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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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@@ -109,11 +109,6 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
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@@ -111,11 +111,6 @@
Get properties of an antibiotic Get properties of an antibiotic
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@@ -167,7 +162,7 @@
<img src="../logo.svg" class="logo" alt=""><h1>How to conduct AMR data analysis</h1> <img src="../logo.svg" class="logo" alt=""><h1>How to conduct AMR data analysis</h1>
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4> <h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
<h4 data-toc-skip class="date">21 August 2022</h4> <h4 data-toc-skip class="date">25 August 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small> <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="d-none name"><code>AMR.Rmd</code></div> <div class="d-none name"><code>AMR.Rmd</code></div>
@@ -175,7 +170,7 @@
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 21 August 2022.</p> <p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 25 August 2022.</p>
<div class="section level2"> <div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a> <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2> </h2>
@@ -206,21 +201,21 @@
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">2022-08-21</td> <td align="center">2022-08-25</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</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>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2022-08-21</td> <td align="center">2022-08-25</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</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">R</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">2022-08-21</td> <td align="center">2022-08-25</td>
<td align="center">efgh</td> <td align="center">efgh</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">R</td> <td align="center">R</td>
@@ -317,71 +312,71 @@
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">2011-06-19</td> <td align="center">2010-03-22</td>
<td align="center">N8</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-04-13</td>
<td align="center">G1</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2014-11-21</td>
<td align="center">D5</td>
<td align="center">Hospital D</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">2014-07-29</td>
<td align="center">J1</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus 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">M</td>
</tr>
<tr class="odd">
<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">Staphylococcus aureus</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-01-18</td>
<td align="center">T4</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</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">F</td> <td align="center">F</td>
</tr> </tr>
<tr class="odd">
<td align="center">2012-07-14</td>
<td align="center">M9</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-02-17</td>
<td align="center">H3</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>
</tbody> </tbody>
</table> </table>
<p>Now, let’s start the cleaning and the analysis!</p> <p>Now, let’s start the cleaning and the analysis!</p>
@@ -414,16 +409,16 @@ Longest: 1</p>
<tr class="odd"> <tr class="odd">
<td align="left">1</td> <td align="left">1</td>
<td align="left">M</td> <td align="left">M</td>
<td align="right">10,328</td> <td align="right">10,334</td>
<td align="right">51.64%</td> <td align="right">51.67%</td>
<td align="right">10,328</td> <td align="right">10,334</td>
<td align="right">51.64%</td> <td align="right">51.67%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">2</td> <td align="left">2</td>
<td align="left">F</td> <td align="left">F</td>
<td align="right">9,672</td> <td align="right">9,666</td>
<td align="right">48.36%</td> <td align="right">48.33%</td>
<td align="right">20,000</td> <td align="right">20,000</td>
<td align="right">100.00%</td> <td align="right">100.00%</td>
</tr> </tr>
@@ -477,9 +472,9 @@ Longest: 1</p>
<span><span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span></span> <span><span class="co"># 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"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span> <span><span class="co"># 2</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"># =&gt; Found 10,754 'phenotype-based' first isolates (53.8% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div> <span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<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> <p>So only 53.8% 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"> <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> <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> <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>
@@ -487,10 +482,10 @@ Longest: 1</p>
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> <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> <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> <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 10,619 isolates for analysis. Now our data looks like:</p> <p>So we end up with 10,754 isolates for analysis. Now our data looks like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> <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> <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"> <table class="table">
<colgroup> <colgroup>
<col width="2%"> <col width="2%">
<col width="9%"> <col width="9%">
@@ -503,7 +498,7 @@ Longest: 1</p>
<col width="3%"> <col width="3%">
<col width="6%"> <col width="6%">
<col width="11%"> <col width="11%">
<col width="12%"> <col width="11%">
<col width="9%"> <col width="9%">
<col width="5%"> <col width="5%">
</colgroup> </colgroup>
@@ -525,74 +520,26 @@ Longest: 1</p>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="left">5</td> <td align="left">2</td>
<td align="center">2015-03-05</td> <td align="center">2012-04-13</td>
<td align="center">A9</td> <td align="center">G1</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="even">
<td align="left">6</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="even">
<td align="left">9</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">Hospital B</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">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="left">4</td>
<td align="center">2010-01-18</td>
<td align="center">T4</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</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>
@@ -604,17 +551,65 @@ Longest: 1</p>
<td align="center">pneumoniae</td> <td align="center">pneumoniae</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">2010-02-17</td>
<td align="center">H3</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"> <tr class="even">
<td align="left">13</td> <td align="left">7</td>
<td align="center">2012-03-06</td> <td align="center">2013-01-04</td>
<td align="center">R5</td> <td align="center">C5</td>
<td align="center">Hospital B</td> <td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">10</td>
<td align="center">2014-12-10</td>
<td align="center">G7</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">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>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">11</td>
<td align="center">2015-10-09</td>
<td align="center">B3</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">M</td>
<td align="center">Gram-negative</td> <td align="center">Gram-negative</td>
<td align="center">Escherichia</td> <td align="center">Escherichia</td>
<td align="center">coli</td> <td align="center">coli</td>
@@ -641,8 +636,8 @@ 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> <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><strong>Frequency table</strong></p>
<p>Class: character<br> <p>Class: character<br>
Length: 10,619<br> Length: 10,754<br>
Available: 10,619 (100.0%, NA: 0 = 0.0%)<br> Available: 10,754 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p> Unique: 4</p>
<p>Shortest: 16<br> <p>Shortest: 16<br>
Longest: 24</p> Longest: 24</p>
@@ -659,33 +654,33 @@ Longest: 24</p>
<tr class="odd"> <tr class="odd">
<td align="left">1</td> <td align="left">1</td>
<td align="left">Escherichia coli</td> <td align="left">Escherichia coli</td>
<td align="right">4,632</td> <td align="right">4,654</td>
<td align="right">43.62%</td> <td align="right">43.28%</td>
<td align="right">4,632</td> <td align="right">4,654</td>
<td align="right">43.62%</td> <td align="right">43.28%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">2</td> <td align="left">2</td>
<td align="left">Staphylococcus aureus</td> <td align="left">Staphylococcus aureus</td>
<td align="right">2,742</td> <td align="right">2,782</td>
<td align="right">25.82%</td> <td align="right">25.87%</td>
<td align="right">7,374</td> <td align="right">7,436</td>
<td align="right">69.44%</td> <td align="right">69.15%</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">3</td> <td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td> <td align="left">Streptococcus pneumoniae</td>
<td align="right">2,062</td> <td align="right">2,109</td>
<td align="right">19.42%</td> <td align="right">19.61%</td>
<td align="right">9,436</td> <td align="right">9,545</td>
<td align="right">88.86%</td> <td align="right">88.76%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">4</td> <td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td> <td align="left">Klebsiella pneumoniae</td>
<td align="right">1,183</td> <td align="right">1,209</td>
<td align="right">11.14%</td> <td align="right">11.24%</td>
<td align="right">10,619</td> <td align="right">10,754</td>
<td align="right">100.00%</td> <td align="right">100.00%</td>
</tr> </tr>
</tbody> </tbody>
@@ -704,14 +699,14 @@ Longest: 24</p>
<col width="9%"> <col width="9%">
<col width="9%"> <col width="9%">
<col width="9%"> <col width="9%">
<col width="10%"> <col width="11%">
<col width="3%"> <col width="3%">
<col width="3%"> <col width="3%">
