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@ -380,12 +380,12 @@ data set:</p>
<col width="13%">
<col width="13%">
<col width="13%">
<col width="26%">
<col width="28%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="9%">
<col width="8%">
</colgroup>
<thead><tr class="header">
<th align="center">date</th>
@ -400,70 +400,70 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-09-07</td>
<td align="center">C1</td>
<td align="center">2013-10-31</td>
<td align="center">J1</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-06-25</td>
<td align="center">F2</td>
<td align="center">2014-11-26</td>
<td align="center">I8</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2011-12-31</td>
<td align="center">A5</td>
<td align="center">Hospital D</td>
<td align="center">2015-03-23</td>
<td align="center">L5</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-12-18</td>
<td align="center">H2</td>
<td align="center">2013-01-05</td>
<td align="center">Q3</td>
<td align="center">Hospital C</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-05-11</td>
<td align="center">S9</td>
<td align="center">2017-12-24</td>
<td align="center">E9</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-02-06</td>
<td align="center">S9</td>
<td align="center">2017-04-23</td>
<td align="center">E8</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
@ -499,16 +499,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,446</td>
<td align="right">52.23%</td>
<td align="right">10,446</td>
<td align="right">52.23%</td>
<td align="right">10,481</td>
<td align="right">52.41%</td>
<td align="right">10,481</td>
<td align="right">52.41%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,554</td>
<td align="right">47.77%</td>
<td align="right">9,519</td>
<td align="right">47.60%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -621,9 +621,9 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 12,360 'phenotype-based' first isolates (61.8% of total where a</span></span>
<span><span class="co"># =&gt; Found 12,319 'phenotype-based' first isolates (61.6% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 61.8% is suitable for resistance analysis! We can now filter
<p>So only 61.6% is suitable for resistance analysis! We can now filter
on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
<code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
@ -634,25 +634,25 @@ 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 12,360 isolates for analysis. Now our data looks
<p>So we end up with 12,319 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%">
<col width="9%">
<col width="9%">
<col width="11%">
<col width="4%">
<col width="4%">
<col width="4%">
<col width="4%">
<col width="6%">
<col width="12%">
<col width="10%">
<col width="7%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
<thead><tr class="header">
@ -673,15 +673,15 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">2</td>
<td align="center">2010-06-25</td>
<td align="center">F2</td>
<td align="left">1</td>
<td align="center">2013-10-31</td>
<td align="center">J1</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">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
@ -689,79 +689,79 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">3</td>
<td align="center">2011-12-31</td>
<td align="center">A5</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="left">2</td>
<td align="center">2014-11-26</td>
<td align="center">I8</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">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2013-01-05</td>
<td align="center">Q3</td>
<td align="center">Hospital C</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</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">2017-12-24</td>
<td align="center">E9</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2014-12-06</td>
<td align="center">Q7</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</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="odd">
<td align="left">5</td>
<td align="center">2014-05-11</td>
<td align="center">S9</td>
<tr class="even">
<td align="left">10</td>
<td align="center">2014-08-11</td>
<td align="center">X6</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">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">2011-02-06</td>
<td align="center">S9</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</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">8</td>
<td align="center">2014-02-12</td>
<td align="center">E6</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">I</td>
