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@ -395,21 +395,43 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-08-16</td>
<td align="center">S1</td>
<td align="center">2012-03-28</td>
<td align="center">G1</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-09-12</td>
<td align="center">E1</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">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2015-07-10</td>
<td align="center">N9</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-12-04</td>
<td align="center">J1</td>
<td align="center">2016-02-13</td>
<td align="center">B8</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
@ -417,48 +439,26 @@ data set:</p>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-07-21</td>
<td align="center">R6</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-11-26</td>
<td align="center">K8</td>
<td align="center">2016-12-26</td>
<td align="center">X3</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</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>
<tr class="odd">
<td align="center">2011-07-23</td>
<td align="center">Z2</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-05-31</td>
<td align="center">S7</td>
<td align="center">2014-04-05</td>
<td align="center">K5</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">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
@ -494,16 +494,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,563</td>
<td align="right">52.82%</td>
<td align="right">10,563</td>
<td align="right">52.82%</td>
<td align="right">10,517</td>
<td align="right">52.59%</td>
<td align="right">10,517</td>
<td align="right">52.59%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,437</td>
<td align="right">47.19%</td>
<td align="right">9,483</td>
<td align="right">47.42%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -616,10 +616,10 @@ 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"># =&gt; Found 10,633 'phenotype-based' first isolates (53.2% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,603 'phenotype-based' first isolates (53.0% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.2% 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% is suitable for resistance analysis! We can now filter on
it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
<code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@ -629,7 +629,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,633 isolates for analysis. Now our data looks
<p>So we end up with 10,603 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>
@ -646,8 +646,8 @@ like:</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="7%">
<col width="10%">
<col width="9%">
<col width="5%">
</colgroup>
<thead><tr class="header">
@ -669,92 +669,60 @@ like:</p>
<tbody>
<tr class="odd">
<td align="left">3</td>
<td align="center">2012-07-21</td>
<td align="center">R6</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">4</td>
<td align="center">2012-11-26</td>
<td align="center">K8</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</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">5</td>
<td align="center">2011-07-23</td>
<td align="center">Z2</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="even">
<td align="left">6</td>
<td align="center">2016-05-31</td>
<td align="center">S7</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">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">7</td>
<td align="center">2011-07-29</td>
<td align="center">C9</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">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="even">
<td align="left">14</td>
<td align="center">2016-07-22</td>
<td align="center">N8</td>
<td align="center">2015-07-10</td>
<td align="center">N9</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2013-12-26</td>
<td align="center">K2</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">11</td>
<td align="center">2017-12-04</td>
<td align="center">B10</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">12</td>
<td align="center">2010-03-06</td>
<td align="center">X9</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
@ -763,6 +731,38 @@ like:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">14</td>
<td align="center">2017-11-16</td>
<td align="center">K5</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">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">15</td>
<td align="center">2012-05-28</td>
<td align="center">X4</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</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>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -796,8 +796,8 @@ readable:</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,633<br>
Available: 10,633 (100%, NA: 0 = 0%)<br>
Length: 10,603<br>
Available: 10,603 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -822,33 +822,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,624</td>
<td align="right">43.49%</td>
<td align="right">4,624</td>
<td align="right">43.49%</td>
<td align="right">4,605</td>
<td align="right">43.43%</td>
<td align="right">4,605</td>
