Built site for AMR: 1.8.2.9062@8da2467
@ -38,7 +38,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9061</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@ -380,12 +380,12 @@ data set:</p>
|
||||
<col width="13%">
|
||||
<col width="13%">
|
||||
<col width="13%">
|
||||
<col width="28%">
|
||||
<col width="26%">
|
||||
<col width="5%">
|
||||
<col width="5%">
|
||||
<col width="5%">
|
||||
<col width="5%">
|
||||
<col width="8%">
|
||||
<col width="9%">
|
||||
</colgroup>
|
||||
<thead><tr class="header">
|
||||
<th align="center">date</th>
|
||||
@ -400,66 +400,66 @@ data set:</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2014-06-10</td>
|
||||
<td align="center">K4</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">2017-09-13</td>
|
||||
<td align="center">T10</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2016-10-31</td>
|
||||
<td align="center">G8</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2011-07-13</td>
|
||||
<td align="center">Q7</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Staphylococcus aureus</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2016-05-04</td>
|
||||
<td align="center">F6</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Streptococcus pneumoniae</td>
|
||||
<td align="center">R3</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2010-05-15</td>
|
||||
<td align="center">N5</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Streptococcus pneumoniae</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2015-12-18</td>
|
||||
<td align="center">O8</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">2013-09-12</td>
|
||||
<td align="center">A3</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">Klebsiella pneumoniae</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2016-12-01</td>
|
||||
<td align="center">T2</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2010-05-10</td>
|
||||
<td align="center">W4</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">2011-12-19</td>
|
||||
<td align="center">R10</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">Staphylococcus aureus</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@ -499,16 +499,16 @@ Longest: 1</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">M</td>
|
||||
<td align="right">10,335</td>
|
||||
<td align="right">51.68%</td>
|
||||
<td align="right">10,335</td>
|
||||
<td align="right">51.68%</td>
|
||||
<td align="right">10,363</td>
|
||||
<td align="right">51.82%</td>
|
||||
<td align="right">10,363</td>
|
||||
<td align="right">51.82%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">F</td>
|
||||
<td align="right">9,665</td>
|
||||
<td align="right">48.33%</td>
|
||||
<td align="right">9,637</td>
|
||||
<td align="right">48.19%</td>
|
||||
<td align="right">20,000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
@ -621,10 +621,10 @@ takes into account the antimicrobial susceptibility test results using
|
||||
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
|
||||
<span><span class="co"># 2</span></span>
|
||||
<span><span class="co"># Including isolates from ICU.</span></span>
|
||||
<span><span class="co"># => Found 10,609 'phenotype-based' first isolates (53.0% of total where a</span></span>
|
||||
<span><span class="co"># => Found 10,615 'phenotype-based' first isolates (53.1% of total where a</span></span>
|
||||
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
|
||||
<p>So only 53% is suitable for resistance analysis! We can now filter on
|
||||
it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
|
||||
<p>So only 53.1% is suitable for resistance analysis! We can now filter
|
||||
on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
|
||||
<code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
@ -634,11 +634,11 @@ it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" cl
|
||||
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
|
||||
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
|
||||
<p>So we end up with 10,609 isolates for analysis. Now our data looks
|
||||
<p>So we end up with 10,615 isolates for analysis. Now our data looks
|
||||
like:</p>
|
||||
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
|
||||
<table class="table">