<col width="3%"> <col width="3%">
<col width="3%"> <col width="3%">
<col width="6%"> <col width="6%">
<col width="11%"> <col width="11%">
<col width="12%"> <col width="11%">
<col width="9%"> <col width="9%">
<col width="5%"> <col width="5%">
</colgroup> </colgroup>
@@ -732,9 +727,24 @@ Longest: 24</p>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">2010-11-23</td> <td align="center">2012-04-13</td>
<td align="center">V10</td> <td align="center">G1</td>
<td align="center">Hospital B</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">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">2010-01-18</td>
<td align="center">T4</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</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>
@@ -746,24 +756,24 @@ Longest: 24</p>
<td align="center">pneumoniae</td> <td align="center">pneumoniae</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="even"> <tr class="odd">
<td align="center">2011-11-01</td> <td align="center">2014-06-06</td>
<td align="center">B1</td> <td align="center">Y10</td>
<td align="center">Hospital D</td> <td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td> <td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">M</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">Gram-positive</td>
<td align="center">Streptococcus</td> <td align="center">Streptococcus</td>
<td align="center">pneumoniae</td> <td align="center">pneumoniae</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="odd"> <tr class="even">
<td align="center">2017-01-30</td> <td align="center">2011-12-29</td>
<td align="center">H5</td> <td align="center">J7</td>
<td align="center">Hospital C</td> <td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td> <td align="center">B_STRPT_PNMN</td>
<td align="center">S</td> <td align="center">S</td>
@@ -776,43 +786,28 @@ Longest: 24</p>
<td align="center">pneumoniae</td> <td align="center">pneumoniae</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="even"> <tr class="odd">
<td align="center">2015-12-11</td> <td align="center">2010-05-28</td>
<td align="center">I5</td> <td align="center">C3</td>
<td align="center">Hospital B</td> <td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td> <td align="center">B_KLBSL_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">S</td>
<td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">M</td> <td align="center">M</td>
<td align="center">Gram-positive</td> <td align="center">Gram-negative</td>
<td align="center">Streptococcus</td> <td align="center">Klebsiella</td>
<td align="center">pneumoniae</td> <td align="center">pneumoniae</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="odd">
<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"> <tr class="even">
<td align="center">2014-10-06</td> <td align="center">2012-12-04</td>
<td align="center">V8</td> <td align="center">V6</td>
<td align="center">Hospital A</td> <td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td> <td align="center">B_STRPT_PNMN</td>
<td align="center">S</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">F</td> <td align="center">F</td>
@@ -842,50 +837,50 @@ Longest: 24</p>
<tr class="odd"> <tr class="odd">
<td align="center">E. coli</td> <td align="center">E. coli</td>
<td align="center">AMX</td> <td align="center">AMX</td>
<td align="center">2203</td> <td align="center">2225</td>
<td align="center">123</td> <td align="center">122</td>
<td align="center">2306</td> <td align="center">2307</td>
<td align="center">4632</td> <td align="center">4654</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">E. coli</td> <td align="center">E. coli</td>
<td align="center">AMC</td> <td align="center">AMC</td>
<td align="center">3385</td> <td align="center">3423</td>
<td align="center">145</td> <td align="center">151</td>
<td align="center">1102</td> <td align="center">1080</td>
<td align="center">4632</td> <td align="center">4654</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">E. coli</td> <td align="center">E. coli</td>
<td align="center">CIP</td> <td align="center">CIP</td>
<td align="center">3390</td> <td align="center">3411</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">1242</td> <td align="center">1243</td>
<td align="center">4632</td> <td align="center">4654</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">E. coli</td> <td align="center">E. coli</td>
<td align="center">GEN</td> <td align="center">GEN</td>
<td align="center">4049</td> <td align="center">4041</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">583</td> <td align="center">613</td>
<td align="center">4632</td> <td align="center">4654</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">K. pneumoniae</td> <td align="center">K. pneumoniae</td>
<td align="center">AMX</td> <td align="center">AMX</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">1183</td> <td align="center">1209</td>
<td align="center">1183</td> <td align="center">1209</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">K. pneumoniae</td> <td align="center">K. pneumoniae</td>
<td align="center">AMC</td> <td align="center">AMC</td>
<td align="center">929</td> <td align="center">948</td>
<td align="center">54</td> <td align="center">54</td>
<td align="center">200</td> <td align="center">207</td>
<td align="center">1183</td> <td align="center">1209</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@@ -908,34 +903,34 @@ Longest: 24</p>
<tr class="odd"> <tr class="odd">
<td align="center">E. coli</td> <td align="center">E. coli</td>
<td align="center">GEN</td> <td align="center">GEN</td>
<td align="center">4049</td> <td align="center">4041</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">583</td> <td align="center">613</td>
<td align="center">4632</td> <td align="center">4654</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">K. pneumoniae</td> <td align="center">K. pneumoniae</td>
<td align="center">GEN</td> <td align="center">GEN</td>
<td align="center">1078</td> <td align="center">1069</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">105</td> <td align="center">140</td>
<td align="center">1183</td> <td align="center">1209</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">S. aureus</td> <td align="center">S. aureus</td>
<td align="center">GEN</td> <td align="center">GEN</td>
<td align="center">2430</td> <td align="center">2474</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">312</td> <td align="center">308</td>
<td align="center">2742</td> <td align="center">2782</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">S. pneumoniae</td> <td align="center">S. pneumoniae</td>
<td align="center">GEN</td> <td align="center">GEN</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">0</td> <td align="center">0</td>
<td align="center">2062</td> <td align="center">2109</td>
<td align="center">2062</td> <td align="center">2109</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@@ -949,7 +944,7 @@ 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> <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"> <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> <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] 0.5432715</span></span></code></pre></div> <span><span class="co"># [1] 0.5432397</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> <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"> <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> <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 +958,19 @@ Longest: 24</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">Hospital A</td> <td align="center">Hospital A</td>
<td align="center">0.5382868</td> <td align="center">0.5458167</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital B</td> <td align="center">Hospital B</td>
<td align="center">0.5447543</td> <td align="center">0.5334954</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Hospital C</td> <td align="center">Hospital C</td>
<td align="center">0.5595602</td> <td align="center">0.5404571</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital D</td> <td align="center">Hospital D</td>
<td align="center">0.5353630</td> <td align="center">0.5580645</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@@ -994,23 +989,23 @@ Longest: 24</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">Hospital A</td> <td align="center">Hospital A</td>
<td align="center">0.5382868</td> <td align="center">0.5458167</td>
<td align="center">3082</td> <td align="center">3263</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital B</td> <td align="center">Hospital B</td>
<td align="center">0.5447543</td> <td align="center">0.5334954</td>
<td align="center">3765</td> <td align="center">3702</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Hospital C</td> <td align="center">Hospital C</td>
<td align="center">0.5595602</td> <td align="center">0.5404571</td>
<td align="center">1637</td> <td align="center">1619</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital D</td> <td align="center">Hospital D</td>
<td align="center">0.5353630</td> <td align="center">0.5580645</td>
<td align="center">2135</td> <td align="center">2170</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@@ -1031,27 +1026,27 @@ Longest: 24</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">Escherichia</td> <td align="center">Escherichia</td>
<td align="center">0.7620898</td> <td align="center">0.7679416</td>
<td align="center">0.8741364</td> <td align="center">0.8682853</td>
<td align="center">0.9771157</td> <td align="center">0.9735711</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Klebsiella</td> <td align="center">Klebsiella</td>
<td align="center">0.8309383</td> <td align="center">0.8287841</td>
<td align="center">0.9112426</td> <td align="center">0.8842018</td>
<td align="center">0.9805579</td> <td align="center">0.9809760</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Staphylococcus</td> <td align="center">Staphylococcus</td>
<td align="center">0.7884756</td> <td align="center">0.7890007</td>
<td align="center">0.8862144</td> <td align="center">0.8892883</td>