<td align="right">43.43%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,730</td>
<td align="right">25.67%</td>
<td align="right">7,354</td>
<td align="right">69.16%</td>
<td align="right">2,704</td>
<td align="right">25.50%</td>
<td align="right">7,309</td>
<td align="right">68.93%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,082</td>
<td align="right">19.58%</td>
<td align="right">9,436</td>
<td align="right">88.74%</td>
<td align="right">2,080</td>
<td align="right">19.62%</td>
<td align="right">9,389</td>
<td align="right">88.55%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,197</td>
<td align="right">11.26%</td>
<td align="right">10,633</td>
<td align="right">1,214</td>
<td align="right">11.45%</td>
<td align="right">10,603</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -869,14 +869,14 @@ 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>
@ -897,92 +897,92 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-12-19</td>
<td align="center">S3</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-04-29</td>
<td align="center">E8</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">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">2014-11-08</td>
<td align="center">R2</td>
<td align="center">2012-05-28</td>
<td align="center">X4</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>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-09-13</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">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-11-23</td>
<td align="center">F9</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="even">
<td align="center">2014-07-26</td>
<td align="center">R5</td>
<td align="center">Hospital C</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">R</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="center">2013-02-21</td>
<td align="center">Q4</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-12-17</td>
<td align="center">V4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-01-20</td>
<td align="center">E6</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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="center">2014-01-15</td>
<td align="center">Y1</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-02-24</td>
<td align="center">I1</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
@ -1009,50 +1009,50 @@ 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">2175</td>
<td align="center">124</td>
<td align="center">2325</td>
<td align="center">4624</td>
<td align="center">2153</td>
<td align="center">133</td>
<td align="center">2319</td>
<td align="center">4605</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3402</td>
<td align="center">145</td>
<td align="center">1077</td>
<td align="center">4624</td>
<td align="center">3353</td>
<td align="center">146</td>
<td align="center">1106</td>
<td align="center">4605</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3385</td>
<td align="center">3357</td>
<td align="center">0</td>
<td align="center">1239</td>
<td align="center">4624</td>
<td align="center">1248</td>
<td align="center">4605</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4046</td>
<td align="center">4032</td>
<td align="center">0</td>
<td align="center">578</td>
<td align="center">4624</td>
<td align="center">573</td>
<td align="center">4605</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">1197</td>
<td align="center">1197</td>
<td align="center">1214</td>
<td align="center">1214</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">922</td>
<td align="center">67</td>
<td align="center">208</td>
<td align="center">1197</td>
<td align="center">938</td>
<td align="center">48</td>
<td align="center">228</td>
<td align="center">1214</td>
</tr>
</tbody>
</table>
@ -1075,34 +1075,34 @@ 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">4046</td>
<td align="center">4032</td>
<td align="center">0</td>
<td align="center">578</td>
<td align="center">4624</td>
<td align="center">573</td>
<td align="center">4605</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1060</td>
<td align="center">1077</td>
<td align="center">0</td>
<td align="center">137</td>
<td align="center">1197</td>
<td align="center">1214</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2411</td>
<td align="center">2407</td>
<td align="center">0</td>
<td align="center">319</td>
<td align="center">2730</td>
<td align="center">297</td>
<td align="center">2704</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">2082</td>
<td align="center">2082</td>
<td align="center">2080</td>
<td align="center">2080</td>
</tr>
</tbody>
</table>
@ -1134,7 +1134,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
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] 0.5444371</span></span></code></pre></div>
<span><span class="co"># [1] 0.5472036</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">
@ -1149,19 +1149,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5425466</td>
<td align="center">0.5600486</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5360493</td>
<td align="center">0.5391692</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5492327</td>
