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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="">1.8.2.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9033</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">
@ -325,71 +325,71 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-03-10</td>
<td align="center">E9</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-04-01</td>
<td align="center">U4</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2013-08-12</td>
<td align="center">S7</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-05-02</td>
<td align="center">K4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-07-08</td>
<td align="center">E6</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-10-16</td>
<td align="center">Q1</td>
<td align="center">2010-01-20</td>
<td align="center">Z10</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-09-08</td>
<td align="center">C9</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">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-07-12</td>
<td align="center">K7</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-11-04</td>
<td align="center">C6</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2017-04-16</td>
<td align="center">Y8</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-07-17</td>
<td align="center">C7</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">S</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -422,16 +422,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,416</td>
<td align="right">52.08%</td>
<td align="right">10,416</td>
<td align="right">52.08%</td>
<td align="right">10,226</td>
<td align="right">51.13%</td>
<td align="right">10,226</td>
<td align="right">51.13%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,584</td>
<td align="right">47.92%</td>
<td align="right">9,774</td>
<td align="right">48.87%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -488,7 +488,7 @@ Longest: 1</p>
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,729 'phenotype-based' first isolates (53.6% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,719 'phenotype-based' first isolates (53.6% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.6% 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">
@ -499,10 +499,10 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,729 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,719 isolates for analysis. Now our data looks like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<table style="width:100%;" class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -516,7 +516,7 @@ Longest: 1</p>
<col width="6%">
<col width="11%">
<col width="12%">
<col width="7%">
<col width="9%">
<col width="5%">
</colgroup>
<thead><tr class="header">
@ -537,10 +537,10 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">2</td>
<td align="center">2013-04-01</td>
<td align="center">U4</td>
<td align="center">Hospital D</td>
<td align="left">1</td>
<td align="center">2010-01-20</td>
<td align="center">Z10</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -553,30 +553,14 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">3</td>
<td align="center">2013-08-12</td>
<td align="center">S7</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2014-05-02</td>
<td align="center">K4</td>
<td align="center">Hospital B</td>
<td align="center">2014-11-04</td>
<td align="center">C6</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
@ -584,49 +568,65 @@ Longest: 1</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">2016-07-08</td>
<td align="center">E6</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">7</td>
<td align="center">2017-02-23</td>
<td align="center">B4</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2016-11-10</td>
<td align="center">V1</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">2011-08-14</td>
<td align="center">S4</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">11</td>
<td align="center">2013-07-11</td>
<td align="center">X7</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">13</td>
<td align="center">2013-09-05</td>
<td align="center">O5</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="even">
<td align="left">14</td>
<td align="center">2016-11-07</td>
<td align="center">H9</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">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>
@ -653,8 +653,8 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,729<br>
Available: 10,729 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,719<br>
Available: 10,719 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -671,33 +671,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,633</td>
<td align="right">43.18%</td>
<td align="right">4,633</td>
<td align="right">43.18%</td>
<td align="right">4,673</td>
<td align="right">43.60%</td>
<td align="right">4,673</td>