<td align="center">0.9817651</td> <td align="center">0.9780733</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Streptococcus</td> <td align="center">Streptococcus</td>
<td align="center">0.5354025</td> <td align="center">0.5372214</td>
<td align="center">0.0000000</td> <td align="center">0.0000000</td>
<td align="center">0.5354025</td> <td align="center">0.5372214</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@@ -1076,23 +1071,23 @@ Longest: 24</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="left">Hospital A</td> <td align="left">Hospital A</td>
<td align="right">53.8%</td> <td align="right">54.6%</td>
<td align="right">26.2%</td> <td align="right">26.9%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">Hospital B</td> <td align="left">Hospital B</td>
<td align="right">54.5%</td> <td align="right">53.3%</td>
<td align="right">27.0%</td> <td align="right">25.9%</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">Hospital C</td> <td align="left">Hospital C</td>
<td align="right">56.0%</td> <td align="right">54.0%</td>
<td align="right">27.9%</td> <td align="right">25.6%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">Hospital D</td> <td align="left">Hospital D</td>
<td align="right">53.5%</td> <td align="right">55.8%</td>
<td align="right">26.1%</td> <td align="right">27.5%</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@@ -1176,16 +1171,16 @@ 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> <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="va">mic_values</span></span>
<span><span class="co"># Class &lt;mic&gt;</span></span> <span><span class="co"># Class &lt;mic&gt;</span></span>
<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"># [1] 2 0.01 128 2 128 0.001 0.025 0.5 2 0.025 </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"># [11] 0.0625 0.125 256 0.125 4 256 4 4 0.0625 256 </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"># [21] 0.125 2 64 16 0.5 0.5 0.0625 4 256 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"># [31] 0.005 0.125 0.002 4 32 0.01 0.01 0.002 0.25 0.125 </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"># [41] 0.025 0.01 64 32 0.001 0.5 16 32 0.5 0.01 </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"># [51] 0.001 4 0.001 16 8 0.001 4 0.25 64 0.002 </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"># [61] 0.01 32 0.005 0.25 4 0.002 0.002 16 32 1 </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"># [71] 0.0625 32 0.001 256 0.25 2 0.025 4 0.0625 16 </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"># [81] 0.002 32 256 0.0625 0.125 0.001 128 0.001 0.01 64 </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> <span><span class="co"># [91] 2 64 1 256 0.01 8 32 8 128 0.002</span></span></code></pre></div>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span> <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> <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>
@@ -1214,10 +1209,10 @@ Longest: 24</p>
<span><span class="co"># coli). Run `mo_uncertainties()` to review this.</span></span> <span><span class="co"># coli). Run `mo_uncertainties()` to review this.</span></span>
<span><span class="va">disk_values</span></span> <span><span class="va">disk_values</span></span>
<span><span class="co"># Class &lt;disk&gt;</span></span> <span><span class="co"># Class &lt;disk&gt;</span></span>
<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"># [1] 25 31 18 30 19 28 18 31 17 30 31 30 20 20 25 18 30 28 18 22 25 28 17 21 22</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"># [26] 22 29 30 28 29 19 21 21 30 21 28 22 19 27 26 31 21 22 31 31 29 28 31 27 28</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"># [51] 28 30 24 27 21 23 26 23 22 19 25 21 30 25 26 29 31 18 18 21 26 23 19 18 24</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> <span><span class="co"># [76] 20 30 28 22 31 21 28 28 24 23 21 24 17 28 18 29 28 31 21 23 24 19 17 29 17</span></span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span> <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> <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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articles/EUCAST.html
+1 -6
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@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -111,11 +111,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="nav-item"> <li class="nav-item">
articles/MDR.html
+27 -32
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@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -111,11 +111,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="nav-item"> <li class="nav-item">
@@ -313,19 +308,19 @@ Unique: 2</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> <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> <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"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 S S R I R I</span></span> <span><span class="co"># 1 R S I R I I</span></span>
<span><span class="co"># 2 I R S S S S</span></span> <span><span class="co"># 2 S R R S R S</span></span>
<span><span class="co"># 3 I R S I S S</span></span> <span><span class="co"># 3 R R S R S S</span></span>
<span><span class="co"># 4 R I S I S R</span></span> <span><span class="co"># 4 I R S R I I</span></span>
<span><span class="co"># 5 I I S R S R</span></span> <span><span class="co"># 5 S R S I S I</span></span>
<span><span class="co"># 6 S I S S R R</span></span> <span><span class="co"># 6 R S R R S R</span></span>
<span><span class="co"># kanamycin</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"># 2 S</span></span>
<span><span class="co"># 3 I</span></span> <span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 R</span></span> <span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 I</span></span> <span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div> <span><span class="co"># 6 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p> <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"> <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></span></code></pre></div> <code class="sourceCode R"><span><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></span></code></pre></div>
@@ -356,40 +351,40 @@ Unique: 5</p>
<tr class="odd"> <tr class="odd">
<td align="left">1</td> <td align="left">1</td>
<td align="left">Mono-resistant</td> <td align="left">Mono-resistant</td>
<td align="right">3182</td> <td align="right">3214</td>
<td align="right">63.64%</td> <td align="right">64.28%</td>
<td align="right">3182</td> <td align="right">3214</td>
<td align="right">63.64%</td> <td align="right">64.28%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">2</td> <td align="left">2</td>
<td align="left">Negative</td> <td align="left">Negative</td>
<td align="right">993</td> <td align="right">977</td>
<td align="right">19.86%</td> <td align="right">19.54%</td>
<td align="right">4175</td> <td align="right">4191</td>
<td align="right">83.50%</td> <td align="right">83.82%</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">3</td> <td align="left">3</td>
<td align="left">Multi-drug-resistant</td> <td align="left">Multi-drug-resistant</td>
<td align="right">477</td> <td align="right">450</td>
<td align="right">9.54%</td> <td align="right">9.00%</td>
<td align="right">4652</td> <td align="right">4641</td>
<td align="right">93.04%</td> <td align="right">92.82%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">4</td> <td align="left">4</td>
<td align="left">Poly-resistant</td> <td align="left">Poly-resistant</td>
<td align="right">250</td> <td align="right">255</td>
<td align="right">5.00%</td> <td align="right">5.10%</td>
<td align="right">4902</td> <td align="right">4896</td>
<td align="right">98.04%</td> <td align="right">97.92%</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">5</td> <td align="left">5</td>
<td align="left">Extensively drug-resistant</td> <td align="left">Extensively drug-resistant</td>
<td align="right">98</td> <td align="right">104</td>
<td align="right">1.96%</td> <td align="right">2.08%</td>
<td align="right">5000</td> <td align="right">5000</td>
<td align="right">100.00%</td> <td align="right">100.00%</td>
</tr> </tr>
articles/PCA.html
+1 -6
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@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -111,11 +111,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="nav-item"> <li class="nav-item">
articles/SPSS.html
+2 -7
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@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -111,11 +111,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="nav-item"> <li class="nav-item">
@@ -167,7 +162,7 @@
<img src="../logo.svg" class="logo" alt=""><h1>How to import data from SPSS / SAS / Stata</h1> <img src="../logo.svg" class="logo" alt=""><h1>How to import data from SPSS / SAS / Stata</h1>
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4> <h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
<h4 data-toc-skip class="date">21 August 2022</h4> <h4 data-toc-skip class="date">25 August 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small> <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="d-none name"><code>SPSS.Rmd</code></div> <div class="d-none name"><code>SPSS.Rmd</code></div>
articles/WHONET.html
+1 -6
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@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -111,11 +111,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="nav-item"> <li class="nav-item">
articles/datasets.html
+9 -14
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@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -111,11 +111,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="nav-item"> <li class="nav-item">
@@ -166,7 +161,7 @@
<main id="main" class="col-md-9"><div class="page-header"> <main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1> <img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">21 August 2022</h4> <h4 data-toc-skip class="date">25 August 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small> <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div> <div class="d-none name"><code>datasets.Rmd</code></div>
