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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</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">
@ -317,69 +317,69 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-01-13</td>
<td align="center">A7</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2011-06-19</td>
<td align="center">N8</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia 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>
</tr>
<tr class="even">
<td align="center">2013-07-08</td>
<td align="center">U10</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-07-14</td>
<td align="center">N3</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-07-17</td>
<td align="center">K10</td>
<td align="center">2014-07-29</td>
<td align="center">J1</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2013-12-06</td>
<td align="center">Z6</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</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>
</tr>
<tr class="even">
<td align="center">2013-09-04</td>
<td align="center">U4</td>
<td align="center">Hospital C</td>
<td align="center">Klebsiella pneumoniae</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">M</td>
</tr>
<tr class="odd">
<td align="center">2010-05-09</td>
<td align="center">B3</td>
<td align="center">2015-03-05</td>
<td align="center">A9</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-10-20</td>
<td align="center">P10</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-12-21</td>
<td align="center">U3</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
</tbody>
@ -414,16 +414,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,403</td>
<td align="right">52.02%</td>
<td align="right">10,403</td>
<td align="right">52.02%</td>
<td align="right">10,328</td>
<td align="right">51.64%</td>
<td align="right">10,328</td>
<td align="right">51.64%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,597</td>
<td align="right">47.99%</td>
<td align="right">9,672</td>
<td align="right">48.36%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -477,9 +477,9 @@ Longest: 1</p>
<span><span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span></span>
<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"># =&gt; Found 10,723 'phenotype-based' first isolates (53.6% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,619 '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 53.6% 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>
<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">&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="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
@ -487,7 +487,7 @@ Longest: 1</p>
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>So we end up with 10,723 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,619 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 style="width:100%;" class="table">
@ -525,101 +525,101 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2014-01-13</td>
<td align="center">A7</td>
<td align="center">Hospital C</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">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">3</td>
<td align="center">2013-12-06</td>
<td align="center">Z6</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">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="center">2010-05-09</td>
<td align="center">B3</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">2015-03-05</td>
<td align="center">A9</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">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<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">2013-12-21</td>
<td align="center">U3</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">2017-10-20</td>
<td align="center">P10</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">8</td>
<td align="center">2013-03-11</td>
<td align="center">S7</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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">7</td>
<td align="center">2011-06-10</td>
<td align="center">D8</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2012-03-02</td>
<td align="center">K7</td>
<td align="center">2012-06-14</td>
<td align="center">I1</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">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="odd">
<td align="left">10</td>
<td align="center">2010-11-23</td>
<td align="center">V10</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">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">13</td>
<td align="center">2012-03-06</td>
<td align="center">R5</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>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -641,8 +641,8 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,723<br>
Available: 10,723 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,619<br>
Available: 10,619 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -659,33 +659,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,683</td>
<td align="right">43.67%</td>
<td align="right">4,683</td>
<td align="right">43.67%</td>
<td align="right">4,632</td>
<td align="right">43.62%</td>
<td align="right">4,632</td>
<td align="right">43.62%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,727</td>
<td align="right">25.43%</td>
<td align="right">7,410</td>
<td align="right">69.10%</td>