<td align="right">43.60%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,796</td>
<td align="right">26.06%</td>
<td align="right">7,429</td>
<td align="right">69.24%</td>
<td align="right">2,754</td>
<td align="right">25.69%</td>
<td align="right">7,427</td>
<td align="right">69.29%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,137</td>
<td align="right">19.92%</td>
<td align="right">9,566</td>
<td align="right">89.16%</td>
<td align="right">2,094</td>
<td align="right">19.54%</td>
<td align="right">9,521</td>
<td align="right">88.82%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,163</td>
<td align="right">10.84%</td>
<td align="right">10,729</td>
<td align="right">1,198</td>
<td align="right">11.18%</td>
<td align="right">10,719</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -716,14 +716,14 @@ Longest: 24</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="10%">
<col width="11%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@ -744,23 +744,23 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-02-23</td>
<td align="center">B4</td>
<td align="center">2013-09-05</td>
<td align="center">O5</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-01-27</td>
<td align="center">M1</td>
<td align="center">2017-10-30</td>
<td align="center">K1</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
@ -774,39 +774,39 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-07-10</td>
<td align="center">U10</td>
<td align="center">2012-03-15</td>
<td align="center">L1</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</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">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">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-03-06</td>
<td align="center">X10</td>
<td align="center">Hospital D</td>
<td align="center">2014-11-12</td>
<td align="center">E8</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">R</td>
<td align="center">F</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-08-29</td>
<td align="center">F1</td>
<td align="center">Hospital B</td>
<td align="center">2015-08-26</td>
<td align="center">A3</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
@ -819,8 +819,8 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-05-24</td>
<td align="center">N8</td>
<td align="center">2012-07-18</td>
<td align="center">R9</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
@ -854,50 +854,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2202</td>
<td align="center">119</td>
<td align="center">2312</td>
<td align="center">4633</td>
<td align="center">2221</td>
<td align="center">115</td>
<td align="center">2337</td>
<td align="center">4673</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3411</td>
<td align="center">175</td>
<td align="center">1047</td>
<td align="center">4633</td>
<td align="center">3415</td>
<td align="center">161</td>
<td align="center">1097</td>
<td align="center">4673</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3383</td>
<td align="center">3488</td>
<td align="center">0</td>
<td align="center">1250</td>
<td align="center">4633</td>
<td align="center">1185</td>
<td align="center">4673</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4044</td>
<td align="center">4081</td>
<td align="center">0</td>
<td align="center">589</td>
<td align="center">4633</td>
<td align="center">592</td>
<td align="center">4673</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1163</td>
<td align="center">1163</td>
<td align="center">1198</td>
<td align="center">1198</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">917</td>
<td align="center">41</td>
<td align="center">205</td>
<td align="center">1163</td>
<td align="center">959</td>
<td align="center">35</td>
<td align="center">204</td>
<td align="center">1198</td>
</tr>
</tbody>
</table>
@ -920,34 +920,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4044</td>
<td align="center">4081</td>
<td align="center">0</td>
<td align="center">589</td>
<td align="center">4633</td>
<td align="center">592</td>
<td align="center">4673</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1035</td>
<td align="center">1069</td>
<td align="center">0</td>
<td align="center">128</td>
<td align="center">1163</td>
<td align="center">129</td>
<td align="center">1198</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2484</td>
<td align="center">2441</td>
<td align="center">0</td>
<td align="center">312</td>
<td align="center">2796</td>
<td align="center">313</td>
<td align="center">2754</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">2137</td>
<td align="center">2137</td>
<td align="center">2094</td>
<td align="center">2094</td>
</tr>
</tbody>
</table>
@ -961,7 +961,7 @@ Longest: 24</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5444123</span></span></code></pre></div>
<span><span class="co"># [1] 0.5500513</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@ -975,19 +975,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5464199</td>