@@ -184,7 +179,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</h2> </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>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>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 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>It was last updated on 25 August 2022 17:23:20 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> <p><strong>Direct download links:</strong></p>
<ul> <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> <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 +400,7 @@ 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>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><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>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 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>It was last updated on 25 August 2022 17:23:20 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> <p><strong>Direct download links:</strong></p>
<ul> <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> <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 +465,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</h2> </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>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>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 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>It was last updated on 25 August 2022 17:23:20 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> <p><strong>Direct download links:</strong></p>
<ul> <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> <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 +633,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</h2> </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>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>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 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>It was last updated on 25 August 2022 17:23:20 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> <p><strong>Direct download links:</strong></p>
<ul> <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> <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 +760,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</h2> </h2>
<p>A data set with 20,369 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p> <p>A data set with 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>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 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>It was last updated on 25 August 2022 17:23:20 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> <p><strong>Direct download links:</strong></p>
<ul> <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> <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 +914,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</h2> </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>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>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 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>It was last updated on 25 August 2022 17:23:20 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> <p><strong>Direct download links:</strong></p>
<ul> <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> <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 +1181,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</h2> </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>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>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 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>It was last updated on 25 August 2022 17:23:20 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> <p><strong>Direct download links:</strong></p>
<ul> <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> <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>
articles/index.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
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articles/resistance_predict.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -111,11 +111,6 @@
Get properties of an antibiotic Get properties of an antibiotic
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<a class="dropdown-item" href="../articles/benchmarks.html">
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Other: benchmarks
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articles/welcome_to_AMR.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -111,11 +111,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
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authors.html
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
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@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
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deps/bootstrap-5.1.3/bootstrap.min.css
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index.html
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -117,11 +117,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
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news/index.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
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@@ -131,37 +126,6 @@
<small>Source: <a href="https://github.com/msberends/AMR/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small> <small>Source: <a href="https://github.com/msberends/AMR/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
</div> </div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="1.8.1.9021" id="amr-1819021">AMR 1.8.1.9021<a class="anchor" aria-label="anchor" href="#amr-1819021"></a></h2>
<div class="section level4">
<h4 id="new-1-8-1-9021">New<a class="anchor" aria-label="anchor" href="#new-1-8-1-9021"></a></h4>
<ul><li>EUCAST 2022 and CLSI 2022 guidelines have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.</li>
<li>Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. The <code>AMR</code> package is now available in 16 languages.</li>
</ul></div>
<div class="section level4">
<h4 id="changed-1-8-1-9021">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9021"></a></h4>
<ul><li>Fix for <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</li>
<li>Removed <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> for MIC values, since MIC are not integer values and running <code><a href="https://rdrr.io/r/base/table.html" class="external-link">table()</a></code> on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on <code>factor</code>s work)</li>
<li>
<code><a href="https://rdrr.io/r/base/droplevels.html" class="external-link">droplevels()</a></code> on MIC will now return a common <code>factor</code> at default and will lose the <code>&lt;mic&gt;</code> class. Use <code>droplevels(..., as.mic = TRUE)</code> to keep the <code>&lt;mic&gt;</code> class.</li>
<li>Small fix for using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>
</li>
<li>Fixes for reading in text files using <code><a href="../reference/mo_source.html">set_mo_source()</a></code>, which now also allows the source file to contain valid taxonomic names instead of only valid microorganism ID of this package</li>
<li>Using any <code>random_*()</code> function (such as <code><a href="../reference/random.html">random_mic()</a></code>) is now possible by directly calling the package without loading it first: <code>AMR::random_mic(10)</code>
</li>
<li>Added <em>Toxoplasma gondii</em> (<code>P_TXPL_GOND</code>) to the <code>microorganisms</code> data set, together with its genus, family, and order</li>
<li>Changed value in column <code>prevalence</code> of the <code>microorganisms</code> data set from 3 to 2 for these genera: <em>Acholeplasma</em>, <em>Alistipes</em>, <em>Alloprevotella</em>, <em>Bergeyella</em>, <em>Borrelia</em>, <em>Brachyspira</em>, <em>Butyricimonas</em>, <em>Cetobacterium</em>, <em>Chlamydia</em>, <em>Chlamydophila</em>, <em>Deinococcus</em>, <em>Dysgonomonas</em>, <em>Elizabethkingia</em>, <em>Empedobacter</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Myroides</em>, <em>Odoribacter</em>, <em>Ornithobacterium</em>, <em>Parabacteroides</em>, <em>Pedobacter</em>, <em>Phocaeicola</em>, <em>Porphyromonas</em>, <em>Riemerella</em>, <em>Sphingobacterium</em>, <em>Streptobacillus</em>, <em>Tenacibaculum</em>, <em>Terrimonas</em>, <em>Victivallis</em>, <em>Wautersiella</em>, <em>Weeksella</em>
</li>
<li>Fix for using the form <code>df[carbapenems() == "R", ]</code> using the latest <code>vctrs</code> package</li>
<li>Fix for using <code>info = FALSE</code> in <code><a href="../reference/mdro.html">mdro()</a></code>
</li>
</ul></div>
<div class="section level4">
<h4 id="other-1-8-1-9021">Other<a class="anchor" aria-label="anchor" href="#other-1-8-1-9021"></a></h4>
<ul><li>New website to make use of the new Bootstrap 5 and pkgdown v2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions</li>
<li>Added Peter Dutey-Magni and Anton Mymrikov as contributors, to thank them for their valuable input</li>
</ul></div>
</div>
<div class="section level2"> <div class="section level2">
<h2 class="pkg-version" data-toc-text="1.8.1" id="amr-181"> <h2 class="pkg-version" data-toc-text="1.8.1" id="amr-181">
<code>AMR</code> 1.8.1<a class="anchor" aria-label="anchor" href="#amr-181"></a></h2><p class="text-muted">CRAN release: 2022-03-24</p> <code>AMR</code> 1.8.1<a class="anchor" aria-label="anchor" href="#amr-181"></a></h2><p class="text-muted">CRAN release: 2022-03-24</p>
pkgdown.yml
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datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2022-08-21T15:26Z last_built: 2022-08-25T17:26Z
urls: urls:
reference: https://msberends.github.io/AMR/reference reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles article: https://msberends.github.io/AMR/articles
reference/AMR-deprecated.html
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@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
