">as.rsi()</a></code>, <code><a href="../reference/AMR-deprecated.html">rsi_df()</a></code> and <code><a href="../reference/AMR-deprecated.html">ggplot_rsi()</a></code> still work, their replacements <code><a href="../reference/as.sir.html">as.sir()</a></code>, <code><a href="../reference/proportion.html">sir_df()</a></code>, <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a></code> are now the current functions for AMR data analysis. A warning will be thrown once a session to remind users about this. The data set <code>rsi_translation</code> is now called <code>clinical_breakpoints</code> to better reflect its content.</p>
<p>The ‘RSI functions’ will be removed in a future version, but not before late 2023 / early 2024.</p>
</div>
<div class="section level4">
<h4 id="new-antibiogram-function-1-8-2-9145">New antibiogram function<a class="anchor" aria-label="anchor" href="#new-antibiogram-function-1-8-2-9145"></a></h4>
<h4 id="new-antibiogram-function-1-8-2-9146">New antibiogram function<a class="anchor" aria-label="anchor" href="#new-antibiogram-function-1-8-2-9146"></a></h4>
<p>With the new <code><a href="../reference/antibiogram.html">antibiogram()</a></code> function, users can now generate traditional, combined, syndromic, and even weighted-incidence syndromic combination antibiograms (WISCA). With this, we follow the logic in the previously described work of Klinker <em>et al.</em> (2021, DOI <a href="https://doi.org/10.1177/20499361211011373" class="external-link">10.1177/20499361211011373</a>) and Barbieri <em>et al.</em> (2021, DOI <a href="https://doi.org/10.1186/s13756-021-00939-2" class="external-link">10.1186/s13756-021-00939-2</a>).</p>
<p>The help page for <code><a href="../reference/antibiogram.html">antibiogram()</a></code> extensively elaborates on use cases, and <code><a href="../reference/antibiogram.html">antibiogram()</a></code> also supports printing in R Markdown and Quarto, with support for 20 languages.</p>
<p>Furthermore, different plotting methods were implemented to allow for graphical visualisations as well.</p>
</div>
<div class="section level4">
<h4 id="interpretation-of-mic-and-disk-diffusion-values-1-8-2-9145">Interpretation of MIC and disk diffusion values<a class="anchor" aria-label="anchor" href="#interpretation-of-mic-and-disk-diffusion-values-1-8-2-9145"></a></h4>
<h4 id="interpretation-of-mic-and-disk-diffusion-values-1-8-2-9146">Interpretation of MIC and disk diffusion values<a class="anchor" aria-label="anchor" href="#interpretation-of-mic-and-disk-diffusion-values-1-8-2-9146"></a></h4>
<p>The clinical breakpoints and intrinsic resistance of EUCAST 2022 and CLSI 2022 have been added for <code><a href="../reference/as.sir.html">as.sir()</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>With the new arguments <code>include_PKPD</code> (default: <code>TRUE</code>) and <code>include_screening</code> (default: <code>FALSE</code>), users can now specify whether breakpoints for screening and from the PK/PD table should be included when interpreting MICs and disks diffusion values. These options can be set globally, which can be read in <a href="https://msberends.github.io/AMR/reference/AMR-options.html">our new manual</a>.</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-1-8-2-9145">Supported languages<a class="anchor" aria-label="anchor" href="#supported-languages-1-8-2-9145"></a></h4>
<h4 id="supported-languages-1-8-2-9146">Supported languages<a class="anchor" aria-label="anchor" href="#supported-languages-1-8-2-9146"></a></h4>
<p>We added support for the following ten languages: Chinese (simplified), Czech, Finnish, Greek, Japanese, Norwegian (bokmål), Polish, Romanian, 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’s 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 20 languages in total, and according to download stats used in almost all countries in the world!</p>
</div>
<div class="section level4">
<h4 id="microbiological-taxonomy-1-8-2-9145">Microbiological taxonomy<a class="anchor" aria-label="anchor" href="#microbiological-taxonomy-1-8-2-9145"></a></h4>
<h4 id="microbiological-taxonomy-1-8-2-9146">Microbiological taxonomy<a class="anchor" aria-label="anchor" href="#microbiological-taxonomy-1-8-2-9146"></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>
@ -205,7 +205,7 @@
<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-1-8-2-9145">Antibiotic agents and selectors<a class="anchor" aria-label="anchor" href="#antibiotic-agents-and-selectors-1-8-2-9145"></a></h4>
<h4 id="antibiotic-agents-and-selectors-1-8-2-9146">Antibiotic agents and selectors<a class="anchor" aria-label="anchor" href="#antibiotic-agents-and-selectors-1-8-2-9146"></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>
@ -217,14 +217,14 @@
</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-1-8-2-9145">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents-1-8-2-9145"></a></h4>
<h4 id="antiviral-agents-1-8-2-9146">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents-1-8-2-9146"></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-1-8-2-9145">Other new functions<a class="anchor" aria-label="anchor" href="#other-new-functions-1-8-2-9145"></a></h4>
<h4 id="other-new-functions-1-8-2-9146">Other new functions<a class="anchor" aria-label="anchor" href="#other-new-functions-1-8-2-9146"></a></h4>
<ul><li>Function <code><a href="../reference/proportion.html">sir_confidence_interval()</a></code> to add confidence intervals in AMR calculation. This is now also included in <code><a href="../reference/proportion.html">sir_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.sir.html">sir_interpretation_history()</a></code> to view the history of previous runs of <code><a href="../reference/as.sir.html">as.sir()</a></code> (previously <code><a href="../reference/AMR-deprecated.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.sir.html">as.sir()</a></code> was run.</li>
@ -233,7 +233,7 @@
</ul></div>
</div>
<div class="section level3">
<h3 id="changes-1-8-2-9145">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9145"></a></h3>
<h3 id="changes-1-8-2-9146">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9146"></a></h3>
<ul><li>
<code><a href="../reference/get_episode.html">get_episode()</a></code> (and its wrapper <code><a href="../reference/get_episode.html">is_new_episode()</a></code>):
<ul><li>Gained an argument <code>new_after_days</code> to determine episodes based on epidemic periods</li>
@ -282,7 +282,7 @@
<code>mo_synonyns()</code> now contains the scientific reference as names</li>
</ul></div>
<div class="section level3">
<h3 id="other-1-8-2-9145">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9145"></a></h3>
<h3 id="other-1-8-2-9146">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9146"></a></h3>
<ul><li>Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, Andrew Norgan, Jonas Salm, and Anita Williams as contributors, to thank them for their valuable input</li>