<td align="center">0.5483379</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5451604</td>
<td align="center">0.5483871</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5317705</td>
<td align="center">0.5518331</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5496909</td>
<td align="center">0.5542563</td>
</tr>
</tbody>
</table>
@ -1008,23 +1008,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5464199</td>
<td align="center">3296</td>
<td align="center">0.5483379</td>
<td align="center">3279</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5451604</td>
<td align="center">3709</td>
<td align="center">0.5483871</td>
<td align="center">3720</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5317705</td>
<td align="center">1621</td>
<td align="center">0.5518331</td>
<td align="center">1582</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5496909</td>
<td align="center">2103</td>
<td align="center">0.5542563</td>
<td align="center">2138</td>
</tr>
</tbody>
</table>
@ -1047,27 +1047,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7740125</td>
<td align="center">0.8728686</td>
<td align="center">0.9769048</td>
<td align="center">0.7652472</td>
<td align="center">0.8733148</td>
<td align="center">0.9736786</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8237317</td>
<td align="center">0.8899398</td>
<td align="center">0.9724850</td>
<td align="center">0.8297162</td>
<td align="center">0.8923205</td>
<td align="center">0.9774624</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7914878</td>
<td align="center">0.8884120</td>
<td align="center">0.9846209</td>
<td align="center">0.7803195</td>
<td align="center">0.8863471</td>
<td align="center">0.9803922</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5297146</td>
<td align="center">0.5272206</td>
<td align="center">0.0000000</td>
<td align="center">0.5297146</td>
<td align="center">0.5272206</td>
</tr>
</tbody>
</table>
@ -1092,23 +1092,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.6%</td>
<td align="right">27.2%</td>
<td align="right">54.8%</td>
<td align="right">26.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.5%</td>
<td align="right">26.0%</td>
<td align="right">54.8%</td>
<td align="right">27.2%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">53.2%</td>
<td align="right">25.6%</td>
<td align="right">55.2%</td>
<td align="right">27.4%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">55.0%</td>
<td align="right">26.9%</td>
<td align="right">55.4%</td>
<td align="right">27.7%</td>
</tr>
</tbody>
</table>
@ -1206,18 +1206,16 @@ Longest: 24</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] &lt;=0.001 2 0.25 0.002 0.0625 1 0.002 32 1 </span></span>
<span><span class="co"># [10] 0.5 1 0.025 0.5 &lt;=0.001 0.005 4 &gt;=256 4 </span></span>
<span><span class="co"># [19] 8 1 16 0.002 &lt;=0.001 0.002 4 0.025 8 </span></span>
<span><span class="co"># [28] 16 16 1 0.25 &lt;=0.001 16 0.005 0.005 &lt;=0.001</span></span>
<span><span class="co"># [37] &lt;=0.001 16 &gt;=256 16 128 0.0625 1 0.25 0.005 </span></span>
<span><span class="co"># [46] 0.01 0.002 0.5 128 64 0.01 8 128 1 </span></span>
<span><span class="co"># [55] &gt;=256 &gt;=256 1 0.125 &lt;=0.001 0.25 64 2 0.002 </span></span>
<span><span class="co"># [64] &gt;=256 16 1 &gt;=256 0.5 8 &gt;=256 &gt;=256 0.005 </span></span>
<span><span class="co"># [73] 0.002 2 0.25 0.25 &lt;=0.001 0.0625 0.01 0.125 1 </span></span>
<span><span class="co"># [82] 0.005 0.125 0.25 2 0.025 0.025 32 1 0.25 </span></span>
<span><span class="co"># [91] 0.005 0.01 1 0.5 1 0.0625 0.5 4 1 </span></span>
<span><span class="co"># [100] 64</span></span></code></pre></div>
<span><span class="co"># [1] 4 0.001 0.005 0.25 0.125 0.25 32 64 32 128 </span></span>
<span><span class="co"># [11] 128 128 0.5 0.001 0.002 16 0.0625 4 0.0625 2 </span></span>
<span><span class="co"># [21] 0.002 0.025 0.5 0.01 1 32 0.5 0.5 4 0.125 </span></span>
<span><span class="co"># [31] 16 0.0625 32 4 32 256 0.001 0.001 0.25 0.01 </span></span>
<span><span class="co"># [41] 0.5 2 64 0.125 128 4 0.001 32 0.01 0.125 </span></span>
<span><span class="co"># [51] 64 0.005 0.001 64 0.005 256 0.001 0.01 0.5 32 </span></span>
<span><span class="co"># [61] 256 0.01 32 16 1 0.005 128 0.0625 0.001 0.001 </span></span>
<span><span class="co"># [71] 2 64 0.002 32 4 0.01 256 0.001 0.005 32 </span></span>
<span><span class="co"># [81] 128 0.002 16 0.125 0.025 2 64 2 0.5 0.001 </span></span>
<span><span class="co"># [91] 0.005 2 0.005 64 0.025 1 0.005 16 64 1</span></span></code></pre></div>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1244,10 +1242,10 @@ Longest: 24</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 27 30 17 21 31 26 25 21 24 31 20 28 23 26 30 22 30 17 23 29 24 30 23 26 19</span></span>