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reference/AMR.html
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@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
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<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
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reference/WHOCC.html
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
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@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
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reference/WHONET.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
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@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
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<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
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reference/ab_from_text.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
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Get properties of an antibiotic Get properties of an antibiotic
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Other: benchmarks
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reference/ab_property.html
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@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
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<a class="dropdown-item" href="../articles/benchmarks.html">
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reference/age.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
@@ -195,16 +190,16 @@
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span> <span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span> <span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1955-03-05 67 67.46301 44</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 1964-06-04 58 58.22466 35</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1969-09-23 52 52.90959 30</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 1982-09-15 39 39.94247 17</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1952-10-15 69 69.84932 47</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 1966-11-08 55 55.79452 33</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1940-09-07 81 81.95342 59</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 1971-11-11 50 50.78630 28</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1956-10-12 65 65.85753 43</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 1960-06-12 62 62.20274 39</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1997-03-26 25 25.40548 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 1992-06-01 30 30.23288 7</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1946-04-17 76 76.34521 53</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 1953-06-03 69 69.22740 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1987-04-28 35 35.31507 12</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 1977-05-25 45 45.25205 22</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1957-09-27 64 64.89863 42</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 1945-02-11 77 77.53425 54</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1949-07-17 73 73.09589 50</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 1972-07-19 50 50.10137 27</span>
</code></pre></div> </code></pre></div>
</div> </div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
reference/age_groups.html
+1 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
reference/antibiotic_class_selectors.html
+1 -17
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
@@ -315,7 +310,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> NA NA </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> NA NA </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,990 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'</span></span></span> <span class="r-in"><span><span class="co"># select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mo"</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span></span> <span class="r-in"><span><span class="va">df</span><span class="op">[</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mo"</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span></span>
@@ -335,7 +329,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B_STPHY_EPDR NA NA </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B_STPHY_EPDR NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B_STPHY_EPDR NA NA </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B_STPHY_EPDR NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,990 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># select only antibiotic columns with DDDs for oral treatment</span></span></span> <span class="r-in"><span><span class="co"># select only antibiotic columns with DDDs for oral treatment</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span>, <span class="fu">administrable_per_os</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span> <span class="r-in"><span><span class="va">df</span><span class="op">[</span>, <span class="fu">administrable_per_os</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
@@ -356,7 +349,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> NA NA R R S </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> NA NA R R S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> NA NA S R S </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> NA NA S R S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,990 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter using any() or all()</span></span></span> <span class="r-in"><span><span class="co"># filter using any() or all()</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span></span> <span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span></span>
@@ -376,7 +368,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> A B_PROTS_MRBL NA S S S S S S R R </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> A B_PROTS_MRBL NA S S S S S S R R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 45 more rows, 3 more variables: MEM &lt;rsi&gt;, TEC &lt;rsi&gt;, VAN &lt;rsi&gt;, and</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 45 more rows, 3 more variables: MEM &lt;rsi&gt;, TEC &lt;rsi&gt;, VAN &lt;rsi&gt;, and</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># abbreviated variable name ¹​hospital_id</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># abbreviated variable name ¹​hospital_id</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">df</span>, <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">df</span>, <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 55 × 14</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 55 × 14</span></span>
@@ -394,7 +385,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> A B_PROTS_MRBL NA S S S S S S R R </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> A B_PROTS_MRBL NA S S S S S S R R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 45 more rows, 3 more variables: MEM &lt;rsi&gt;, TEC &lt;rsi&gt;, VAN &lt;rsi&gt;, and</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 45 more rows, 3 more variables: MEM &lt;rsi&gt;, TEC &lt;rsi&gt;, VAN &lt;rsi&gt;, and</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># abbreviated variable name ¹​hospital_id</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># abbreviated variable name ¹​hospital_id</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter on any or all results in the carbapenem columns (i.e., IPM, MEM):</span></span></span> <span class="r-in"><span><span class="co"># filter on any or all results in the carbapenem columns (i.e., IPM, MEM):</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span> <span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span>
@@ -415,7 +405,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> C B_ESCHR_COLI R R NA R S S NA NA S </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> C B_ESCHR_COLI R R NA R S S NA NA S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 952 more rows, 3 more variables: MEM &lt;rsi&gt;, TEC &lt;rsi&gt;, VAN &lt;rsi&gt;, and</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 952 more rows, 3 more variables: MEM &lt;rsi&gt;, TEC &lt;rsi&gt;, VAN &lt;rsi&gt;, and</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># abbreviated variable name ¹​hospital_id</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># abbreviated variable name ¹​hospital_id</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span> <span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Filtering all of columns 'IPM' and 'MEM' to contain value "R", "S" or "I"</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Filtering all of columns 'IPM' and 'MEM' to contain value "R", "S" or "I"</span>
@@ -434,7 +423,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B B_ESCHR_COLI NA S S S S S S NA S </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B B_ESCHR_COLI NA S S S S S S NA S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 746 more rows, 3 more variables: MEM &lt;rsi&gt;, TEC &lt;rsi&gt;, VAN &lt;rsi&gt;, and</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 746 more rows, 3 more variables: MEM &lt;rsi&gt;, TEC &lt;rsi&gt;, VAN &lt;rsi&gt;, and</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># abbreviated variable name ¹​hospital_id</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># abbreviated variable name ¹​hospital_id</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter with multiple antibiotic selectors using c()</span></span></span> <span class="r-in"><span><span class="co"># filter with multiple antibiotic selectors using c()</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span></span> <span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span></span>