<td align="center">R</td>
<td align="center">I</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">2015-08-18</td>
<td align="center">Q1</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
@ -801,8 +801,8 @@ readable:</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 12,360<br>
Available: 12,360 (100%, NA: 0 = 0%)<br>
Length: 12,319<br>
Available: 12,319 (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">5,843</td>
<td align="right">47.27%</td>
<td align="right">5,843</td>
<td align="right">47.27%</td>
<td align="right">5,888</td>
<td align="right">47.80%</td>
<td align="right">5,888</td>
<td align="right">47.80%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,316</td>
<td align="right">26.83%</td>
<td align="right">9,159</td>
<td align="right">74.10%</td>
<td align="right">3,213</td>
<td align="right">26.08%</td>
<td align="right">9,101</td>
<td align="right">73.88%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,866</td>
<td align="right">15.10%</td>
<td align="right">11,025</td>
<td align="right">1,887</td>
<td align="right">15.32%</td>
<td align="right">10,988</td>
<td align="right">89.20%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,335</td>
<td align="right">1,331</td>
<td align="right">10.80%</td>
<td align="right">12,360</td>
<td align="right">12,319</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -902,13 +902,28 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-05-11</td>
<td align="center">S9</td>
<td align="center">2014-11-26</td>
<td align="center">I8</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">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-08-11</td>
<td align="center">X6</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
@ -916,13 +931,28 @@ antibiotic class they are in:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-09-06</td>
<td align="center">N1</td>
<tr class="odd">
<td align="center">2015-06-18</td>
<td align="center">D8</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">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="even">
<td align="center">2017-10-11</td>
<td align="center">L2</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">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
@ -932,65 +962,35 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-10-21</td>
<td align="center">U6</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">2011-02-28</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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">S</td>
<td align="center">I</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="even">
<td align="center">2016-07-17</td>
<td align="center">T2</td>
<td align="center">Hospital A</td>
<td align="center">2012-10-28</td>
<td align="center">L6</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">I</td>
<td align="center">R</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">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">2014-09-22</td>
<td align="center">F8</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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">2014-04-21</td>
<td align="center">E7</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</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>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in
@ -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">1469</td>
<td align="center">1254</td>
<td align="center">3120</td>
<td align="center">5843</td>
<td align="center">1515</td>
<td align="center">1214</td>
<td align="center">3159</td>
<td align="center">5888</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">2702</td>
<td align="center">1194</td>
<td align="center">1947</td>
<td align="center">5843</td>
<td align="center">2728</td>
<td align="center">1171</td>
<td align="center">1989</td>
<td align="center">5888</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">1973</td>
<td align="center">1812</td>
<td align="center">2058</td>
<td align="center">5843</td>
<td align="center">1970</td>
<td align="center">1842</td>
<td align="center">2076</td>
<td align="center">5888</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2020</td>
<td align="center">1806</td>
<td align="center">2017</td>
<td align="center">5843</td>
<td align="center">2001</td>
<td align="center">1793</td>
<td align="center">2094</td>
<td align="center">5888</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">1335</td>
<td align="center">1335</td>
<td align="center">1331</td>
<td align="center">1331</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">599</td>