<span><span class="co"># [26] 29 24 23 19 19 30 27 23 31 27 26 24 27 26 20 17 22 29 17 23 20 19 26 28 30</span></span>
<span><span class="co"># [51] 21 30 23 30 30 17 26 25 30 20 24 27 24 20 28 23 22 22 29 18 20 27 22 22 17</span></span>
<span><span class="co"># [76] 30 19 27 27 23 19 23 31 19 26 30 25 22 23 27 28 19 29 19 19 26 26 17 23 17</span></span></code></pre></div>
<span><span class="co"># [1] 29 28 23 31 30 24 29 31 28 24 25 28 30 25 27 21 31 23 30 19 22 28 26 24 28</span></span>
<span><span class="co"># [26] 22 27 28 31 20 24 22 26 17 27 17 17 25 27 23 24 20 26 27 17 22 21 17 23 26</span></span>
<span><span class="co"># [51] 18 25 22 17 24 23 29 20 20 22 19 18 26 28 18 23 28 21 29 23 20 30 19 26 29</span></span>
<span><span class="co"># [76] 19 25 29 23 30 23 26 20 19 27 18 31 29 19 20 17 25 29 23 27 18 28 17 22 28</span></span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>

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2
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="">1.8.2.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9033</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">

58
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="">1.8.2.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9033</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -314,19 +314,19 @@ Unique: 2</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 S R I S S S</span></span>
<span><span class="co"># 2 I S R R R S</span></span>
<span><span class="co"># 3 S R S S I S</span></span>
<span><span class="co"># 4 I R S S R S</span></span>
<span><span class="co"># 5 I S I S S R</span></span>
<span><span class="co"># 6 R I I S S I</span></span>
<span><span class="co"># 1 I S S R S R</span></span>
<span><span class="co"># 2 I R R R S S</span></span>
<span><span class="co"># 3 I I S S R R</span></span>
<span><span class="co"># 4 R R I I R I</span></span>
<span><span class="co"># 5 R I R S S R</span></span>
<span><span class="co"># 6 I I I S I I</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"># 1 S</span></span>
<span><span class="co"># 2 I</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 I</span></span></code></pre></div>
<span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></span></code></pre></div>
@ -357,40 +357,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3216</td>
<td align="right">64.32%</td>
<td align="right">3216</td>
<td align="right">64.32%</td>
<td align="right">3193</td>
<td align="right">63.86%</td>
<td align="right">3193</td>
<td align="right">63.86%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1022</td>
<td align="right">20.44%</td>
<td align="right">4238</td>
<td align="right">84.76%</td>
<td align="right">988</td>
<td align="right">19.76%</td>
<td align="right">4181</td>
<td align="right">83.62%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">414</td>
<td align="right">8.28%</td>
<td align="right">4652</td>
<td align="right">93.04%</td>
<td align="right">429</td>
<td align="right">8.58%</td>
<td align="right">4610</td>
<td align="right">92.20%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">239</td>
<td align="right">4.78%</td>
<td align="right">4891</td>
<td align="right">97.82%</td>
<td align="right">282</td>
<td align="right">5.64%</td>
<td align="right">4892</td>
<td align="right">97.84%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">109</td>
<td align="right">2.18%</td>
<td align="right">108</td>
<td align="right">2.16%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
articles/PCA.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="">1.8.2.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9033</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
articles/SPSS.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9033</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">

18
articles/WHONET.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9033</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">
@ -209,7 +209,7 @@
<p>Class: character<br>
Length: 500<br>
Available: 500 (100.0%, NA: 0 = 0.0%)<br>
Unique: 37</p>
Unique: 38</p>
<p>Shortest: 11<br>
Longest: 40</p>
<table class="table">
@ -256,7 +256,7 @@ Longest: 40</p>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Staphylococcus hominis</td>
<td align="left">Staphylococcus hominis hominis</td>
<td align="right">21</td>
<td align="right">4.2%</td>
<td align="right">409</td>
@ -296,15 +296,15 @@ Longest: 40</p>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="left">Streptococcus anginosus</td>
<td align="right">5</td>
<td align="right">1.0%</td>
<td align="right">444</td>
<td align="right">88.8%</td>
<td align="left">Enterococcus columbae</td>
<td align="right">4</td>
<td align="right">0.8%</td>
<td align="right">443</td>
<td align="right">88.6%</td>
</tr>
</tbody>
</table>
<p>(omitted 27 entries, n = 56 [11.20%])</p>