<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>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>

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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: 2023-02-24T16:10Z
last_built: 2023-02-24T18:58Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

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@ -18,7 +18,7 @@ The AMR package is available in English, Chinese, Danish, Dutch, French, German,
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@ -10,7 +10,7 @@
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reference/ab_from_text.html
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@ -10,7 +10,7 @@
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reference/ab_property.html
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reference/add_custom_antimicrobials.html
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@ -10,7 +10,7 @@
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reference/add_custom_microorganisms.html
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@ -10,7 +10,7 @@
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reference/age.html
View File

@ -10,7 +10,7 @@
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@ -205,16 +205,16 @@
<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 1951-07-26 71 71.58356 48</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1957-01-31 66 66.06575 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1986-04-15 36 36.86301 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1942-10-08 80 80.38082 57</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-02-25 90 90.99726 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1986-05-12 36 36.78904 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1986-10-24 36 36.33699 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1969-12-26 53 53.16438 30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1941-07-07 81 81.63562 58</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1984-12-17 38 38.18904 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1977-05-02 45 45.81644 22</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1988-09-17 34 34.43836 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1942-02-25 80 80.99726 57</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1991-02-14 32 32.02740 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1985-03-09 37 37.96438 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1980-07-27 42 42.58082 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1942-06-08 80 80.71507 57</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1954-12-30 68 68.15342 45</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-30 50 50.65479 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1935-07-18 87 87.60548 64</span>
</code></pre></div>
</div>
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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reference/as.mo.html
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@ -10,7 +10,7 @@
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reference/as.sir.html
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@ -12,7 +12,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
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@ -534,16 +534,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 17</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_guid…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> 2023-02-24 <span style="color: #949494;">16:11:48</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;"> 2</span> 2023-02-24 <span style="color: #949494;">16:11:47</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;"> 3</span> 2023-02-24 <span style="color: #949494;">16:11:47</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> 2023-02-24 <span style="color: #949494;">16:11:47</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;"> 5</span> 2023-02-24 <span style="color: #949494;">16:11:40</span> 1 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-02-24 <span style="color: #949494;">16:11:40</span> 2 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-02-24 <span style="color: #949494;">16:11:40</span> 3 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-02-24 <span style="color: #949494;">16:11:40</span> 4 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-02-24 <span style="color: #949494;">16:11:40</span> 5 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-02-24 <span style="color: #949494;">16:11:40</span> 6 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-02-24 <span style="color: #949494;">18:59:29</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;"> 2</span> 2023-02-24 <span style="color: #949494;">18:59:29</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;"> 3</span> 2023-02-24 <span style="color: #949494;">18:59:28</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> 2023-02-24 <span style="color: #949494;">18:59:28</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;"> 5</span> 2023-02-24 <span style="color: #949494;">18:59:23</span> 1 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-02-24 <span style="color: #949494;">18:59:23</span> 2 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-02-24 <span style="color: #949494;">18:59:23</span> 3 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-02-24 <span style="color: #949494;">18:59:23</span> 4 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-02-24 <span style="color: #949494;">18:59:23</span> 5 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-02-24 <span style="color: #949494;">18:59:23</span> 6 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 10 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;sir&gt;, breakpoint_S_R &lt;chr&gt;, ab_considered &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># mo_considered &lt;lgl&gt;, breakpoint_S &lt;lgl&gt;, breakpoint_R &lt;lgl&gt;,</span></span>

2
reference/atc_online.html
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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2
reference/dosage.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</small>
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2
reference/eucast_rules.html
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@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<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="">1.8.2.9145</small>
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2
reference/example_isolates.html
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@ -10,7 +10,7 @@
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reference/example_isolates_unclean.html
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@ -10,7 +10,7 @@
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2
reference/first_isolate.html
