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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
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@@ -162,7 +162,7 @@
<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="date">21 October 2022</h4>
<h4 data-toc-skip class="date">22 October 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>
<div class="d-none name"><code>AMR.Rmd</code></div>
@@ -170,7 +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 October 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 22 October 2022.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@@ -201,21 +201,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-10-21</td>
<td align="center">2022-10-22</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2022-10-21</td>
<td align="center">2022-10-22</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2022-10-21</td>
<td align="center">2022-10-22</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@@ -325,71 +325,71 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-06-09</td>
<td align="center">Z9</td>
<td align="center">Hospital A</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">F</td>
</tr>
<tr class="even">
<td align="center">2010-11-06</td>
<td align="center">Z5</td>
<td align="center">Hospital D</td>
<td align="center">2013-03-10</td>
<td align="center">E9</td>
<td align="center">Hospital B</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">F</td>
</tr>
<tr class="odd">
<td align="center">2013-05-18</td>
<td align="center">R5</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">F</td>
</tr>
<tr class="even">
<td align="center">2015-05-02</td>
<td align="center">R2</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">F</td>
</tr>
<tr class="odd">
<td align="center">2015-07-14</td>
<td align="center">P2</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-09-28</td>
<td align="center">G7</td>
<td align="center">Hospital D</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">2013-04-01</td>
<td align="center">U4</td>
<td align="center">Hospital D</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">2013-08-12</td>
<td align="center">S7</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-05-02</td>
<td align="center">K4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-07-08</td>
<td align="center">E6</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-10-16</td>
<td align="center">Q1</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@@ -422,16 +422,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,457</td>
<td align="right">52.29%</td>
<td align="right">10,457</td>
<td align="right">52.29%</td>
<td align="right">10,416</td>
<td align="right">52.08%</td>
<td align="right">10,416</td>
<td align="right">52.08%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,543</td>
<td align="right">47.72%</td>
<td align="right">9,584</td>
<td align="right">47.92%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@@ -488,9 +488,9 @@ Longest: 1</p>
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,731 'phenotype-based' first isolates (53.7% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,729 'phenotype-based' first isolates (53.6% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.7% 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 53.6% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<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>
@@ -499,10 +499,10 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,731 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,729 isolates for analysis. Now our data looks like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
<table style="width:100%;" class="table">
<table class="table">
<colgroup>
<col width="2%">
<col width="9%">
@@ -516,7 +516,7 @@ Longest: 1</p>
<col width="6%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="7%">
<col width="5%">
</colgroup>
<thead><tr class="header">
@@ -537,41 +537,25 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2012-06-09</td>
<td align="center">Z9</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="left">2</td>
<td align="center">2013-04-01</td>
<td align="center">U4</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">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">2015-05-02</td>
<td align="center">R2</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="center">2015-07-14</td>
<td align="center">P2</td>
<td align="left">3</td>
<td align="center">2013-08-12</td>
<td align="center">S7</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
@@ -584,14 +568,30 @@ Longest: 1</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2014-05-02</td>
<td align="center">K4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2012-06-15</td>
<td align="center">G7</td>
<td align="left">5</td>
<td align="center">2016-07-08</td>
<td align="center">E6</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
@@ -601,35 +601,35 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">10</td>
<td align="center">2016-01-05</td>
<td align="center">N3</td>
<td align="left">7</td>
<td align="center">2017-02-23</td>
<td align="center">B4</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">11</td>
<td align="center">2017-09-24</td>
<td align="center">T7</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="left">9</td>
<td align="center">2016-11-10</td>
<td align="center">V1</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@@ -653,8 +653,8 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,731<br>
Available: 10,731 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,729<br>
Available: 10,729 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@@ -671,33 +671,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,682</td>
<td align="right">43.63%</td>
<td align="right">4,682</td>