<p>(omitted 28 entries, n = 57 [11.40%])</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># our transformed antibiotic columns</span></span>
<span><span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span></span>

56
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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="">1.8.2.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9033</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">
@ -175,9 +175,9 @@
<h2 id="microorganisms-full-microbial-taxonomy">
<code>microorganisms</code>: Full Microbial Taxonomy<a class="anchor" aria-label="anchor" href="#microorganisms-full-microbial-taxonomy"></a>
</h2>
<p>A data set with 48,787 rows and 22 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>source</em>, <em>lpsn</em>, <em>lpsn_parent</em>, <em>lpsn_renamed_to</em>, <em>gbif</em>, <em>gbif_parent</em>, <em>gbif_renamed_to</em>, <em>prevalence</em> and <em>snomed</em>.</p>
<p>A data set with 48,788 rows and 22 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>source</em>, <em>lpsn</em>, <em>lpsn_parent</em>, <em>lpsn_renamed_to</em>, <em>gbif</em>, <em>gbif_parent</em>, <em>gbif_renamed_to</em>, <em>prevalence</em> and <em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 22 October 2022 08:21:06 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p>It was last updated on 22 October 2022 20:03:38 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">original R Data Structure (RDS) file</a> (1.1 MB)<br>
@ -232,7 +232,7 @@
</tr>
<tr class="even">
<td align="center">Bacteria</td>
<td align="center">33,713</td>
<td align="center">33,714</td>
</tr>
<tr class="odd">
<td align="center">Fungi</td>
@ -449,7 +449,7 @@
</h2>
<p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 22 October 2022 08:21:06 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 22 October 2022 20:03:38 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">original R Data Structure (RDS) file</a> (36 kB)<br>
@ -622,7 +622,7 @@
</h2>
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 22 October 2022 08:21:06 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 22 October 2022 20:03:38 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">original R Data Structure (RDS) file</a> (4 kB)<br>
@ -752,31 +752,31 @@
<h2 id="rsi_translation-interpretation-from-mic-values-disk-diameters-to-rsi">
<code>rsi_translation</code>: Interpretation from MIC values / disk diameters to R/SI<a class="anchor" aria-label="anchor" href="#rsi_translation-interpretation-from-mic-values-disk-diameters-to-rsi"></a>
</h2>
<p>A data set with 20,369 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>A data set with 18,308 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 22 October 2022 08:21:06 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p>It was last updated on 22 October 2022 20:03:38 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">original R Data Structure (RDS) file</a> (49 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">original R Data Structure (RDS) file</a> (42 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">tab-separated text file</a> (2 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">tab-separated text file</a> (1.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Microsoft Excel workbook</a> (0.9 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Microsoft Excel workbook</a> (0.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.feather" class="external-link">Apache Feather file</a> (0.8 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.feather" class="external-link">Apache Feather file</a> (0.7 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.parquet" class="external-link">Apache Parquet file</a> (99 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.parquet" class="external-link">Apache Parquet file</a> (87 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS data file</a> (4 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS data file</a> (3.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">IBM SPSS Statistics data file</a> (2.6 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">IBM SPSS Statistics data file</a> (2.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata DTA file</a> (3.8 MB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata DTA file</a> (3.4 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-3">Source<a class="anchor" aria-label="anchor" href="#source-3"></a>
</h3>
<p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2011-2022) and EUCAST (2011-2022).</p>
<p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2013-2022) and EUCAST (2013-2022).</p>
</div>
<div class="section level3">
<h3 id="example-content-3">Example content<a class="anchor" aria-label="anchor" href="#example-content-3"></a>
@ -847,9 +847,9 @@
<td align="center">EUCAST 2022</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_CANDD</td>