@@ -456,7 +444,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> D B_STPHY_CONS R R R R R R R R R </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> D B_STPHY_CONS R R R R R R R R R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 16 more rows, 3 more variables: MEM &lt;rsi&gt;, TEC &lt;rsi&gt;, VAN &lt;rsi&gt;, and</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 16 more rows, 3 more variables: MEM &lt;rsi&gt;, TEC &lt;rsi&gt;, VAN &lt;rsi&gt;, and</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># abbreviated variable name ¹​hospital_id</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># abbreviated variable name ¹​hospital_id</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter + select in one go: get penicillins in carbapenems-resistant strains</span></span></span> <span class="r-in"><span><span class="co"># filter + select in one go: get penicillins in carbapenems-resistant strains</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="fu">penicillins</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span> <span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="fu">penicillins</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
@@ -477,7 +464,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> NA S S </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> NA S S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> NA S S </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> NA S S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 45 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 45 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># You can combine selectors with '&amp;' to be more specific. For example,</span></span></span> <span class="r-in"><span><span class="co"># You can combine selectors with '&amp;' to be more specific. For example,</span></span></span>
<span class="r-in"><span><span class="co"># penicillins() would select benzylpenicillin ('peni G') and</span></span></span> <span class="r-in"><span><span class="co"># penicillins() would select benzylpenicillin ('peni G') and</span></span></span>
@@ -504,7 +490,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> NA NA </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> NA NA </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,990 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># ab_selector() applies a filter in the `antibiotics` data set and is thus very</span></span></span> <span class="r-in"><span><span class="co"># ab_selector() applies a filter in the `antibiotics` data set and is thus very</span></span></span>
<span class="r-in"><span><span class="co"># flexible. For instance, to select antibiotic columns with an oral DDD of at</span></span></span> <span class="r-in"><span><span class="co"># flexible. For instance, to select antibiotic columns with an oral DDD of at</span></span></span>
@@ -526,7 +511,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> NA NA S </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> NA NA S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> NA NA S </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> NA NA S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,990 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># dplyr -------------------------------------------------------------------</span></span></span> <span class="r-in"><span><span class="co"># dplyr -------------------------------------------------------------------</span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span> <span class="r-in"><span><span class="co"># \donttest{</span></span></span>
reference/antibiotics.html
+1 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
reference/as.ab.html
+1 -7
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
@@ -290,7 +285,6 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div> </code></pre></div>
</div> </div>
reference/as.disk.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
reference/as.mic.html
+1 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
reference/as.mo.html
+1 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
reference/as.rsi.html
+1 -8
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
@@ -340,7 +335,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><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">example_isolates</span><span class="op">)</span> <span class="co"># see all R/SI results at a glance</span></span></span> <span class="r-in"><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">example_isolates</span><span class="op">)</span> <span class="co"># see all R/SI results at a glance</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date hospital_id ward_icu ward_clinical </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date hospital_id ward_icu ward_clinical </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Min. :2002-01-02 A:321 Mode :logical Mode :logical </span> <span class="r-out co"><span class="r-pr">#&gt;</span> Min. :2002-01-02 A:321 Mode :logical Mode :logical </span>
@@ -736,7 +730,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div> </code></pre></div>
</div> </div>
reference/atc_online.html
+1 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
reference/availability.html
+1 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
reference/bug_drug_combinations.html
+1 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
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reference/catalogue_of_life.html
+2 -7
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
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@@ -168,7 +163,7 @@ Function <code><a href="as.mo.html">as.mo()</a></code> to use the data for intel
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Get version info of included data set</span></span></span> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Get version info of included data set</span></span></span>
<span class="r-in"><span><span class="fu"><a href="catalogue_of_life_version.html">catalogue_of_life_version</a></span><span class="op">(</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="catalogue_of_life_version.html">catalogue_of_life_version</a></span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Included in this AMR package (v1.8.1.9021) are:</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Included in this AMR package (v1.8.1.9026) are:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Catalogue of Life: 2019 Annual Checklist</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Catalogue of Life: 2019 Annual Checklist</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Available at: http://www.catalogueoflife.org</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Available at: http://www.catalogueoflife.org</span>
reference/catalogue_of_life_version.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
reference/count.html
+1 -6
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@@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -84,11 +84,6 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
reference/custom_eucast_rules.html
+1 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
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reference/dosage.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
reference/eucast_rules.html
+1 -6
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@@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -84,11 +84,6 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
reference/example_isolates.html
+1 -7
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
@@ -180,7 +175,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;, TCY &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;, TCY &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;, IPM &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;, IPM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, RIF &lt;rsi&gt;, and …</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, RIF &lt;rsi&gt;, and …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `colnames()` to see all variable names</span></span>
</code></pre></div> </code></pre></div>
</div> </div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
reference/example_isolates_unclean.html
+1 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
reference/first_isolate.html
+1 -8
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@@ -12,7 +12,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -84,11 +84,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
@@ -349,7 +344,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span> <span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># get all first Gram-negatives</span></span></span> <span class="r-in"><span><span class="co"># get all first Gram-negatives</span></span></span>
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu"><a href="mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span> <span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu"><a href="mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span>
@@ -374,7 +368,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span> <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># filter on first isolates using dplyr:</span></span></span> <span class="r-in"><span> <span class="co"># filter on first isolates using dplyr:</span></span></span>
reference/g.test.html
+1 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
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@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
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reference/get_episode.html
+29 -36
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
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@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