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@ -12,7 +12,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/g.test.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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122
reference/get_episode.html
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2
reference/ggplot_pca.html
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@ -10,7 +10,7 @@
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2
reference/ggplot_sir.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="">1.8.2.9145</small>
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2
reference/guess_ab_col.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="">1.8.2.9145</small>
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2
reference/index.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</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="">1.8.2.9145</small>
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2
reference/italicise_taxonomy.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="">1.8.2.9145</small>
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2
reference/join.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</small>
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2
reference/key_antimicrobials.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9146</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="">1.8.2.9145</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9146</small>
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@ -182,9 +182,9 @@
<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] 2.965401</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.980001</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] 0.03055707</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.02531765</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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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/mdro.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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73
reference/mean_amr_distance.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</small>
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@ -201,31 +201,30 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</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">sir</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S S I I R I I R I R</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S R I S S R S I I S</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.621059 -0.621059 -0.621059 -0.621059 1.449138 -0.621059 -0.621059</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [8] 1.449138 -0.621059 1.449138</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.4743416 1.8973666 -0.4743416 -0.4743416 -0.4743416 1.8973666</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.4743416 -0.4743416 -0.4743416 -0.4743416</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 0.5 0.0625 &lt;=0.001 &gt;=128 0.5 32 &gt;=128 0.002 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.25 64 64 0.01 0.025 128 256 4 128 256 </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] -0.90187954 -0.05159359 -0.50356433 -1.40235097 1.15366171 -0.05159359</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.85234788 1.15366171 -1.25169406 1.00300479</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.8840919 0.5294878 0.5294878 -1.7046495 -1.4710682 0.7061853</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.8828827 -0.1773020 0.7061853 0.8828827</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] -0.90187954 -0.05159359 -0.50356433 -1.40235097 1.15366171 -0.05159359</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.85234788 1.15366171 -1.25169406 1.00300479</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.8840919 0.5294878 0.5294878 -1.7046495 -1.4710682 0.7061853</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.8828827 -0.1773020 0.7061853 0.8828827</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] 31 43 47 11 50 40 41 6 40 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 13 36 18 50 14 40 38 15 45 48</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] -0.06075813 0.66833944 0.91137196 -1.27592075 1.09364635 0.48606505</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.54682318 -1.57971140 0.48606505 -1.27592075</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.2438749 0.2860247 -0.9112880 1.2172680 -1.1773575 0.5520942</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.4190595 -1.1108402 0.8846811 1.0842332</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>
@ -235,22 +234,22 @@
<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 S 23 &lt;=0.25 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B S 22 &lt;=0.25 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C R 22 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D S 29 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E R 25 &gt;=4 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F I 17 0.5 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G R 29 &gt;=4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H R 19 0.5 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I R 24 1 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J I 22 0.5 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A I 17 &lt;=1 &lt;=0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B R 20 &lt;=1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C R 28 &gt;=16 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D R 22 &gt;=16 &lt;=0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E I 24 &gt;=16 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F R 30 &gt;=16 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G R 17 &gt;=16 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H I 23 2 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I I 27 8 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 19 8 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> and "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.6549761 -0.4877892 0.2461508 0.2294569 0.3737749 -0.4180608</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.8678531 0.1870373 -0.0197123 -0.3237347</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.29633203 -0.33470083 0.68999803 0.04843526 0.30058957 0.64264079</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.40191868 -0.19451042 -0.15234167 -0.10569739</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
@ -266,17 +265,17 @@