<td align="center">Candida</td>
<td align="center">3</td>
<td align="center">F_CANDD_ALBC</td>
<td align="center">Candida albicans</td>
<td align="center">2</td>
<td align="center">AMB</td>
<td align="center">Amphotericin B</td>
<td align="center">Candida</td>
@ -862,8 +862,8 @@
<td align="center">EUCAST 2022</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_CANDD_ALBC</td>
<td align="center">Candida albicans</td>
<td align="center">F_CANDD_DBLN</td>
<td align="center">Candida dubliniensis</td>
<td align="center">2</td>
<td align="center">AMB</td>
<td align="center">Amphotericin B</td>
@ -877,8 +877,8 @@
<td align="center">EUCAST 2022</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_CANDD_DBLN</td>
<td align="center">Candida dubliniensis</td>
<td align="center">F_CANDD_GLBR</td>
<td align="center">Candida glabrata</td>
<td align="center">2</td>
<td align="center">AMB</td>
<td align="center">Amphotericin B</td>
@ -913,7 +913,7 @@
</h2>
<p>A data set with 134,659 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 22 October 2022 08:21:06 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p>It was last updated on 22 October 2022 20:03:38 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">original R Data Structure (RDS) file</a> (78 kB)<br>
@ -1185,7 +1185,7 @@
</h2>
<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 22 October 2022 08:21:06 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p>It was last updated on 22 October 2022 20:03:38 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">original R Data Structure (RDS) file</a> (3 kB)<br>
@ -1302,7 +1302,7 @@
</h2>
<p>A data set with 2,000 rows and 46 columns, containing the following column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>, <em>ward</em>, <em>mo</em>, <em>PEN</em>, <em>OXA</em>, <em>FLC</em>, <em>AMX</em>, <em>AMC</em>, <em>AMP</em>, <em>TZP</em>, <em>CZO</em>, <em>FEP</em>, <em>CXM</em>, <em>FOX</em>, <em>CTX</em>, <em>CAZ</em>, <em>CRO</em>, <em>GEN</em>, <em>TOB</em>, <em>AMK</em>, <em>KAN</em>, <em>TMP</em>, <em>SXT</em>, <em>NIT</em>, <em>FOS</em>, <em>LNZ</em>, <em>CIP</em>, <em>MFX</em>, <em>VAN</em>, <em>TEC</em>, <em>TCY</em>, <em>TGC</em>, <em>DOX</em>, <em>ERY</em>, <em>CLI</em>, <em>AZM</em>, <em>IPM</em>, <em>MEM</em>, <em>MTR</em>, <em>CHL</em>, <em>COL</em>, <em>MUP</em> and <em>RIF</em>.</p>
<p>This data set is in R available as <code>example_isolates</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 22 October 2022 08:21:06 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
<p>It was last updated on 22 October 2022 20:03:38 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
<div class="section level3">
<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
</h3>
@ -1707,7 +1707,7 @@
</h2>
<p>A data set with 3,000 rows and 8 columns, containing the following column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>, <em>bacteria</em>, <em>AMX</em>, <em>AMC</em>, <em>CIP</em> and <em>GEN</em>.</p>
<p>This data set is in R available as <code>example_isolates_unclean</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 22 October 2022 08:21:06 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
<p>It was last updated on 22 October 2022 20:03:38 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
<div class="section level3">
<h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>
</h3>

2
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@ -10,7 +10,7 @@
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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="">1.8.2.9032</small>
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@ -172,7 +172,7 @@
<hr>
<p>The <code>AMR</code> package is a <a href="https://msberends.github.io/AMR/#copyright">free and open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero dependencies</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
<p>This work was published in the Journal of Statistical Software (Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">DOI 10.18637/jss.v104.i03</a>) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>).</p>
<p>After installing this package, R knows ~49,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>After installing this package, R knows ~49,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. The integral breakpoint guidelines from CLSI and EUCAST are included from the last 10 years. It supports and can read any data format, including WHONET data.</p>
<p>The <code>AMR</code> package is available in English, Chinese, Danish, Dutch, French, German, Greek, Italian, Japanese, Polish, Portuguese, Russian, Spanish, Swedish, Turkish and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
<p>This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. Since its first public release in early 2018, this package has been downloaded from more than 175 countries.</p>
<p>This package can be used for:</p>