<td align="right">43.63%</td>
<td align="right">4,633</td>
<td align="right">43.18%</td>
<td align="right">4,633</td>
<td align="right">43.18%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,733</td>
<td align="right">25.47%</td>
<td align="right">7,415</td>
<td align="right">69.10%</td>
<td align="right">2,796</td>
<td align="right">26.06%</td>
<td align="right">7,429</td>
<td align="right">69.24%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,132</td>
<td align="right">19.87%</td>
<td align="right">9,547</td>
<td align="right">88.97%</td>
<td align="right">2,137</td>
<td align="right">19.92%</td>
<td align="right">9,566</td>
<td align="right">89.16%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,184</td>
<td align="right">11.03%</td>
<td align="right">10,731</td>
<td align="right">1,163</td>
<td align="right">10.84%</td>
<td align="right">10,729</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@@ -716,14 +716,14 @@ Longest: 24</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="11%">
<col width="10%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@@ -744,43 +744,43 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-06-09</td>
<td align="center">Z9</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">2017-02-23</td>
<td align="center">B4</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-05-02</td>
<td align="center">R2</td>
<td align="center">2016-01-27</td>
<td align="center">M1</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2010-11-28</td>
<td align="center">Q9</td>
<td align="center">Hospital C</td>
<td align="center">2012-07-10</td>
<td align="center">U10</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@@ -789,12 +789,12 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-11-10</td>
<td align="center">V1</td>
<td align="center">Hospital B</td>
<td align="center">2017-03-06</td>
<td align="center">X10</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">R</td>
<td align="center">F</td>
@@ -804,30 +804,30 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-06-17</td>
<td align="center">Y3</td>
<td align="center">Hospital A</td>
<td align="center">2017-08-29</td>
<td align="center">F1</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-06-19</td>
<td align="center">H1</td>
<td align="center">Hospital D</td>
<td align="center">2014-05-24</td>
<td align="center">N8</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
@@ -854,50 +854,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2224</td>
<td align="center">132</td>
<td align="center">2326</td>
<td align="center">4682</td>
<td align="center">2202</td>
<td align="center">119</td>
<td align="center">2312</td>
<td align="center">4633</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3427</td>
<td align="center">152</td>
<td align="center">1103</td>
<td align="center">4682</td>
<td align="center">3411</td>
<td align="center">175</td>
<td align="center">1047</td>
<td align="center">4633</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3453</td>
<td align="center">3383</td>
<td align="center">0</td>
<td align="center">1229</td>
<td align="center">4682</td>
<td align="center">1250</td>
<td align="center">4633</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4086</td>
<td align="center">4044</td>
<td align="center">0</td>
<td align="center">596</td>
<td align="center">4682</td>
<td align="center">589</td>
<td align="center">4633</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1184</td>
<td align="center">1184</td>
<td align="center">1163</td>
<td align="center">1163</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">950</td>
<td align="center">43</td>
<td align="center">191</td>
<td align="center">1184</td>
<td align="center">917</td>
<td align="center">41</td>
<td align="center">205</td>
<td align="center">1163</td>
</tr>
</tbody>
</table>
@@ -920,34 +920,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4086</td>
<td align="center">4044</td>
<td align="center">0</td>
<td align="center">596</td>
<td align="center">4682</td>
<td align="center">589</td>
<td align="center">4633</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1083</td>
<td align="center">1035</td>
<td align="center">0</td>
<td align="center">101</td>
<td align="center">1184</td>
<td align="center">128</td>
<td align="center">1163</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2453</td>
<td align="center">2484</td>
<td align="center">0</td>
<td align="center">280</td>
<td align="center">2733</td>
<td align="center">312</td>
<td align="center">2796</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">2132</td>
<td align="center">2132</td>
<td align="center">2137</td>
<td align="center">2137</td>
</tr>
</tbody>
</table>
@@ -961,7 +961,7 @@ Longest: 24</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5461746</span></span></code></pre></div>
<span><span class="co"># [1] 0.5444123</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@@ -975,19 +975,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5456783</td>
<td align="center">0.5464199</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5524140</td>
<td align="center">0.5451604</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5469820</td>
<td align="center">0.5317705</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5353107</td>
<td align="center">0.5496909</td>
</tr>
</tbody>
</table>
@@ -1008,23 +1008,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5456783</td>
<td align="center">3251</td>
<td align="center">0.5464199</td>
<td align="center">3296</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5524140</td>
<td align="center">3749</td>
<td align="center">0.5451604</td>
<td align="center">3709</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5469820</td>
<td align="center">1607</td>