<td align="center">293</td>
<td align="center">443</td>
<td align="center">1335</td>
<td align="center">593</td>
<td align="center">289</td>
<td align="center">449</td>
<td align="center">1331</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">2020</td>
<td align="center">1806</td>
<td align="center">2017</td>
<td align="center">5843</td>
<td align="center">2001</td>
<td align="center">1793</td>
<td align="center">2094</td>
<td align="center">5888</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">471</td>
<td align="center">430</td>
<td align="center">434</td>
<td align="center">1335</td>
<td align="center">400</td>
<td align="center">460</td>
<td align="center">1331</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1109</td>
<td align="center">1086</td>
<td align="center">1121</td>
<td align="center">3316</td>
<td align="center">1094</td>
<td align="center">982</td>
<td align="center">1137</td>
<td align="center">3213</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">1866</td>
<td align="center">1866</td>
<td align="center">1887</td>
<td align="center">1887</td>
</tr>
</tbody>
</table>
@ -1137,7 +1137,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5817152</span></span></code></pre></div>
<span><span class="co"># [1] 0.5826772</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">0.5845627</td>
<td align="center">0.5808320</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5830477</td>
<td align="center">0.5845366</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5790359</td>
<td align="center">0.5761047</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5767790</td>
<td align="center">0.5873016</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">0.5845627</td>
<td align="center">3796</td>
<td align="center">0.5808320</td>
<td align="center">3798</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5830477</td>
<td align="center">4377</td>
<td align="center">0.5845366</td>
<td align="center">4294</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5790359</td>
<td align="center">1784</td>
<td align="center">0.5761047</td>
<td align="center">1833</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5767790</td>
<td align="center">2403</td>
<td align="center">0.5873016</td>
<td align="center">2394</td>
</tr>
</tbody>
</table>
@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6667808</td>
<td align="center">0.6548006</td>
<td align="center">0.8867020</td>
<td align="center">0.6621943</td>
<td align="center">0.6443614</td>
<td align="center">0.8773777</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6681648</td>
<td align="center">0.6749064</td>
<td align="center">0.8936330</td>
<td align="center">0.6626597</td>
<td align="center">0.6543952</td>
<td align="center">0.8918107</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6628468</td>
<td align="center">0.6619421</td>
<td align="center">0.8808806</td>
<td align="center">0.6644880</td>
<td align="center">0.6461251</td>
<td align="center">0.8801743</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4764202</td>
<td align="center">0.4886063</td>
<td align="center">0.0000000</td>
<td align="center">0.4764202</td>
<td align="center">0.4886063</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">58.5%</td>
<td align="right">36.8%</td>
<td align="right">58.1%</td>
<td align="right">36.1%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">58.3%</td>
<td align="right">36.2%</td>
<td align="right">58.5%</td>
<td align="right">36.4%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">57.9%</td>
<td align="right">37.7%</td>
<td align="right">57.6%</td>
<td align="right">36.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">57.7%</td>
<td align="right">34.5%</td>
<td align="right">58.7%</td>
<td align="right">36.9%</td>
</tr>
</tbody>
</table>
@ -1410,18 +1410,16 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 0.002 64 16 0.125 2 64 8 0.025 0.01 </span></span>
<span><span class="co"># [10] 0.002 128 0.5 1 0.01 0.005 &gt;=256 0.0625 4 </span></span>
<span><span class="co"># [19] 64 0.01 128 2 0.25 0.5 0.0625 64 8 </span></span>
<span><span class="co"># [28] &gt;=256 8 0.0625 0.5 0.005 0.025 2 0.005 4 </span></span>
<span><span class="co"># [37] 64 &lt;=0.001 0.01 1 &lt;=0.001 0.0625 1 64 32 </span></span>
<span><span class="co"># [46] 0.5 0.005 4 0.25 0.01 64 0.5 &lt;=0.001 0.25 </span></span>
<span><span class="co"># [55] &lt;=0.001 1 0.002 4 32 0.005 4 128 &lt;=0.001</span></span>