<td align="center">0.5552826</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5585458</td>
<td align="center">0.5345403</td>
</tr>
</tbody>
</table>
@ -1186,23 +1186,23 @@ 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">0.5425466</td>
<td align="center">3220</td>
<td align="center">0.5600486</td>
<td align="center">3289</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5360493</td>
<td align="center">3731</td>
<td align="center">0.5391692</td>
<td align="center">3587</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5492327</td>
<td align="center">1564</td>
<td align="center">0.5552826</td>
<td align="center">1628</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5585458</td>
<td align="center">2118</td>
<td align="center">0.5345403</td>
<td align="center">2099</td>
</tr>
</tbody>
</table>
@ -1227,27 +1227,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7670848</td>
<td align="center">0.8750000</td>
<td align="center">0.9764273</td>
<td align="center">0.7598263</td>
<td align="center">0.8755700</td>
<td align="center">0.9774159</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8262322</td>
<td align="center">0.8855472</td>
<td align="center">0.9791145</td>
<td align="center">0.8121911</td>
<td align="center">0.8871499</td>
<td align="center">0.9728171</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7908425</td>
<td align="center">0.8831502</td>
<td align="center">0.9754579</td>
<td align="center">0.7917899</td>
<td align="center">0.8901627</td>
<td align="center">0.9822485</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5317003</td>
<td align="center">0.5423077</td>
<td align="center">0.0000000</td>
<td align="center">0.5317003</td>
<td align="center">0.5423077</td>
</tr>
</tbody>
</table>
@ -1275,23 +1275,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.3%</td>
<td align="right">25.2%</td>
<td align="right">56.0%</td>
<td align="right">28.0%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">53.6%</td>
<td align="right">26.7%</td>
<td align="right">53.9%</td>
<td align="right">27.0%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">54.9%</td>
<td align="right">25.9%</td>
<td align="right">55.5%</td>
<td align="right">25.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">55.9%</td>
<td align="right">29.3%</td>
<td align="right">53.5%</td>
<td align="right">26.1%</td>
</tr>
</tbody>
</table>
@ -1407,16 +1407,18 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 0.001 0.5 0.002 4 0.025 8 4 32 0.025 32 </span></span>
<span><span class="co"># [11] &gt;=256 0.001 0.5 0.5 0.002 0.002 0.025 16 1 0.025 </span></span>
<span><span class="co"># [21] &gt;=256 0.0625 0.002 0.5 0.0625 4 1 0.001 16 &gt;=256 </span></span>
<span><span class="co"># [31] 0.005 0.002 0.002 &gt;=256 0.005 0.025 0.5 8 0.125 0.125 </span></span>
<span><span class="co"># [41] 0.005 0.005 &gt;=256 4 0.005 0.001 0.025 0.01 0.01 128 </span></span>
<span><span class="co"># [51] 0.001 0.5 0.005 32 64 8 0.005 8 0.001 32 </span></span>
<span><span class="co"># [61] 0.5 128 0.001 2 32 0.125 16 16 8 0.002 </span></span>
<span><span class="co"># [71] 0.25 4 0.25 128 0.002 0.5 0.25 0.025 0.025 4 </span></span>
<span><span class="co"># [81] &gt;=256 8 0.002 1 0.001 64 0.25 0.5 0.005 16 </span></span>
<span><span class="co"># [91] 0.025 0.25 0.025 1 2 2 &gt;=256 1 0.5 0.125</span></span></code></pre></div>
<span><span class="co"># [1] 32 &lt;=0.001 16 16 0.5 0.5 0.0625 4 0.25 </span></span>
<span><span class="co"># [10] 0.01 128 256 0.01 &lt;=0.001 0.25 0.25 128 256 </span></span>
<span><span class="co"># [19] 8 64 256 256 1 32 0.0625 0.005 4 </span></span>
<span><span class="co"># [28] 0.005 0.125 0.025 0.125 8 64 &lt;=0.001 0.5 0.025 </span></span>
<span><span class="co"># [37] 0.002 0.5 0.002 4 &lt;=0.001 0.25 1 0.125 4 </span></span>
<span><span class="co"># [46] 128 256 0.01 0.002 0.01 32 32 0.005 4 </span></span>
<span><span class="co"># [55] 0.0625 256 0.25 2 32 0.01 &lt;=0.001 4 0.5 </span></span>
<span><span class="co"># [64] 8 0.125 0.005 &lt;=0.001 64 1 0.5 16 1 </span></span>
<span><span class="co"># [73] 2 0.005 0.25 64 32 16 &lt;=0.001 128 0.025 </span></span>
<span><span class="co"># [82] 4 256 16 0.125 2 0.005 &lt;=0.001 0.0625 0.005 </span></span>
<span><span class="co"># [91] 0.5 2 128 0.5 2 16 0.002 &lt;=0.001 0.125 </span></span>
<span><span class="co"># [100] 0.002</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>
@ -1450,10 +1452,10 @@ plotting:</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 30 31 30 24 26 25 23 24 17 22 30 27 20 19 24 21 21 20 21 26 22 24 18 30 17</span></span>
<span><span class="co"># [26] 28 30 22 27 27 31 19 24 27 23 18 30 21 20 18 19 21 26 18 18 20 17 27 30 25</span></span>
<span><span class="co"># [51] 31 21 23 23 27 19 24 30 25 22 31 19 26 26 24 27 19 17 25 20 28 28 26 24 19</span></span>
<span><span class="co"># [76] 22 18 30 23 27 27 21 28 21 24 23 17 23 20 24 31 17 21 17 19 26 18 29 20 25</span></span></code></pre></div>
<span><span class="co"># [1] 20 26 25 18 21 30 25 24 29 29 18 31 24 22 19 21 21 30 18 22 27 20 25 19 28</span></span>