|
||||
<table style="width:100%;" class="table">
|
||||
<colgroup>
|
||||
<col width="2%">
|
||||
<col width="9%">
|
||||
@ -651,7 +651,7 @@ like:</p>
|
||||
<col width="3%">
|
||||
<col width="6%">
|
||||
<col width="11%">
|
||||
<col width="11%">
|
||||
<col width="12%">
|
||||
<col width="9%">
|
||||
<col width="5%">
|
||||
</colgroup>
|
||||
@ -673,99 +673,99 @@ like:</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">2</td>
|
||||
<td align="center">2016-05-04</td>
|
||||
<td align="center">F6</td>
|
||||
<td align="left">8</td>
|
||||
<td align="center">2014-11-28</td>
|
||||
<td align="center">R9</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">3</td>
|
||||
<td align="center">2010-05-15</td>
|
||||
<td align="center">N5</td>
|
||||
<td align="left">10</td>
|
||||
<td align="center">2011-11-04</td>
|
||||
<td align="center">U10</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">4</td>
|
||||
<td align="center">2015-12-18</td>
|
||||
<td align="center">O8</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_KLBSL_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">5</td>
|
||||
<td align="center">2016-12-01</td>
|
||||
<td align="center">T2</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="left">11</td>
|
||||
<td align="center">2011-05-17</td>
|
||||
<td align="center">F5</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">7</td>
|
||||
<td align="center">2012-12-26</td>
|
||||
<td align="center">U7</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<tr class="even">
|
||||
<td align="left">12</td>
|
||||
<td align="center">2016-12-09</td>
|
||||
<td align="center">A9</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">13</td>
|
||||
<td align="center">2011-06-24</td>
|
||||
<td align="center">M5</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">9</td>
|
||||
<td align="center">2010-11-22</td>
|
||||
<td align="center">R6</td>
|
||||
<td align="left">16</td>
|
||||
<td align="center">2010-11-26</td>
|
||||
<td align="center">F5</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
@ -801,8 +801,8 @@ readable:</p>
|
||||
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
|
||||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: character<br>
|
||||
Length: 10,609<br>
|
||||
Available: 10,609 (100%, NA: 0 = 0%)<br>
|
||||
Length: 10,615<br>
|
||||
Available: 10,615 (100%, NA: 0 = 0%)<br>
|
||||
Unique: 4</p>
|
||||
<p>Shortest: 16<br>
|
||||
Longest: 24</p>
|
||||
@ -827,33 +827,33 @@ Longest: 24</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Escherichia coli</td>
|
||||
<td align="right">4,637</td>
|
||||
<td align="right">43.71%</td>
|
||||
<td align="right">4,637</td>
|
||||
<td align="right">43.71%</td>
|
||||
<td align="right">4,550</td>
|
||||
<td align="right">42.86%</td>
|
||||
<td align="right">4,550</td>
|
||||
<td align="right">42.86%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Staphylococcus aureus</td>
|
||||
<td align="right">2,731</td>
|
||||
<td align="right">25.74%</td>
|
||||
<td align="right">7,368</td>
|
||||
<td align="right">69.45%</td>
|
||||
<td align="right">2,715</td>
|
||||
<td align="right">25.58%</td>
|
||||
<td align="right">7,265</td>
|
||||
<td align="right">68.44%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Streptococcus pneumoniae</td>
|
||||
<td align="right">2,078</td>
|
||||
<td align="right">19.59%</td>
|
||||
<td align="right">9,446</td>
|
||||
<td align="right">89.04%</td>
|
||||
<td align="right">2,147</td>
|
||||
<td align="right">20.23%</td>
|
||||
<td align="right">9,412</td>
|
||||
<td align="right">88.67%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Klebsiella pneumoniae</td>
|
||||
<td align="right">1,163</td>
|
||||
<td align="right">10.96%</td>
|
||||
<td align="right">10,609</td>
|
||||
<td align="right">1,203</td>
|
||||
<td align="right">11.33%</td>
|
||||
<td align="right">10,615</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
@ -874,14 +874,14 @@ antibiotic class they are in:</p>
|
||||
<col width="9%">
|
||||
<col width="9%">
|
||||
<col width="9%">
|
||||
<col width="11%">
|
||||
<col width="10%">
|
||||
<col width="3%">
|
||||
<col width="3%">
|
||||
<col width="3%">
|
||||
<col width="3%">