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@@ -182,41 +177,40 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">200</span><span class="op">)</span>, <span class="op">]</span></span></span> <span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">200</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span> <span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 63 42 61 46 22 21 21 10 46 12 31 47 53 64 9 27 12 7 30 25 15 61 52 20 18</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 6 17 60 34 7 61 19 35 61 38 26 59 25 61 25 20 50 2 20 5 53 35 67 48 5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 46 53 39 38 54 61 58 12 58 39 21 27 35 66 46 59 57 13 43 30 29 60 51 25 35</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [26] 11 17 20 59 66 54 26 60 44 48 20 12 23 37 4 5 36 21 28 59 20 44 11 60 49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 22 4 56 20 5 18 18 22 9 21 50 9 58 38 59 44 46 11 41 55 55 5 14 56 26</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [51] 6 12 16 16 62 40 4 17 64 52 33 20 3 1 55 46 12 12 30 64 22 8 2 30 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 53 63 33 20 5 31 32 10 1 51 46 2 28 24 40 10 13 26 55 12 49 54 16 43 26</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [76] 28 61 31 52 63 35 15 7 45 51 65 41 36 33 14 53 18 40 12 42 55 2 15 14 38</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 51 37 60 27 49 23 42 63 5 60 7 23 4 37 47 22 52 45 65 56 11 38 17 36 12</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [101] 23 9 9 23 22 58 3 26 20 6 1 68 43 39 24 46 12 40 56 29 39 1 8 59 65</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 9 47 25 14 1 56 38 66 42 53 19 51 10 34 16 11 15 62 31 40 22 63 49 32 62</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [126] 57 14 64 65 37 41 42 37 20 24 32 59 14 61 52 10 13 59 18 24 40 52 62 30 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 45 6 48 5 58 57 7 56 46 13 58 65 15 21 7 42 8 5 6 6 28 29 4 26 19</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [151] 10 35 65 61 10 16 20 4 53 16 24 47 2 67 27 58 64 1 11 62 12 40 47 1 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 3 56 3 60 61 63 63 56 65 16 21 40 57 23 16 47 58 61 21 32 9 60 3 17 62</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [176] 22 54 21 29 11 23 59 61 40 39 42 14 14 17 66 17 2 52 23 29 2 68 24 46 14</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span> <span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE TRUE FALSE TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE TRUE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [85] TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [97] TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] TRUE TRUE FALSE TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [145] TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [193] TRUE TRUE TRUE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span> <span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span> <span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 49</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 49</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date hospita…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date hospita…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;fct&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;fct&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-06-06 D FALSE TRUE FALSE 20 F 24D393 B_ESCHR_COLI</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-06-04 B TRUE FALSE FALSE 78 M 082413 B_STRPT_PNMN</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-06-18 B TRUE FALSE FALSE 30 M 012595 B_CRYNB </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-06-06 D FALSE TRUE FALSE 20 F 24D393 B_ESCHR_COLI</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-07-23 B TRUE FALSE FALSE 51 M F35553 B_STPHY_AURS</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more variables: PEN &lt;rsi&gt;, OXA &lt;rsi&gt;, FLC &lt;rsi&gt;, AMX &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more variables: PEN &lt;rsi&gt;, OXA &lt;rsi&gt;, FLC &lt;rsi&gt;, AMX &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;, CZO &lt;rsi&gt;, FEP &lt;rsi&gt;, CXM &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;, CZO &lt;rsi&gt;, FEP &lt;rsi&gt;, CXM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOX &lt;rsi&gt;, CTX &lt;rsi&gt;, CAZ &lt;rsi&gt;, CRO &lt;rsi&gt;, GEN &lt;rsi&gt;, TOB &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOX &lt;rsi&gt;, CTX &lt;rsi&gt;, CAZ &lt;rsi&gt;, CRO &lt;rsi&gt;, GEN &lt;rsi&gt;, TOB &lt;rsi&gt;,</span></span>
@@ -224,7 +218,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;, TCY &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;, TCY &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;, IPM &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;, IPM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, RIF &lt;rsi&gt;, and …</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, RIF &lt;rsi&gt;, and …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `colnames()` to see all variable names</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># the functions also work for less than a day, e.g. to include one per hour:</span></span></span> <span class="r-in"><span><span class="co"># the functions also work for less than a day, e.g. to include one per hour:</span></span></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span>,</span></span> <span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
reference/ggplot_pca.html
+1 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
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reference/ggplot_rsi.html
+1 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
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reference/guess_ab_col.html
+1 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
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reference/index.html
+1 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
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@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
reference/intrinsic_resistant.html
+1 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
reference/italicise_taxonomy.html
+1 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
reference/join.html
+1 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
reference/key_antimicrobials.html
+1 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
reference/kurtosis.html
+3 -8
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
@@ -172,9 +167,9 @@
<div class="section level2"> <div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.031812</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.056791</span>
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.03994734</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.006309202</span>
</code></pre></div> </code></pre></div>
</div> </div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
reference/like.html
+1 -9
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
@@ -230,7 +225,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span> <span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># faster way, since mo_name() is context-aware:</span></span></span> <span class="r-in"><span><span class="co"># faster way, since mo_name() is context-aware:</span></span></span>
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%like%</span> <span class="st">"^ent"</span><span class="op">)</span>, <span class="op">]</span></span></span> <span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%like%</span> <span class="st">"^ent"</span><span class="op">)</span>, <span class="op">]</span></span></span>
@@ -255,7 +249,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span> <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><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="r-in"><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>
@@ -282,7 +275,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div> </code></pre></div>
</div> </div>
reference/mdro.html
+1 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
reference/microorganisms.codes.html
+1 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
reference/microorganisms.html
+1 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
reference/microorganisms.old.html
+1 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
reference/mo_matching_score.html
+1 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</div> </div>
</li> </li>
<li class="active nav-item"> <li class="active nav-item">
reference/mo_property.html
+1 -7
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@@ -10,7 +10,7 @@
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@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
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@@ -470,7 +465,6 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;rsi&gt;, LNZ &lt;rsi&gt;, CIP &lt;rsi&gt;, MFX &lt;rsi&gt;, VAN &lt;rsi&gt;, TEC &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;rsi&gt;, TGC &lt;rsi&gt;, DOX &lt;rsi&gt;, ERY &lt;rsi&gt;, CLI &lt;rsi&gt;, AZM &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;rsi&gt;, MEM &lt;rsi&gt;, MTR &lt;rsi&gt;, CHL &lt;rsi&gt;, COL &lt;rsi&gt;, MUP &lt;rsi&gt;, …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># get a list with the complete taxonomy (from kingdom to subspecies)</span></span></span> <span class="r-in"><span><span class="co"># get a list with the complete taxonomy (from kingdom to subspecies)</span></span></span>
reference/mo_source.html
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@@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@@ -84,11 +84,6 @@ resistance() should be used to calculate resistance, susceptibility() should be
Get properties of an antibiotic Get properties of an antibiotic
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reference/random.html
+18 -22
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@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
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@@ -183,42 +178,43 @@