<td align="right">2,742</td>
<td align="right">25.82%</td>
<td align="right">7,374</td>
<td align="right">69.44%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,104</td>
<td align="right">19.62%</td>
<td align="right">9,514</td>
<td align="right">88.73%</td>
<td align="right">2,062</td>
<td align="right">19.42%</td>
<td align="right">9,436</td>
<td align="right">88.86%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,209</td>
<td align="right">11.27%</td>
<td align="right">10,723</td>
<td align="right">1,183</td>
<td align="right">11.14%</td>
<td align="right">10,619</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -704,14 +704,14 @@ Longest: 24</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>
@ -732,13 +732,13 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-12-06</td>
<td align="center">Z6</td>
<td align="center">Hospital A</td>
<td align="center">2010-11-23</td>
<td align="center">V10</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@ -747,23 +747,8 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-12-21</td>
<td align="center">U3</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">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-06-10</td>
<td align="center">D8</td>
<td align="center">2011-11-01</td>
<td align="center">B1</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
@ -776,9 +761,24 @@ Longest: 24</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-01-30</td>
<td align="center">H5</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">2012-03-02</td>
<td align="center">K7</td>
<td align="center">2015-12-11</td>
<td align="center">I5</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
@ -792,9 +792,24 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-12-25</td>
<td align="center">W10</td>
<td align="center">2017-08-04</td>
<td align="center">O3</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">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-10-06</td>
<td align="center">V8</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
@ -806,21 +821,6 @@ Longest: 24</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-02-13</td>
<td align="center">E5</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>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> function:</p>
@ -842,50 +842,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2228</td>
<td align="center">121</td>
<td align="center">2334</td>
<td align="center">4683</td>
<td align="center">2203</td>
<td align="center">123</td>
<td align="center">2306</td>
<td align="center">4632</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3423</td>
<td align="center">156</td>
<td align="center">1104</td>
<td align="center">4683</td>
<td align="center">3385</td>
<td align="center">145</td>
<td align="center">1102</td>
<td align="center">4632</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3439</td>
<td align="center">3390</td>
<td align="center">0</td>
<td align="center">1244</td>
<td align="center">4683</td>
<td align="center">1242</td>
<td align="center">4632</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4064</td>
<td align="center">4049</td>
<td align="center">0</td>
<td align="center">619</td>
<td align="center">4683</td>
<td align="center">583</td>
<td align="center">4632</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">1209</td>
<td align="center">1209</td>
<td align="center">1183</td>
<td align="center">1183</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">960</td>
<td align="center">46</td>
<td align="center">203</td>
<td align="center">1209</td>
<td align="center">929</td>
<td align="center">54</td>
<td align="center">200</td>
<td align="center">1183</td>
</tr>
</tbody>
</table>
@ -908,34 +908,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4064</td>
<td align="center">4049</td>
<td align="center">0</td>
<td align="center">619</td>
<td align="center">4683</td>
<td align="center">583</td>
<td align="center">4632</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1075</td>
<td align="center">1078</td>
<td align="center">0</td>
<td align="center">134</td>
<td align="center">1209</td>
<td align="center">105</td>
<td align="center">1183</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2421</td>
<td align="center">2430</td>
<td align="center">0</td>
<td align="center">306</td>
<td align="center">2727</td>
<td align="center">312</td>
<td align="center">2742</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">2104</td>
<td align="center">2104</td>
<td align="center">2062</td>
<td align="center">2062</td>
</tr>
</tbody>
</table>
@ -949,7 +949,7 @@ Longest: 24</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5465821</span></span></code></pre></div>
<span><span class="co"># [1] 0.5432715</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
@ -963,19 +963,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5332098</td>
<td align="center">0.5382868</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5497618</td>
<td align="center">0.5447543</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5499058</td>
<td align="center">0.5595602</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5588652</td>
<td align="center">0.5353630</td>
</tr>
</tbody>
</table>
@ -994,23 +994,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5332098</td>
<td align="center">3237</td>