|
||||
<col width="6%">
|
||||
<col width="11%">
|
||||
<col width="11%">
|
||||
<col width="12%">
|
||||
<col width="9%">
|
||||
<col width="5%">
|
||||
</colgroup>
|
||||
@ -902,42 +902,12 @@ antibiotic class they are in:</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2016-05-04</td>
|
||||
<td align="center">F6</td>
|
||||
<td align="center">2014-11-28</td>
|
||||
<td align="center">R9</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2010-05-15</td>
|
||||
<td align="center">N5</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2012-12-26</td>
|
||||
<td align="center">U7</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
@ -947,43 +917,73 @@ antibiotic class they are in:</p>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2010-11-22</td>
|
||||
<td align="center">R6</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2015-02-05</td>
|
||||
<td align="center">U1</td>
|
||||
<td align="center">2016-12-17</td>
|
||||
<td align="center">M1</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2017-05-10</td>
|
||||
<td align="center">T3</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<tr class="odd">
|
||||
<td align="center">2016-09-19</td>
|
||||
<td align="center">B9</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2016-12-18</td>
|
||||
<td align="center">N3</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2010-04-19</td>
|
||||
<td align="center">N5</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2016-09-02</td>
|
||||
<td align="center">W3</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
@ -1013,50 +1013,50 @@ different bug/drug combinations, you can use the
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">AMX</td>
|
||||
<td align="center">2169</td>
|
||||
<td align="center">134</td>
|
||||
<td align="center">2334</td>
|
||||
<td align="center">4637</td>
|
||||
<td align="center">2178</td>
|
||||
<td align="center">98</td>
|
||||
<td align="center">2274</td>
|
||||
<td align="center">4550</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">AMC</td>
|
||||
<td align="center">3403</td>
|
||||
<td align="center">162</td>
|
||||
<td align="center">1072</td>
|
||||
<td align="center">4637</td>
|
||||
<td align="center">3344</td>
|
||||
<td align="center">135</td>
|
||||
<td align="center">1071</td>
|
||||
<td align="center">4550</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">CIP</td>
|
||||
<td align="center">3398</td>
|
||||
<td align="center">3331</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">1239</td>
|
||||
<td align="center">4637</td>
|
||||
<td align="center">1219</td>
|
||||
<td align="center">4550</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">4041</td>
|
||||
<td align="center">3996</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">596</td>
|
||||
<td align="center">4637</td>
|
||||
<td align="center">554</td>
|
||||
<td align="center">4550</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center">AMX</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">1163</td>
|
||||
<td align="center">1163</td>
|
||||
<td align="center">1203</td>
|
||||
<td align="center">1203</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center">AMC</td>
|
||||
<td align="center">906</td>
|
||||
<td align="center">45</td>
|
||||
<td align="center">212</td>
|
||||
<td align="center">1163</td>
|
||||
<td align="center">947</td>
|
||||
<td align="center">52</td>
|
||||
<td align="center">204</td>
|
||||
<td align="center">1203</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1078,34 +1078,34 @@ different bug/drug combinations, you can use the
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">4041</td>
|
||||
<td align="center">3996</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">596</td>
|
||||
<td align="center">4637</td>
|
||||
<td align="center">554</td>
|
||||
<td align="center">4550</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">1041</td>
|
||||
<td align="center">1097</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">122</td>
|
||||
<td align="center">1163</td>
|
||||
<td align="center">106</td>
|
||||
<td align="center">1203</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">S. aureus</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">2436</td>