<span><span class="co"># [64] 0.025 0.25 &lt;=0.001 64 &lt;=0.001 0.0625 128 &gt;=256 8 </span></span>
<span><span class="co"># [73] 2 0.125 &gt;=256 8 0.005 &gt;=256 0.125 16 2 </span></span>
<span><span class="co"># [82] 2 0.025 64 &gt;=256 &lt;=0.001 32 &gt;=256 2 2 </span></span>
<span><span class="co"># [91] 64 0.0625 &gt;=256 0.002 0.025 0.125 64 0.01 0.002 </span></span>
<span><span class="co"># [100] 0.5</span></span></code></pre></div>
<span><span class="co"># [1] 64 0.125 64 4 256 0.01 0.125 2 128 0.002 </span></span>
<span><span class="co"># [11] 2 0.125 0.01 0.01 8 0.0625 0.5 32 0.01 0.0625</span></span>
<span><span class="co"># [21] 8 16 32 16 0.001 0.005 4 128 0.025 128 </span></span>
<span><span class="co"># [31] 2 256 0.5 8 0.25 256 16 0.025 0.001 32 </span></span>
<span><span class="co"># [41] 16 2 16 0.025 1 32 64 4 16 32 </span></span>
<span><span class="co"># [51] 0.005 0.025 0.001 0.025 64 2 0.125 1 0.5 0.125 </span></span>
<span><span class="co"># [61] 16 0.002 0.25 16 0.002 4 0.5 2 128 128 </span></span>
<span><span class="co"># [71] 8 1 0.002 32 0.0625 8 128 0.125 1 0.25 </span></span>
<span><span class="co"># [81] 0.002 8 128 16 256 0.125 2 4 1 0.0625</span></span>
<span><span class="co"># [91] 4 0.025 16 0.5 64 0.002 128 0.0625 1 64</span></span></code></pre></div>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1455,10 +1453,10 @@ plotting:</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 31 28 26 25 25 26 25 19 31 31 30 27 23 29 18 31 21 18 31 19 29 24 20 28 18</span></span>
<span><span class="co"># [26] 28 30 22 18 20 22 19 26 25 29 26 26 31 17 17 18 26 25 26 30 20 27 20 28 20</span></span>
<span><span class="co"># [51] 17 20 30 23 18 31 23 18 22 20 24 31 19 27 18 21 25 25 22 26 21 29 26 24 20</span></span>
<span><span class="co"># [76] 24 20 31 22 18 23 26 28 20 26 20 17 28 31 24 31 28 21 19 26 26 22 24 18 31</span></span></code></pre></div>
<span><span class="co"># [1] 30 20 18 25 20 24 23 23 19 30 23 27 24 19 18 25 21 26 21 26 29 18 25 29 31</span></span>
<span><span class="co"># [26] 19 25 30 19 24 25 26 21 22 28 17 24 17 31 28 20 29 31 21 29 18 25 19 25 22</span></span>
<span><span class="co"># [51] 24 27 29 27 19 26 20 27 24 18 22 22 26 31 19 24 22 29 20 22 31 19 22 21 18</span></span>
<span><span class="co"># [76] 22 17 23 21 20 19 28 21 24 23 25 30 26 26 17 17 20 18 28 24 18 25 29 17 27</span></span></code></pre></div>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>

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@ -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 I S S I S I</span></span>
<span><span class="co"># 2 R R R R I S</span></span>
<span><span class="co"># 3 R I R R I R</span></span>
<span><span class="co"># 4 R S I S S I</span></span>
<span><span class="co"># 5 I I S S S I</span></span>
<span><span class="co"># 6 I I I R R I</span></span>
<span><span class="co"># 1 S I I I S I</span></span>
<span><span class="co"># 2 S S I S I I</span></span>
<span><span class="co"># 3 S S S R I S</span></span>
<span><span class="co"># 4 R S S I S S</span></span>
<span><span class="co"># 5 I S I R I R</span></span>
<span><span class="co"># 6 S R S I S R</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 I</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"># 5 S</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
@ -428,40 +428,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3238</td>
<td align="right">64.76%</td>
<td align="right">3238</td>
<td align="right">64.76%</td>
<td align="right">3193</td>
<td align="right">63.86%</td>
<td align="right">3193</td>
<td align="right">63.86%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">994</td>
<td align="right">19.88%</td>
<td align="right">4232</td>
<td align="right">84.64%</td>
<td align="right">981</td>
<td align="right">19.62%</td>
<td align="right">4174</td>
<td align="right">83.48%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">425</td>
<td align="right">8.50%</td>
<td align="right">4657</td>
<td align="right">93.14%</td>
<td align="right">472</td>
<td align="right">9.44%</td>
<td align="right">4646</td>
<td align="right">92.92%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">247</td>
<td align="right">4.94%</td>
<td align="right">4904</td>
<td align="right">98.08%</td>
<td align="right">262</td>
<td align="right">5.24%</td>
<td align="right">4908</td>
<td align="right">98.16%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">96</td>
<td align="right">1.92%</td>
<td align="right">92</td>
<td align="right">1.84%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>