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 64 8 0.25 8 2 0.005 16 256 32 16 0.125</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=0.001 1 0.25 128 0.01 0.025 0.025 16 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.125 64 32 0.25 256 4 1 0.125 32 0.5 0.025 128 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [10] 128 64 16 &lt;=0.001 0.01 0.0625 0.0625 0.5 0.0625 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 0.25 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.025 8 128 32 0.025 0.0625 0.01 </span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 27 41 44 30 6 49 34 45 48 31 48 31 31 41 49 46 14 24 31 12 45 24 44 36 38</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 30 11 11 41 49 41 47 7 44 29 15 18 25 6 30 49 24 38 15 23 15 17 43 45 6</span>
<span class="r-in"><span><span class="fu">random_rsi</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">random_rsi</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;rsi&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;rsi&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I I R S S R S S S I I R I R I I S R R R S I S I S</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] S I I S R R I I S R S I S R R R R I S I R I I S I</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span> <span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span> <span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span> <span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.125 0.25 0.125 0.002 4 2 8 32 0.0625 0.002 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01 0.025 8 2 1 0.002 0.125 2 64 0.25 16 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.125 0.005 1 0.002 0.001 16 0.025 0.25 0.5 128 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.005 0.125 0.01 256 0.5 1 4 0.25 0.125 0.001 256 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 2 0.005 128 4 0.002 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [25] 128 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span> <span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=1 4 8 8 8 8 8 &gt;=16 2 2 4 2 &lt;=1 8 2 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5 &gt;=64 2 4 8 0.5 &gt;=64 2 1 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] &lt;=1 &gt;=16 2 2 8 4 4 8 &lt;=1 &lt;=1 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [11] &gt;=64 16 8 &lt;=0.25 &lt;=0.25 4 &lt;=0.25 16 16 &lt;=0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 16 32 32 &lt;=0.25 &lt;=0.25</span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span> <span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.125 0.25 2 0.5 0.0625 8 0.25 0.25 0.125 1 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.25 1 &gt;=8 &lt;=0.125 0.25 4 0.5 &gt;=8 &gt;=8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 2 0.125 0.0625 4 0.5 0.125 2 8 4 0.0625</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.25 0.25 0.25 1 4 &lt;=0.125 1 &gt;=8 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.5 0.25 0.5 8 0.25 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [19] 4 0.5 2 &gt;=8 &gt;=8 &gt;=8 0.25 </span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span> <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 42 30 13 25 19 37 49 26 38 8 46 40 23 25 44 11 40 13 22 34 15 36 47 49 49</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 19 46 14 40 42 13 26 42 12 21 41 26 21 12 24 27 40 21 45 37 24 13 41 17 41</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span> <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 15 14 17 16 15 16 15 11 16 16 15 15 13 13 15 11 15 15 15 17 13 11 15 17 11</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 16 17 11 13 14 13 17 17 16 17 12 17 11 16 11 13 15 13 11 16 12 14 16 13</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span> <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 20 25 18 16 15 19 16 21 23 19 25 18 16 16 16 18 16 27 17 27 23 22 17 19 19</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 22 17 19 18 25 20 18 23 18 15 23 20 24 23 21 20 18 21 18 21 23 15 18 25 22</span>
<span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div> </code></pre></div>
</div> </div>
reference/resistance_predict.html
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@@ -10,7 +10,7 @@
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
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@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
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reference/skewness.html
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@@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
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@@ -84,11 +84,6 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
<a class="dropdown-item" href="../articles/benchmarks.html">
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Other: benchmarks
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@@ -171,7 +166,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<div class="section level2"> <div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.06804385</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.04631559</span>
</code></pre></div> </code></pre></div>
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reference/translate.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <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="">1.8.1.9021</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
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@@ -82,11 +82,6 @@
Get properties of an antibiotic Get properties of an antibiotic
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search.json
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@@ -1 +1 @@
[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations RSI values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables.","code":"library(dplyr) library(ggplot2) library(AMR) library(cleaner) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\", \"cleaner\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"creation-of-data","dir":"Articles","previous_headings":"","what":"Creation of data","title":"How to conduct AMR data analysis","text":"create fake example data use analysis. AMR data analysis, need least: patient ID, name code microorganism, date antimicrobial results (antibiogram). also include specimen type (e.g. filter blood urine), ward type (e.g. filter ICUs). additional columns (like hospital name, patients gender even [well-defined] clinical properties) can comparative analysis, tutorial demonstrate .","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"patients","dir":"Articles","previous_headings":"Creation of data","what":"Patients","title":"How to conduct AMR data analysis","text":"start patients, need unique list patients. LETTERS object available R - ’s vector 26 characters: Z. patients object just created now vector length 260, values (patient IDs) varying A1 Z10. Now also set gender patients, putting ID gender table: first 135 patient IDs now male, 125 female.","code":"patients <- unlist(lapply(LETTERS, paste0, 1:10)) patients_table <- data.frame(patient_id = patients, gender = c(rep(\"M\", 135), rep(\"F\", 125)))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"dates","dir":"Articles","previous_headings":"Creation of data","what":"Dates","title":"How to conduct AMR data analysis","text":"Let’s pretend data consists blood cultures isolates 1 January 2010 1 January 2018. dates object now contains days date range.","code":"dates <- seq(as.Date(\"2010-01-01\"), as.Date(\"2018-01-01\"), by = \"day\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"microorganisms","dir":"Articles","previous_headings":"Creation of data > Dates","what":"Microorganisms","title":"How to conduct AMR data analysis","text":"tutorial, uses four different microorganisms: Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae:","code":"bacteria <- c(\"Escherichia coli\", \"Staphylococcus aureus\", \"Streptococcus pneumoniae\", \"Klebsiella pneumoniae\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"put-everyLine truncated [{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations RSI values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables.","code":"library(dplyr) library(ggplot2) library(AMR) library(cleaner) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\", \"cleaner\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"creation-of-data","dir":"Articles","previous_headings":"","what":"Creation of data","title":"How to conduct AMR data analysis","text":"create fake example data use analysis. AMR data analysis, need least: patient ID, name code microorganism, date antimicrobial results (antibiogram). also include specimen type (e.g. filter blood urine), ward type (e.g. filter ICUs). additional columns (like hospital name, patients gender even [well-defined] clinical properties) can comparative analysis, tutorial demonstrate .","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"patients","dir":"Articles","previous_headings":"Creation of data","what":"Patients","title":"How to conduct AMR data analysis","text":"start patients, need unique list patients. LETTERS object available R - ’s vector 26 characters: Z. patients object just created now vector length 260, values (patient IDs) varying A1 Z10. Now also set gender patients, putting ID gender table: first 135 patient IDs now male, 125 female.","code":"patients <- unlist(lapply(LETTERS, paste0, 1:10)) patients_table <- data.frame(patient_id = patients, gender = c(rep(\"M\", 135), rep(\"F\", 125)))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"dates","dir":"Articles","previous_headings":"Creation of data","what":"Dates","title":"How to conduct AMR data analysis","text":"Let’s pretend data consists blood cultures isolates 1 January 2010 1 January 2018. dates object now contains days date range.","code":"dates <- seq(as.Date(\"2010-01-01\"), as.Date(\"2018-01-01\"), by = \"day\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"microorganisms","dir":"Articles","previous_headings":"Creation of data > Dates","what":"Microorganisms","title":"How to conduct AMR data analysis","text":"tutorial, uses four different microorganisms: Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae:","code":"bacteria <- c(\"Escherichia coli\", \"Staphylococcus aureus\", \"Streptococcus pneumoniae\", \"Klebsiella pneumoniae\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"put-everyLine truncated