<span><span class="co"># [26] 28 29 26 17 24 20 30 22 30 24 18 25 27 29 29 22 28 18 29 28 21 29 27 19 29</span></span>
<span><span class="co"># [51] 21 17 17 23 26 22 27 30 29 20 26 18 18 17 24 21 23 25 26 17 24 22 18 31 29</span></span>
<span><span class="co"># [76] 29 21 24 27 22 28 26 25 19 17 23 24 28 31 18 30 30 25 22 22 31 25 31 24 26</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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56
articles/MDR.html
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@ -370,19 +370,19 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 R S R S R R</span></span>
<span><span class="co"># 2 R I R R R I</span></span>
<span><span class="co"># 3 I R S I S R</span></span>
<span><span class="co"># 4 I I I R I S</span></span>
<span><span class="co"># 5 R R S R I S</span></span>
<span><span class="co"># 6 S S R R R I</span></span>
<span><span class="co"># 1 I I I S S R</span></span>
<span><span class="co"># 2 R S S S I I</span></span>
<span><span class="co"># 3 S R R R S R</span></span>
<span><span class="co"># 4 S I R S I I</span></span>
<span><span class="co"># 5 S S S I S R</span></span>
<span><span class="co"># 6 I S R 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"># 3 S</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 R</span></span>
<span><span class="co"># 6 I</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -423,40 +423,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3231</td>
<td align="right">64.62%</td>
<td align="right">3231</td>
<td align="right">64.62%</td>
<td align="right">3140</td>
<td align="right">62.80%</td>
<td align="right">3140</td>
<td align="right">62.80%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">961</td>
<td align="right">19.22%</td>
<td align="right">4192</td>
<td align="right">83.84%</td>
<td align="right">1031</td>
<td align="right">20.62%</td>
<td align="right">4171</td>
<td align="right">83.42%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">445</td>
<td align="right">8.90%</td>
<td align="right">4637</td>
<td align="right">92.74%</td>
<td align="right">463</td>
<td align="right">9.26%</td>
<td align="right">4634</td>
<td align="right">92.68%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">250</td>
<td align="right">5.00%</td>
<td align="right">4887</td>
<td align="right">97.74%</td>
<td align="right">252</td>
<td align="right">5.04%</td>
<td align="right">4886</td>
<td align="right">97.72%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">113</td>
<td align="right">2.26%</td>
<td align="right">114</td>
<td align="right">2.28%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

16
articles/datasets.html
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@ -191,7 +191,7 @@ 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 12 November 2022 08:46:26 UTC. Find more info
<p>It was last updated on 29 October 2022 12:15:23 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>
@ -490,7 +490,7 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
<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 12 November 2022 08:46:26 UTC. Find more info
<p>It was last updated on 30 October 2022 20:05:46 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>
@ -687,7 +687,7 @@ column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</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 12 November 2022 08:46:26 UTC. Find more info
<p>It was last updated on 27 August 2022 18:49:37 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -847,7 +847,7 @@ column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</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 12 November 2022 08:46:26 UTC. Find more info
<p>It was last updated on 29 October 2022 17:01:23 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>
@ -1020,7 +1020,7 @@ Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intri
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 12 November 2022 08:46:26 UTC. Find more info
<p>It was last updated on 31 October 2022 10:19:06 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><strong>Direct download links:</strong></p>
<ul>
@ -1308,7 +1308,7 @@ column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</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 12 November 2022 08:46:26 UTC. Find more info
<p>It was last updated on 30 October 2022 20:05:46 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>
@ -1458,7 +1458,7 @@ column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</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 12 November 2022 08:46:26 UTC. Find more info
<p>It was last updated on 27 August 2022 18:49:37 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
<div class="section level3">
<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
@ -1871,7 +1871,7 @@ column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>,
<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 12 November 2022 08:46:26 UTC. Find more info
<p>It was last updated on 27 August 2022 18:49:37 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
<div class="section level3">
<h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>