<td align="center">0.5317705</td>
<td align="center">1621</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5353107</td>
<td align="center">2124</td>
<td align="center">0.5496909</td>
<td align="center">2103</td>
</tr>
</tbody>
</table>
@@ -1047,27 +1047,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7644169</td>
<td align="center">0.8727040</td>
<td align="center">0.9769329</td>
<td align="center">0.7740125</td>
<td align="center">0.8728686</td>
<td align="center">0.9769048</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8386824</td>
<td align="center">0.9146959</td>
<td align="center">0.9831081</td>
<td align="center">0.8237317</td>
<td align="center">0.8899398</td>
<td align="center">0.9724850</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7969265</td>
<td align="center">0.8975485</td>
<td align="center">0.9849982</td>
<td align="center">0.7914878</td>
<td align="center">0.8884120</td>
<td align="center">0.9846209</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5323640</td>
<td align="center">0.5297146</td>
<td align="center">0.0000000</td>
<td align="center">0.5323640</td>
<td align="center">0.5297146</td>
</tr>
</tbody>
</table>
@@ -1093,22 +1093,22 @@ Longest: 24</p>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.6%</td>
<td align="right">25.6%</td>
<td align="right">27.2%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">55.2%</td>
<td align="right">27.5%</td>
<td align="right">54.5%</td>
<td align="right">26.0%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">54.7%</td>
<td align="right">26.1%</td>
<td align="right">53.2%</td>
<td align="right">25.6%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">53.5%</td>
<td align="right">26.5%</td>
<td align="right">55.0%</td>
<td align="right">26.9%</td>
</tr>
</tbody>
</table>
@@ -1206,16 +1206,18 @@ Longest: 24</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 0.0625 0.0625 0.25 0.025 16 256 8 4 16 0.125 </span></span>
<span><span class="co"># [11] 16 0.0625 128 64 0.025 2 2 0.0625 0.25 0.025 </span></span>
<span><span class="co"># [21] 256 0.125 0.125 4 8 16 4 1 0.002 4 </span></span>
<span><span class="co"># [31] 1 8 1 0.001 16 0.002 64 16 32 0.002 </span></span>
<span><span class="co"># [41] 0.002 0.25 0.25 1 0.5 0.005 0.125 0.0625 4 8 </span></span>
<span><span class="co"># [51] 0.002 0.025 16 2 4 0.025 0.0625 256 64 4 </span></span>
<span><span class="co"># [61] 0.25 0.5 64 128 16 2 0.025 0.002 64 0.0625</span></span>
<span><span class="co"># [71] 64 0.5 0.001 0.025 2 0.5 8 64 0.25 256 </span></span>
<span><span class="co"># [81] 0.025 0.001 0.25 0.125 64 256 256 0.5 0.002 8 </span></span>
<span><span class="co"># [91] 64 64 0.5 4 0.5 0.125 2 32 0.01 0.25</span></span></code></pre></div>
<span><span class="co"># [1] &lt;=0.001 2 0.25 0.002 0.0625 1 0.002 32 1 </span></span>
<span><span class="co"># [10] 0.5 1 0.025 0.5 &lt;=0.001 0.005 4 &gt;=256 4 </span></span>
<span><span class="co"># [19] 8 1 16 0.002 &lt;=0.001 0.002 4 0.025 8 </span></span>
<span><span class="co"># [28] 16 16 1 0.25 &lt;=0.001 16 0.005 0.005 &lt;=0.001</span></span>
<span><span class="co"># [37] &lt;=0.001 16 &gt;=256 16 128 0.0625 1 0.25 0.005 </span></span>
<span><span class="co"># [46] 0.01 0.002 0.5 128 64 0.01 8 128 1 </span></span>
<span><span class="co"># [55] &gt;=256 &gt;=256 1 0.125 &lt;=0.001 0.25 64 2 0.002 </span></span>
<span><span class="co"># [64] &gt;=256 16 1 &gt;=256 0.5 8 &gt;=256 &gt;=256 0.005 </span></span>
<span><span class="co"># [73] 0.002 2 0.25 0.25 &lt;=0.001 0.0625 0.01 0.125 1 </span></span>
<span><span class="co"># [82] 0.005 0.125 0.25 2 0.025 0.025 32 1 0.25 </span></span>
<span><span class="co"># [91] 0.005 0.01 1 0.5 1 0.0625 0.5 4 1 </span></span>
<span><span class="co"># [100] 64</span></span></code></pre></div>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@@ -1242,10 +1244,10 @@ Longest: 24</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 30 27 25 26 26 30 31 29 25 26 25 22 17 25 18 20 18 30 31 28 22 29 26 17 21</span></span>
<span><span class="co"># [26] 27 30 26 29 28 22 21 26 20 24 26 30 27 25 26 30 17 20 18 20 21 24 20 18 21</span></span>
<span><span class="co"># [51] 27 23 23 26 24 20 29 21 22 26 31 28 26 25 18 26 21 19 21 18 23 30 19 27 25</span></span>
<span><span class="co"># [76] 31 31 21 30 24 28 28 26 29 25 23 19 20 29 20 18 17 28 21 28 27 17 21 18 25</span></span></code></pre></div>
<span><span class="co"># [1] 27 30 17 21 31 26 25 21 24 31 20 28 23 26 30 22 30 17 23 29 24 30 23 26 19</span></span>
<span><span class="co"># [26] 29 24 23 19 19 30 27 23 31 27 26 24 27 26 20 17 22 29 17 23 20 19 26 28 30</span></span>
<span><span class="co"># [51] 21 30 23 30 30 17 26 25 30 20 24 27 24 20 28 23 22 22 29 18 20 27 22 22 17</span></span>
<span><span class="co"># [76] 30 19 27 27 23 19 23 31 19 26 30 25 22 23 27 28 19 29 19 19 26 26 17 23 17</span></span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>
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+1 -1
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@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
articles/MDR.html
+30 -30
View File
@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
@@ -314,19 +314,19 @@ Unique: 2</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 S R I R S S</span></span>
<span><span class="co"># 2 I R S I S S</span></span>
<span><span class="co"># 3 I I I I I I</span></span>
<span><span class="co"># 4 S R I R I R</span></span>
<span><span class="co"># 5 S I I I S S</span></span>
<span><span class="co"># 6 I I R R S I</span></span>
<span><span class="co"># 1 S R I S S S</span></span>
<span><span class="co"># 2 I S R R R S</span></span>
<span><span class="co"># 3 S R S S I S</span></span>
<span><span class="co"># 4 I R S S R S</span></span>