|
||||
<td align="center">2393</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">295</td>
|
||||
<td align="center">2731</td>
|
||||
<td align="center">322</td>
|
||||
<td align="center">2715</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">S. pneumoniae</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">2078</td>
|
||||
<td align="center">2078</td>
|
||||
<td align="center">2147</td>
|
||||
<td align="center">2147</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1137,7 +1137,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
|
||||
own:</p>
|
||||
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
|
||||
<span><span class="co"># [1] 0.5435951</span></span></code></pre></div>
|
||||
<span><span class="co"># [1] 0.5501649</span></span></code></pre></div>
|
||||
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
|
||||
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
|
||||
@ -1152,19 +1152,19 @@ own:</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.5376442</td>
|
||||
<td align="center">0.5511084</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.5473011</td>
|
||||
<td align="center">0.5511442</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.5522855</td>
|
||||
<td align="center">0.5606154</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.5400188</td>
|
||||
<td align="center">0.5390071</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1189,23 +1189,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.5376442</td>
|
||||
<td align="center">3294</td>
|
||||
<td align="center">0.5511084</td>
|
||||
<td align="center">3248</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.5473011</td>
|
||||
<td align="center">3594</td>
|
||||
<td align="center">0.5511442</td>
|
||||
<td align="center">3627</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.5522855</td>
|
||||
<td align="center">1597</td>
|
||||
<td align="center">0.5606154</td>
|
||||
<td align="center">1625</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.5400188</td>
|
||||
<td align="center">2124</td>
|
||||
<td align="center">0.5390071</td>
|
||||
<td align="center">2115</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1230,27 +1230,27 @@ therapies very easily:</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">0.7688160</td>
|
||||
<td align="center">0.8714686</td>
|
||||
<td align="center">0.9775717</td>
|
||||
<td align="center">0.7646154</td>
|
||||
<td align="center">0.8782418</td>
|
||||
<td align="center">0.9764835</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">0.8177128</td>
|
||||
<td align="center">0.8950989</td>
|
||||
<td align="center">0.9819433</td>
|
||||
<td align="center">0.8304239</td>
|
||||
<td align="center">0.9118869</td>
|
||||
<td align="center">0.9825436</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">0.8033687</td>
|
||||
<td align="center">0.8919810</td>
|
||||
<td align="center">0.9794947</td>
|
||||
<td align="center">0.8040516</td>
|
||||
<td align="center">0.8813996</td>
|
||||
<td align="center">0.9793738</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">0.5413859</td>
|
||||
<td align="center">0.5365626</td>
|
||||
<td align="center">0.0000000</td>
|
||||
<td align="center">0.5413859</td>
|
||||
<td align="center">0.5365626</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1278,23 +1278,23 @@ classes, use a antibiotic class selector such as
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">Hospital A</td>
|
||||
<td align="right">53.8%</td>
|
||||
<td align="right">26.2%</td>
|
||||
<td align="right">55.1%</td>
|
||||
<td align="right">26.8%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Hospital B</td>
|
||||
<td align="right">54.7%</td>
|
||||
<td align="right">26.7%</td>
|
||||
<td align="right">55.1%</td>
|
||||
<td align="right">26.1%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Hospital C</td>
|
||||
<td align="right">55.2%</td>
|
||||
<td align="right">25.7%</td>
|
||||
<td align="right">56.1%</td>
|
||||
<td align="right">26.2%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Hospital D</td>
|
||||
<td align="right">54.0%</td>
|
||||
<td align="right">25.4%</td>
|
||||
<td align="right">53.9%</td>