<td align="center">0.5382868</td>
<td align="center">3082</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5497618</td>
<td align="center">3778</td>
<td align="center">0.5447543</td>
<td align="center">3765</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5499058</td>
<td align="center">1593</td>
<td align="center">0.5595602</td>
<td align="center">1637</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5588652</td>
<td align="center">2115</td>
<td align="center">0.5353630</td>
<td align="center">2135</td>
</tr>
</tbody>
</table>
@ -1031,27 +1031,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7642537</td>
<td align="center">0.8678198</td>
<td align="center">0.9750160</td>
<td align="center">0.7620898</td>
<td align="center">0.8741364</td>
<td align="center">0.9771157</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8320926</td>
<td align="center">0.8891646</td>
<td align="center">0.9743590</td>
<td align="center">0.8309383</td>
<td align="center">0.9112426</td>
<td align="center">0.9805579</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7920792</td>
<td align="center">0.8877888</td>
<td align="center">0.9845985</td>
<td align="center">0.7884756</td>
<td align="center">0.8862144</td>
<td align="center">0.9817651</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5361217</td>
<td align="center">0.5354025</td>
<td align="center">0.0000000</td>
<td align="center">0.5361217</td>
<td align="center">0.5354025</td>
</tr>
</tbody>
</table>
@ -1076,23 +1076,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">53.3%</td>
<td align="right">53.8%</td>
<td align="right">26.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">55.0%</td>
<td align="right">54.5%</td>
<td align="right">27.0%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">55.0%</td>
<td align="right">25.5%</td>
<td align="right">56.0%</td>
<td align="right">27.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">55.9%</td>
<td align="right">27.3%</td>
<td align="right">53.5%</td>
<td align="right">26.1%</td>
</tr>
</tbody>
</table>
@ -1176,18 +1176,16 @@ Longest: 24</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class &lt;mic&gt;</span></span>
<span><span class="co"># [1] 32 64 128 128 64 8 32 0.002 0.025 </span></span>
<span><span class="co"># [10] 0.5 32 &lt;=0.001 2 128 0.01 1 2 0.01 </span></span>
<span><span class="co"># [19] 128 0.5 4 0.002 0.125 256 0.0625 4 0.002 </span></span>
<span><span class="co"># [28] 0.005 4 0.002 32 0.01 0.0625 0.25 2 64 </span></span>
<span><span class="co"># [37] 0.0625 0.5 256 4 1 0.025 128 0.0625 16 </span></span>
<span><span class="co"># [46] 0.5 0.005 0.01 1 2 0.01 2 8 0.125 </span></span>
<span><span class="co"># [55] 0.25 256 0.0625 0.025 0.002 8 &lt;=0.001 1 0.002 </span></span>
<span><span class="co"># [64] 256 8 4 0.005 0.025 4 0.002 &lt;=0.001 2 </span></span>
<span><span class="co"># [73] 256 0.005 256 2 4 16 128 256 &lt;=0.001</span></span>
<span><span class="co"># [82] 1 2 1 1 &lt;=0.001 0.5 4 0.25 32 </span></span>
<span><span class="co"># [91] 0.002 0.0625 0.01 32 0.005 0.01 2 64 64 </span></span>
<span><span class="co"># [100] 2</span></span></code></pre></div>
<span><span class="co"># [1] 256 16 0.002 0.025 8 0.025 32 0.025 0.01 256 </span></span>
<span><span class="co"># [11] 16 0.01 32 0.025 0.01 0.0625 2 0.25 128 0.005 </span></span>
<span><span class="co"># [21] 0.01 16 0.125 0.25 0.01 0.001 8 0.025 8 1 </span></span>
<span><span class="co"># [31] 0.025 0.25 0.0625 256 0.001 0.025 0.001 8 0.01 0.025 </span></span>
<span><span class="co"># [41] 0.25 8 64 8 0.25 4 1 0.0625 0.0625 0.5 </span></span>
<span><span class="co"># [51] 2 0.002 16 0.002 0.01 16 0.25 64 8 256 </span></span>
<span><span class="co"># [61] 0.005 0.0625 1 64 64 0.5 128 0.002 32 0.002 </span></span>
<span><span class="co"># [71] 128 128 0.5 0.002 0.25 0.5 0.125 1 16 64 </span></span>
<span><span class="co"># [81] 128 32 0.025 128 16 32 32 32 0.002 0.125 </span></span>
<span><span class="co"># [91] 0.5 0.0625 0.5 128 0.125 128 8 0.25 128 0.25</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>
@ -1216,10 +1214,10 @@ Longest: 24</p>
<span><span class="co"># coli). Run `mo_uncertainties()` to review this.</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class &lt;disk&gt;</span></span>
<span><span class="co"># [1] 28 22 30 19 23 20 17 21 22 18 18 27 18 20 24 28 30 20 29 31 22 31 23 24 17</span></span>
<span><span class="co"># [26] 23 18 17 25 30 28 23 30 23 30 31 18 26 26 26 27 17 30 18 27 31 17 24 20 26</span></span>
<span><span class="co"># [51] 30 21 26 27 20 23 28 29 17 29 27 24 22 27 28 27 22 30 18 28 25 18 25 18 31</span></span>
<span><span class="co"># [76] 29 25 17 31 20 20 21 24 24 30 28 30 31 20 30 27 19 24 17 22 30 31 27 28 24</span></span></code></pre></div>
<span><span class="co"># [1] 23 21 25 21 18 21 18 19 23 26 28 30 20 21 17 17 27 26 31 30 25 17 27 27 19</span></span>
<span><span class="co"># [26] 31 23 23 23 22 20 26 17 24 29 26 24 25 29 22 22 29 26 22 24 25 26 18 31 24</span></span>
<span><span class="co"># [51] 25 28 26 27 19 21 21 29 27 21 27 21 18 17 20 20 17 25 30 20 19 20 23 27 31</span></span>
<span><span class="co"># [76] 24 31 24 22 26 19 19 20 20 25 17 21 22 30 25 23 26 31 20 30 18 29 18 29 17</span></span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>

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2