<span><span class="co"># 5 I S I S S R</span></span>
<span><span class="co"># 6 R I I S S I</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 R</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 I</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<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>
@@ -357,40 +357,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3215</td>
<td align="right">64.30%</td>
<td align="right">3215</td>
<td align="right">64.30%</td>
<td align="right">3216</td>
<td align="right">64.32%</td>
<td align="right">3216</td>
<td align="right">64.32%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">993</td>
<td align="right">19.86%</td>
<td align="right">4208</td>
<td align="right">84.16%</td>
<td align="right">1022</td>
<td align="right">20.44%</td>
<td align="right">4238</td>
<td align="right">84.76%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">448</td>
<td align="right">8.96%</td>
<td align="right">4656</td>
<td align="right">93.12%</td>
<td align="right">414</td>
<td align="right">8.28%</td>
<td align="right">4652</td>
<td align="right">93.04%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">233</td>
<td align="right">4.66%</td>
<td align="right">4889</td>
<td align="right">97.78%</td>
<td align="right">239</td>
<td align="right">4.78%</td>
<td align="right">4891</td>
<td align="right">97.82%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">111</td>
<td align="right">2.22%</td>
<td align="right">109</td>
<td align="right">2.18%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>
articles/PCA.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
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articles/SPSS.html
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@@ -38,7 +38,7 @@
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@@ -162,7 +162,7 @@
<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="date">21 October 2022</h4>
<h4 data-toc-skip class="date">22 October 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>
<div class="d-none name"><code>SPSS.Rmd</code></div>
articles/WHONET.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
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articles/datasets.html
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@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</small>
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@@ -161,7 +161,7 @@
<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>
<h4 data-toc-skip class="date">21 October 2022</h4>
<h4 data-toc-skip class="date">22 October 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>
<div class="d-none name"><code>datasets.Rmd</code></div>
@@ -177,7 +177,7 @@
</h2>
<p>A data set with 48,787 rows and 22 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>source</em>, <em>lpsn</em>, <em>lpsn_parent</em>, <em>lpsn_renamed_to</em>, <em>gbif</em>, <em>gbif_parent</em>, <em>gbif_renamed_to</em>, <em>prevalence</em> and <em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 October 2022 19:58:04 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 22 October 2022 08:21:06 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">original R Data Structure (RDS) file</a> (1.1 MB)<br>
@@ -449,7 +449,7 @@
</h2>
<p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 October 2022 19:58:04 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 22 October 2022 08:21:06 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">original R Data Structure (RDS) file</a> (36 kB)<br>
@@ -622,7 +622,7 @@
</h2>
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 October 2022 19:58:04 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 22 October 2022 08:21:06 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">original R Data Structure (RDS) file</a> (4 kB)<br>
@@ -754,7 +754,7 @@
</h2>
<p>A data set with 20,369 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 October 2022 19:58:04 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 22 October 2022 08:21:06 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">original R Data Structure (RDS) file</a> (49 kB)<br>
@@ -913,7 +913,7 @@
</h2>
<p>A data set with 134,659 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 October 2022 19:58:04 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 22 October 2022 08:21:06 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">original R Data Structure (RDS) file</a> (78 kB)<br>
@@ -1185,7 +1185,7 @@
</h2>
<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 October 2022 19:58:04 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 22 October 2022 08:21:06 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">original R Data Structure (RDS) file</a> (3 kB)<br>
@@ -1302,7 +1302,7 @@
</h2>
<p>A data set with 2,000 rows and 46 columns, containing the following column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>, <em>ward</em>, <em>mo</em>, <em>PEN</em>, <em>OXA</em>, <em>FLC</em>, <em>AMX</em>, <em>AMC</em>, <em>AMP</em>, <em>TZP</em>, <em>CZO</em>, <em>FEP</em>, <em>CXM</em>, <em>FOX</em>, <em>CTX</em>, <em>CAZ</em>, <em>CRO</em>, <em>GEN</em>, <em>TOB</em>, <em>AMK</em>, <em>KAN</em>, <em>TMP</em>, <em>SXT</em>, <em>NIT</em>, <em>FOS</em>, <em>LNZ</em>, <em>CIP</em>, <em>MFX</em>, <em>VAN</em>, <em>TEC</em>, <em>TCY</em>, <em>TGC</em>, <em>DOX</em>, <em>ERY</em>, <em>CLI</em>, <em>AZM</em>, <em>IPM</em>, <em>MEM</em>, <em>MTR</em>, <em>CHL</em>, <em>COL</em>, <em>MUP</em> and <em>RIF</em>.</p>
<p>This data set is in R available as <code>example_isolates</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 October 2022 19:58:04 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
<p>It was last updated on 22 October 2022 08:21:06 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
<div class="section level3">