|
||||
<td align="right">26.5%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1410,18 +1410,18 @@ classes) <code><mic></code> and <code><disk></code>:</p>
|
||||
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op"><-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
|
||||
<span><span class="va">mic_values</span></span>
|
||||
<span><span class="co"># Class 'mic'</span></span>
|
||||
<span><span class="co"># [1] 0.005 0.0625 <=0.001 8 0.025 0.01 8 0.0625 128 </span></span>
|
||||
<span><span class="co"># [10] 2 0.025 32 1 128 32 2 0.002 <=0.001</span></span>
|
||||
<span><span class="co"># [19] 8 8 64 64 0.25 0.005 0.0625 8 0.5 </span></span>
|
||||
<span><span class="co"># [28] 0.0625 0.25 1 64 1 32 16 16 1 </span></span>
|
||||
<span><span class="co"># [37] 16 0.005 0.25 64 >=256 0.01 2 0.025 0.01 </span></span>
|
||||
<span><span class="co"># [46] 64 0.5 16 0.01 >=256 0.025 32 0.025 0.5 </span></span>
|
||||
<span><span class="co"># [55] 0.025 16 >=256 0.01 32 0.125 4 1 8 </span></span>
|
||||
<span><span class="co"># [64] 128 128 0.0625 2 >=256 64 0.005 0.0625 0.25 </span></span>
|
||||
<span><span class="co"># [73] 0.002 0.025 2 32 0.005 0.25 64 0.5 4 </span></span>
|
||||
<span><span class="co"># [82] 128 4 1 16 0.01 8 2 64 0.0625 </span></span>
|
||||
<span><span class="co"># [91] 64 32 1 4 16 >=256 32 0.25 2 </span></span>
|
||||
<span><span class="co"># [100] 0.005</span></span></code></pre></div>
|
||||
<span><span class="co"># [1] 64 2 0.01 128 1 8 16 <=0.001 256 </span></span>
|
||||
<span><span class="co"># [10] 0.025 0.005 0.002 256 2 <=0.001 0.5 256 128 </span></span>
|
||||
<span><span class="co"># [19] 16 0.025 0.25 0.002 0.5 8 32 0.125 1 </span></span>
|
||||
<span><span class="co"># [28] 1 0.002 0.125 0.025 32 0.005 0.25 0.0625 0.002 </span></span>
|
||||
<span><span class="co"># [37] 0.01 0.002 32 <=0.001 16 <=0.001 0.125 1 128 </span></span>
|
||||
<span><span class="co"># [46] 0.005 2 0.01 8 0.0625 16 32 0.01 8 </span></span>
|
||||
<span><span class="co"># [55] 256 0.002 0.0625 0.0625 0.005 2 256 4 0.0625 </span></span>
|
||||
<span><span class="co"># [64] 256 4 16 <=0.001 256 0.125 0.002 256 64 </span></span>
|
||||
<span><span class="co"># [73] 4 64 0.0625 0.125 0.25 16 8 1 16 </span></span>
|
||||
<span><span class="co"># [82] 0.125 0.005 128 0.25 16 0.005 256 8 0.01 </span></span>
|
||||
<span><span class="co"># [91] 0.0625 64 4 8 0.01 0.01 128 2 8 </span></span>
|
||||
<span><span class="co"># [100] 8</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
|
||||
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
|
||||
@ -1455,10 +1455,10 @@ plotting:</p>
|
||||
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op"><-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
|
||||
<span><span class="va">disk_values</span></span>
|
||||
<span><span class="co"># Class 'disk'</span></span>
|
||||
<span><span class="co"># [1] 21 23 25 27 17 22 21 27 27 22 29 31 31 29 17 18 20 26 27 29 24 26 30 25 23</span></span>
|
||||
<span><span class="co"># [26] 22 22 19 29 21 31 29 22 29 21 17 26 21 20 28 26 24 21 25 23 25 28 28 29 21</span></span>
|
||||
<span><span class="co"># [51] 28 20 17 18 27 25 30 28 30 18 22 23 26 31 26 28 27 18 19 22 22 27 28 28 30</span></span>
|
||||
<span><span class="co"># [76] 29 26 20 20 26 28 19 27 23 20 21 17 30 24 26 25 30 26 28 20 20 27 31 31 18</span></span></code></pre></div>
|
||||
<span><span class="co"># [1] 20 22 20 20 22 17 24 28 30 26 26 27 18 26 22 21 23 29 27 21 24 29 19 28 30</span></span>
|
||||
<span><span class="co"># [26] 21 31 29 27 20 23 18 20 19 19 23 27 29 24 17 29 17 17 22 31 19 25 20 25 19</span></span>
|
||||
<span><span class="co"># [51] 24 25 21 23 26 28 26 24 17 21 26 23 30 28 19 26 18 28 17 17 27 26 22 26 23</span></span>
|
||||
<span><span class="co"># [76] 21 18 30 23 25 24 25 31 21 31 20 30 17 23 29 27 17 21 30 19 17 17 21 30 23</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
|
||||
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>
|
||||
|
Before Width: | Height: | Size: 38 KiB After Width: | Height: | Size: 37 KiB |
Before Width: | Height: | Size: 54 KiB After Width: | Height: | Size: 51 KiB |
Before Width: | Height: | Size: 28 KiB After Width: | Height: | Size: 27 KiB |