articles/EUCAST.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

58
articles/MDR.html
View File

@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</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">
@ -313,18 +313,18 @@ Unique: 2</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 I I S S I R</span></span>
<span><span class="co"># 2 I R R S I I</span></span>
<span><span class="co"># 3 R I S R R S</span></span>
<span><span class="co"># 4 I S I S I S</span></span>
<span><span class="co"># 5 S R S I S R</span></span>
<span><span class="co"># 6 I S I I S S</span></span>
<span><span class="co"># 1 S S R I R I</span></span>
<span><span class="co"># 2 I R S S S S</span></span>
<span><span class="co"># 3 I R S I S S</span></span>
<span><span class="co"># 4 R I S I S R</span></span>
<span><span class="co"># 5 I I S R S R</span></span>
<span><span class="co"># 6 S I S S R R</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -356,40 +356,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3193</td>
<td align="right">63.86%</td>
<td align="right">3193</td>
<td align="right">63.86%</td>
<td align="right">3182</td>
<td align="right">63.64%</td>
<td align="right">3182</td>
<td align="right">63.64%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">996</td>
<td align="right">19.92%</td>
<td align="right">4189</td>
<td align="right">83.78%</td>
<td align="right">993</td>
<td align="right">19.86%</td>
<td align="right">4175</td>
<td align="right">83.50%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">450</td>
<td align="right">9.00%</td>
<td align="right">4639</td>
<td align="right">92.78%</td>
<td align="right">477</td>
<td align="right">9.54%</td>
<td align="right">4652</td>
<td align="right">93.04%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">241</td>
<td align="right">4.82%</td>
<td align="right">4880</td>
<td align="right">97.60%</td>
<td align="right">250</td>
<td align="right">5.00%</td>
<td align="right">4902</td>
<td align="right">98.04%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">120</td>
<td align="right">2.40%</td>
<td align="right">98</td>
<td align="right">1.96%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
articles/PCA.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
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2
articles/SPSS.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
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2
articles/WHONET.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
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16
articles/datasets.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
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@ -184,7 +184,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</h2>
<p>A data set with 70,764 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</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 21 August 2022 14:52:57 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">R file</a> (1.3 MB)<br>
@ -405,7 +405,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<p>A data set with 14,338 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>prevalence</em>.</p>
<p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
<p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 August 2022 14:52:57 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">R file</a> (0.2 MB)<br>
@ -470,7 +470,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</h2>
<p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 August 2022 14:52:57 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 21 August 2022 15:23:37 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>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">R file</a> (33 kB)<br>
@ -638,7 +638,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</h2>
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 August 2022 14:52:57 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 21 August 2022 15:23:37 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>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">R file</a> (5 kB)<br>
@ -765,7 +765,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</h2>
<p>A data set with 20,369 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>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 21 August 2022 14:52:57 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R file</a> (49 kB)<br>
@ -919,7 +919,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</h2>
<p>A data set with 134,956 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 21 August 2022 14:52:57 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p>It was last updated on 21 August 2022 15:23:37 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">R file</a> (78 kB)<br>
@ -1186,7 +1186,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</h2>
<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 August 2022 14:52:57 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">R file</a> (3 kB)<br>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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articles/resistance_predict.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</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">
@ -176,7 +176,7 @@
<div class="section level2">
<h2 id="needed-r-packages">Needed R packages<a class="anchor" aria-label="anchor" href="#needed-r-packages"></a>