<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
</h3>
@@ -1707,7 +1707,7 @@
</h2>
<p>A data set with 3,000 rows and 8 columns, containing the following column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>, <em>bacteria</em>, <em>AMX</em>, <em>AMC</em>, <em>CIP</em> and <em>GEN</em>.</p>
<p>This data set is in R available as <code>example_isolates_unclean</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 October 2022 19:58:04 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
<p>It was last updated on 22 October 2022 08:21:06 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
<div class="section level3">
<h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>
</h3>
articles/index.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
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articles/resistance_predict.html
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@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
articles/welcome_to_AMR.html
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@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
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authors.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</small>
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index.html
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@@ -42,7 +42,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</small>
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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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
@@ -127,10 +127,10 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="1.8.2.9031" id="amr-1829031">AMR 1.8.2.9031<a class="anchor" aria-label="anchor" href="#amr-1829031"></a></h2>
<h2 class="pkg-version" data-toc-text="1.8.2.9032" id="amr-1829032">AMR 1.8.2.9032<a class="anchor" aria-label="anchor" href="#amr-1829032"></a></h2>
<p>This version will eventually become v2.0! We’re happy to reach a new major milestone soon!</p>
<div class="section level4">
<h4 id="breaking-1-8-2-9031">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9031"></a></h4>
<h4 id="breaking-1-8-2-9032">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9032"></a></h4>
<ul><li>Removed all species of the taxonomic kingdom Chromista from the package. This was done for multiple reasons:<ul><li>CRAN allows packages to be around 5 MB maximum, some packages are exempted but this package is not one of them</li>
<li>Chromista are not relevant when it comes to antimicrobial resistance, thus lacking the primary scope of this package</li>
<li>Chromista are almost never clinically relevant, thus lacking the secondary scope of this package</li>
@@ -141,7 +141,7 @@
<li>Argument <code>combine_IR</code> has been removed from this package (affecting functions <code><a href="../reference/count.html">count_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code>, and <code><a href="../reference/proportion.html">rsi_df()</a></code> and some plotting functions), since it was replaced with <code>combine_SI</code> three years ago</li>
</ul></div>
<div class="section level4">
<h4 id="new-1-8-2-9031">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9031"></a></h4>
<h4 id="new-1-8-2-9032">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9032"></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>All new algorithm for <code><a href="../reference/as.mo.html">as.mo()</a></code> (and thus internally all <code>mo_*()</code> functions) while still following our original set-up as described in our paper (DOI 10.18637/jss.v104.i03).<ul><li>A new argument <code>keep_synonyms</code> allows to <em>not</em> correct for updated taxonomy, in favour of the now deleted argument <code>allow_uncertain</code>
</li>
@@ -162,7 +162,7 @@
</li>
</ul></div>
<div class="section level4">
<h4 id="changed-1-8-2-9031">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9031"></a></h4>
<h4 id="changed-1-8-2-9032">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9032"></a></h4>
<ul><li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</li>
<li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on <code>NA</code> values (e.g. <code>as.rsi(as.disk(NA), ...)</code>)</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>
@@ -187,7 +187,7 @@
<li>Fix for using <code><a href="../reference/as.ab.html">as.ab()</a></code> on <code>NA</code> values</li>
</ul></div>
<div class="section level4">
<h4 id="other-1-8-2-9031">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9031"></a></h4>
<h4 id="other-1-8-2-9032">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9032"></a></h4>
<ul><li>New website to make use of the new Bootstrap 5 and pkgdown 2.0. 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, Dmytro Mykhailenko, Anton Mymrikov, and Jonas Salm as contributors, to thank them for their valuable input</li>
<li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>
pkgdown.yml
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@@ -11,7 +11,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2022-10-21T20:00Z
last_built: 2022-10-22T08:23Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles
reference/AMR-deprecated.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/AMR.html
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@@ -62,7 +62,7 @@ Principal component analysis for AMR
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/Rplot005.png
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reference/WHOCC.html
+1 -1
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/WHONET.html
+1 -1
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/ab_from_text.html
+1 -1
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/ab_property.html
+1 -1
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/add_custom_antimicrobials.html