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and "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 R 22 2 1 0.2461508 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 D S 29 2 1 0.2294569 0.01669387</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 H R 19 0.5 &gt;=4 0.1870373 0.05911349</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 E R 25 &gt;=4 0.5 0.3737749 0.12762412</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 I R 24 1 0.5 -0.0197123 0.26586311</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 J I 22 0.5 2 -0.3237347 0.56988550</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G R 29 &gt;=4 1 0.8678531 0.62170227</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 F I 17 0.5 &gt;=4 -0.4180608 0.66421164</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 B S 22 &lt;=0.25 2 -0.4877892 0.73393999</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 A S 23 &lt;=0.25 1 -0.6549761 0.90112686</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 R 28 &gt;=16 1 0.68999803 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 F R 30 &gt;=16 0.5 0.64264079 0.04735723</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 G R 17 &gt;=16 &gt;=4 0.40191868 0.28807934</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 E I 24 &gt;=16 &gt;=4 0.30058957 0.38940845</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 D R 22 &gt;=16 &lt;=0.25 0.04843526 0.64156276</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 J R 19 8 0.5 -0.10569739 0.79569542</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 I I 27 8 0.5 -0.15234167 0.84233970</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H I 23 2 &gt;=4 -0.19451042 0.88450845</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 B R 20 &lt;=1 1 -0.33470083 1.02469886</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 A I 17 &lt;=1 &lt;=0.25 -1.29633203 1.98633005</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>

2
reference/microorganisms.codes.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/microorganisms.html
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@ -10,7 +10,7 @@
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2
reference/mo_matching_score.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</small>
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2
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="">1.8.2.9145</small>
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2
reference/mo_source.html
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@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -10,7 +10,7 @@
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reference/plot.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</small>
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2
reference/proportion.html
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@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</small>
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35
reference/random.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9146</small>
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@ -193,42 +193,43 @@
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01 1 0.125 &gt;=256 32 0.005 0.25 0.25 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 32 64 0.125 32 4 0.0625 16 &lt;=0.001 &gt;=256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 1 1 32 0.125 2 16 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 256 0.005 0.5 0.001 64 0.0625 0.005 0.005 0.001 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.125 0.0625 0.0625 0.002 32 2 0.0625 4 2 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.005 0.002 0.005 16 128 </span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 18 26 28 25 20 42 41 9 45 22 49 25 50 32 23 20 23 41 46 28 46 40 48 37 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 27 33 26 44 31 47 13 50 24 9 44 6 44 50 7 45 9 21 41 23 15 9 42 9 40</span>
<span class="r-in"><span><span class="fu">random_sir</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S S R R S S R R R I I S S I I I R I I R I R R I S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R R I R S R I R S I S R R S R I S R I S I I I S I</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.001 32 128 128 8 4 0.25 0.005 0.01 128 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.002 0.01 0.25 0.002 0.025 1 4 0.25 16 128 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 128 8 0.5 0.0625 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01 0.25 &lt;=0.001 16 0.002 0.125 4 0.25 &gt;=64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 1 &lt;=0.001 0.005 0.125 0.025 &lt;=0.001 2 0.5 &lt;=0.001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.002 0.25 0.0625 0.025 0.25 0.25 0.01 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5 16 0.5 0.5 &gt;=32 8 8 1 8 &gt;=32 &gt;=32 2 0.5 0.5 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] 2 0.5 4 2 1 0.5 &gt;=32 2 0.5 0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 32 16 0.5 8 4 &lt;=0.25 2 1 2 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 4 0.5 4 16 8 8 &lt;=0.25 4 32 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.5 0.5 16 0.5 16 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 1 0.25 2 &lt;=0.125 2 0.25 1 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.5 4 &lt;=0.125 0.25 4 0.25 0.5 2 &lt;=0.125</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 2 1 1 0.25 &lt;=0.125 0.5 &lt;=0.125</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.25 &gt;=8 0.5 0.0625 0.5 0.0625 0.25 0.5 4 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 4 1 1 &gt;=8 &gt;=8 &gt;=8 2 0.25 0.25 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] &gt;=8 &gt;=8 0.5 0.25 1 </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 41 46 50 12 9 33 34 12 50 35 19 12 41 34 13 48 10 42 16 20 10 49 29 17 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 47 43 49 8 36 33 21 38 30 39 13 41 22 47 21 19 12 47 12 36 46 48 47 27</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 12 13 11 16 16 14 14 12 13 17 17 16 13 13 13 15 15 17 13 17 15 11 12 16 12</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 15 11 17 17 11 17 12 17 16 17 16 13 13 12 16 14 13 11 11 12 13 11 13 12 11</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 23 25 25 19 23 18 25 16 17 15 22 24 15 22 17 15 26 25 25 21 25 22 16 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 20 17 19 16 20 24 17 23 19 25 27 19 22 19 23 18 23 24 21 24 26 21 27 18 17</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>

2
reference/resistance_predict.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</small>
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4
reference/skewness.html
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@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9146</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">
@ -181,7 +181,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.07241631</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.002064919</span>
</code></pre></div>
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reference/translate.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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