Before Width: | Height: | Size: 37 KiB After Width: | Height: | Size: 36 KiB |
Before Width: | Height: | Size: 38 KiB After Width: | Height: | Size: 37 KiB |
Before Width: | Height: | Size: 52 KiB After Width: | Height: | Size: 51 KiB |
Before Width: | Height: | Size: 42 KiB After Width: | Height: | Size: 42 KiB |
Before Width: | Height: | Size: 28 KiB After Width: | Height: | Size: 28 KiB |
Before Width: | Height: | Size: 76 KiB After Width: | Height: | Size: 76 KiB |
Before Width: | Height: | Size: 49 KiB After Width: | Height: | Size: 49 KiB |
@ -38,7 +38,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9061</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
@ -38,7 +38,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9061</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@ -375,18 +375,18 @@ names or codes, this would have worked exactly the same way:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
|
||||
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
|
||||
<span><span class="co"># 1 S S I R R S</span></span>
|
||||
<span><span class="co"># 2 I R I S S R</span></span>
|
||||
<span><span class="co"># 3 S I R S S S</span></span>
|
||||
<span><span class="co"># 4 R S R I I R</span></span>
|
||||
<span><span class="co"># 5 I I R I S I</span></span>
|
||||
<span><span class="co"># 6 S I I S S S</span></span>
|
||||
<span><span class="co"># 1 S S I R I S</span></span>
|
||||
<span><span class="co"># 2 I S I R R R</span></span>
|
||||
<span><span class="co"># 3 R I I R S I</span></span>
|
||||
<span><span class="co"># 4 S S R S S S</span></span>
|
||||
<span><span class="co"># 5 I S S I R I</span></span>
|
||||
<span><span class="co"># 6 I R S R S S</span></span>
|
||||
<span><span class="co"># kanamycin</span></span>
|
||||
<span><span class="co"># 1 I</span></span>
|
||||
<span><span class="co"># 2 I</span></span>
|
||||
<span><span class="co"># 3 R</span></span>
|
||||
<span><span class="co"># 4 I</span></span>
|
||||
<span><span class="co"># 5 S</span></span>
|
||||
<span><span class="co"># 3 S</span></span>
|
||||
<span><span class="co"># 4 R</span></span>
|
||||
<span><span class="co"># 5 I</span></span>
|
||||
<span><span class="co"># 6 I</span></span></code></pre></div>
|
||||
<p>We can now add the interpretation of MDR-TB to our data set. You can
|
||||
use:</p>
|
||||
@ -428,40 +428,40 @@ Unique: 5</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Mono-resistant</td>
|
||||
<td align="right">3201</td>
|
||||
<td align="right">64.02%</td>
|
||||
<td align="right">3201</td>
|
||||
<td align="right">64.02%</td>
|
||||
<td align="right">3173</td>
|
||||
<td align="right">63.46%</td>
|
||||
<td align="right">3173</td>
|
||||
<td align="right">63.46%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">985</td>
|
||||
<td align="right">19.70%</td>
|
||||
<td align="right">4186</td>
|
||||
<td align="right">83.72%</td>
|
||||
<td align="right">1011</td>
|
||||
<td align="right">20.22%</td>
|
||||
<td align="right">4184</td>
|
||||
<td align="right">83.68%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Multi-drug-resistant</td>
|
||||
<td align="right">470</td>
|
||||
<td align="right">9.40%</td>
|
||||
<td align="right">4656</td>
|
||||
<td align="right">93.12%</td>
|
||||
<td align="right">481</td>
|
||||
<td align="right">9.62%</td>
|
||||
<td align="right">4665</td>
|
||||
<td align="right">93.30%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Poly-resistant</td>
|
||||
<td align="right">240</td>
|
||||
<td align="right">4.80%</td>
|
||||
<td align="right">4896</td>
|
||||
<td align="right">97.92%</td>
|
||||
<td align="right">236</td>
|
||||
<td align="right">4.72%</td>
|
||||
<td align="right">4901</td>
|
||||
<td align="right">98.02%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="left">Extensively drug-resistant</td>
|
||||
<td align="right">104</td>
|
||||
<td align="right">2.08%</td>
|
||||
<td align="right">99</td>
|
||||
<td align="right">1.98%</td>
|
||||
<td align="right">5000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
|
@ -38,7 +38,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9061</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