</h2>
<p>As with many uses in R, we need some additional packages for AMR data analysis. Our package works closely together with the <a href="https://www.tidyverse.org" class="external-link">tidyverse packages</a> <a href="https://dplyr.tidyverse.org/" class="external-link"><code>dplyr</code></a> and <a href="https://ggplot2.tidyverse.org" class="external-link"><code>ggplot2</code></a> by Dr Hadley Wickham. The tidyverse tremendously improves the way we conduct data science - it allows for a very natural way of writing syntaxes and creating beautiful plots in R.</p>
<p>As with many uses in R, we need some additional packages for AMR data analysis. Our package works closely together with the <a href="https://www.tidyverse.org" class="external-link">tidyverse packages</a> <a href="https://dplyr.tidyverse.org/" class="external-link"><code>dplyr</code></a> and <a href="https://ggplot2.tidyverse.org" class="external-link"><code>ggplot2</code></a>. The tidyverse tremendously improves the way we conduct data science - it allows for a very natural way of writing syntaxes and creating beautiful plots in R.</p>
<p>Our <code>AMR</code> package depends on these packages and even extends their use and functions.</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
@ -205,9 +205,8 @@
<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a> <span class="at">model =</span> <span class="st">"binomial"</span>)</span></code></pre></div>
<p>The function will look for a date column itself if <code>col_date</code> is not set.</p>
<p>When running any of these commands, a summary of the regression model will be printed unless using <code>resistance_predict(..., info = FALSE)</code>.</p>
<pre><code><span><span class="co"># ℹ Using column 'date' as input for `col_date`.</span></span></code></pre>
<p>This text is only a printed summary - the actual result (output) of the function is a <code>data.frame</code> containing for each year: the number of observations, the actual observed resistance, the estimated resistance and the standard error below and above the estimation:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">predict_TZP</span></span>
<span><span class="co"># year value se_min se_max observations observed estimated</span></span>
<span><span class="co"># 1 2002 0.20000000 NA NA 15 0.20000000 0.05616378</span></span>
@ -242,15 +241,15 @@
<span><span class="co"># 30 2031 0.51109592 0.3973697 0.6248221 NA NA 0.51109592</span></span>
<span><span class="co"># 31 2032 0.53574417 0.4169574 0.6545309 NA NA 0.53574417</span></span></code></pre></div>
<p>The function <code>plot</code> is available in base R, and can be extended by other packages to depend the output based on the type of input. We extended its function to cope with resistance predictions:</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span></span></code></pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-4-1.png" width="720"></p>
<p>This is the fastest way to plot the result. It automatically adds the right axes, error bars, titles, number of available observations and type of model.</p>
<p>We also support the <code>ggplot2</code> package with our custom function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> to create more appealing plots:</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span></span></code></pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-5-1.png" width="720"></p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="co"># choose for error bars instead of a ribbon</span></span>
<span><span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="va">predict_TZP</span>, ribbon <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
@ -259,7 +258,7 @@
<h3 id="choosing-the-right-model">Choosing the right model<a class="anchor" aria-label="anchor" href="#choosing-the-right-model"></a>
</h3>
<p>Resistance is not easily predicted; if we look at vancomycin resistance in Gram-positive bacteria, the spread (i.e. standard error) is enormous:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</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/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"binomial"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
@ -305,7 +304,7 @@
</tbody>
</table>
<p>For the vancomycin resistance in Gram-positive bacteria, a linear model might be more appropriate:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</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/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"linear"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
@ -313,7 +312,7 @@
<span><span class="co"># ℹ Using column 'date' as input for `col_date`.</span></span></code></pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
<p>The model itself is also available from the object, as an <code>attribute</code>:</p>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">model</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/attributes.html" class="external-link">attributes</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span><span class="op">$</span><span class="va">model</span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">$</span><span class="va">family</span></span>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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