@ -38,7 +38,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9061</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@ -247,7 +247,7 @@ data using a custom made website. The webdesign knowledge needed
|
||||
<li>
|
||||
<p><strong>R has a huge community.</strong></p>
|
||||
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest
|
||||
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">473,435
|
||||
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">474,212
|
||||
R-related questions</a> have already been asked on this platform (that
|
||||
covers questions and answers for any programming language). In my own
|
||||
experience, most questions are answered within a couple of
|
||||
|
@ -38,7 +38,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9061</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
@ -38,7 +38,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9061</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@ -187,7 +187,7 @@ of the data sets look like.</p>
|
||||
<h2 id="microorganisms-full-microbial-taxonomy">
|
||||
<code>microorganisms</code>: Full Microbial Taxonomy<a class="anchor" aria-label="anchor" href="#microorganisms-full-microbial-taxonomy"></a>
|
||||
</h2>
|
||||
<p>A data set with 48,883 rows and 22 columns, containing the following
|
||||
<p>A data set with 48,050 rows and 22 columns, containing the following
|
||||
column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>,
|
||||
<em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>,
|
||||
<em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>,
|
||||
@ -196,7 +196,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
|
||||
<em>gbif_renamed_to</em>, <em>prevalence</em> and <em>snomed</em>.</p>
|
||||
<p>This data set is in R available as <code>microorganisms</code>, after
|
||||
you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 9 December 2022 12:37:08 UTC. Find more info
|
||||
<p>It was last updated on 11 December 2022 23:14:56 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
@ -204,25 +204,25 @@ about the structure of this data set <a href="https://msberends.github.io/AMR/re
|
||||
R Data Structure (RDS) file</a> (1.1 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">tab-separated
|
||||
text file</a> (10.6 MB)<br>
|
||||
text file</a> (10.4 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Microsoft
|
||||
Excel workbook</a> (4.8 MB)<br>
|
||||
Excel workbook</a> (4.7 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.feather" class="external-link">Apache
|
||||
Feather file</a> (5.1 MB)<br>
|
||||
Feather file</a> (5 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.parquet" class="external-link">Apache
|
||||
Parquet file</a> (2.5 MB)<br>
|
||||
Parquet file</a> (2.4 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS
|
||||
data file</a> (47.8 MB)<br>
|
||||
data file</a> (46.9 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">IBM
|
||||
SPSS Statistics data file</a> (15.8 MB)<br>
|
||||
SPSS Statistics data file</a> (15.5 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata
|
||||
DTA file</a> (43.8 MB)</li>
|
||||
DTA file</a> (43.4 MB)</li>
|
||||
</ul>
|
||||
<p><strong>NOTE: The exported files for SAS, SPSS and Stata contain only
|
||||
the first 50 SNOMED codes per record, as their file size would otherwise
|
||||
@ -240,9 +240,9 @@ and the Global Biodiversity Information Facility (GBIF):</p>
|
||||
<li>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names
|
||||
with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong>
|
||||
International Journal of Systematic and Evolutionary Microbiology, 70,
|
||||
5607-5612; . Accessed from <a href="https://lpsn.dsmz.de" class="external-link uri">https://lpsn.dsmz.de</a> on 12 September, 2022.</li>
|
||||
<li>GBIF Secretariat (November 26, 2021). GBIF Backbone Taxonomy.
|
||||
Checklist dataset . Accessed from <a href="https://www.gbif.org" class="external-link uri">https://www.gbif.org</a> on 12 September, 2022.</li>
|
||||
5607-5612; . Accessed from <a href="https://lpsn.dsmz.de" class="external-link uri">https://lpsn.dsmz.de</a> on 11 December, 2022.</li>
|
||||
<li>GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset .
|
||||
Accessed from <a href="https://www.gbif.org" class="external-link uri">https://www.gbif.org</a> on 11 December, 2022.</li>
|
||||
<li>Public Health Information Network Vocabulary Access and Distribution
|
||||
System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value
|
||||
Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link uri">https://phinvads.cdc.gov</a>
|
||||
@ -261,27 +261,27 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">(unknown kingdom)</td>
|
||||
<td align="center">5</td>
|
||||
<td align="center">1</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Animalia</td>
|
||||
<td align="center">1,524</td>
|
||||
<td align="center">1,061</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Archaea</td>
|
||||
<td align="center">1,237</td>
|
||||
<td align="center">1,291</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Bacteria</td>
|
||||
<td align="center">33,716</td>
|
||||
<td align="center">34,398</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Fungi</td>
|
||||
<td align="center">7,450</td>
|
||||
<td align="center">6,852</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Protozoa</td>
|
||||
<td align="center">4,951</td>
|
||||
<td align="center">4,447</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -355,7 +355,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
|
||||
<td align="center">482</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">3221780</td>
|
||||
<td align="center">4899</td>
|
||||
<td align="center">11158430</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1</td>
|
||||
<td align="center">407310004, 407251000, 407281008, …</td>
|
||||
@ -450,7 +450,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
|
||||
<td align="center">776057</td>
|
||||
<td align="center">515602</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">6110934</td>
|
||||
<td align="center">11286021</td>
|
||||
<td align="center">3221780</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1</td>
|
||||
@ -1042,37 +1042,37 @@ diffusion diameters. Included guidelines are CLSI (2013-2022) and EUCAST
|
||||
<code>intrinsic_resistant</code>: Intrinsic Bacterial
|
||||
Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intrinsic-bacterial-resistance"></a>
|
||||
</h2>
|
||||
<p>A data set with 134,659 rows and 2 columns, containing the following
|
||||
<p>A data set with 206,832 rows and 2 columns, containing the following
|
||||
column names:<br><em>mo</em> and <em>ab</em>.</p>
|
||||
<p>This data set is in R available as <code>intrinsic_resistant</code>,
|
||||
after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 31 October 2022 10:19:06 UTC. Find more info
|
||||
<p>It was last updated on 11 December 2022 23:14:56 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">original
|
||||
R Data Structure (RDS) file</a> (78 kB)<br>
|
||||
R Data Structure (RDS) file</a> (0.1 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">tab-separated
|
||||
text file</a> (5.1 MB)<br>
|
||||
text file</a> (7.9 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Microsoft
|
||||
Excel workbook</a> (1.3 MB)<br>
|
||||
Excel workbook</a> (1.9 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.feather" class="external-link">Apache
|
||||
Feather file</a> (1.2 MB)<br>
|
||||
Feather file</a> (1.8 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.parquet" class="external-link">Apache
|
||||
Parquet file</a> (0.2 MB)<br>
|
||||
Parquet file</a> (0.3 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS
|
||||
data file</a> (9.8 MB)<br>
|
||||
data file</a> (17.6 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">IBM
|
||||
SPSS Statistics data file</a> (7.4 MB)<br>
|
||||
SPSS Statistics data file</a> (11.4 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata
|
||||
DTA file</a> (9.5 MB)</li>
|
||||
DTA file</a> (17.2 MB)</li>
|
||||
</ul>
|
||||
<div class="section level3">
|
||||
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
|
||||
|
@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9061</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
@ -38,7 +38,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9061</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
@ -38,7 +38,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9061</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@ -192,7 +192,7 @@ treatment evaluation in any setting.</p>
|
||||
10.18637/jss.v104.i03</a>) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI
|
||||
10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI
|
||||
10.33612/diss.192486375</a>).</p>
|
||||
<p>After installing this package, R knows ~49,000 distinct microbial
|
||||
<p>After installing this package, R knows ~48,000 distinct microbial
|
||||
species and all ~600 antibiotic, antimycotic and antiviral drugs by name
|
||||
and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED
|
||||
CT), and knows all about valid R/SI and MIC values. The integral
|
||||
|