+4 -4
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
@@ -205,7 +205,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Test Group"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $atc</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> NULL</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] NA</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $atc_group1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] NA</span>
@@ -214,10 +214,10 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] NA</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $tradenames</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> NULL</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] NA</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $loinc</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> NULL</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] NA</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $ddd</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $ddd$oral</span>
reference/age.html
+11 -11
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
@@ -190,16 +190,16 @@
<span class="r-in"><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> 1 1932-09-10 90 90.11233 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1986-09-23 36 36.07671 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1950-08-19 72 72.17260 49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1943-04-15 79 79.51781 56</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1948-09-12 74 74.10685 51</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1996-04-09 26 26.53425 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1935-06-06 87 87.37534 64</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1990-06-17 32 32.34521 9</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1947-04-20 75 75.50411 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1966-01-18 56 56.75616 33</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1945-06-08 77 77.37260 54</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1932-04-12 90 90.52877 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1956-12-27 65 65.81918 43</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-12-21 74 74.83562 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1954-10-06 68 68.04384 45</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1951-10-15 71 71.01918 48</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1941-11-29 80 80.89589 58</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1992-05-13 30 30.44384 7</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1994-08-11 28 28.19726 5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1934-12-18 87 87.84384 65</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
reference/age_groups.html
+1 -1
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/antibiotic_class_selectors.html
+1 -1
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/antibiotics.html
+1 -1
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/as.ab.html
+5 -3
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
@@ -215,7 +215,8 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"J 01 FA 01"</span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error:</span> in like(): argument `x` must not be NULL</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"Erythromycin"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
@@ -223,7 +224,8 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">" eryt 123"</span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error:</span> in like(): argument `x` must not be NULL</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"ERYT"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
reference/as.disk.html
+1 -1
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/as.mic.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/as.mo.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/as.rsi.html
+11 -11
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
@@ -484,16 +484,16 @@ 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;"># A tibble: 50 × 13</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_consid…¹ mo_in…² mo_conside…³ guide…⁴</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&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 style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-10-21 <span style="color: #949494;">20:01:04</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-10-21 <span style="color: #949494;">20:01:04</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-10-21 <span style="color: #949494;">20:01:04</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-10-21 <span style="color: #949494;">20:01:04</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-10-21 <span style="color: #949494;">20:01:05</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-10-21 <span style="color: #949494;">20:01:05</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-10-21 <span style="color: #949494;">20:01:05</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-10-21 <span style="color: #949494;">20:01:05</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-10-21 <span style="color: #949494;">20:01:05</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-10-21 <span style="color: #949494;">20:01:05</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-10-22 <span style="color: #949494;">08:23:30</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-10-22 <span style="color: #949494;">08:23:30</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-10-22 <span style="color: #949494;">08:23:31</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-10-22 <span style="color: #949494;">08:23:31</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-10-22 <span style="color: #949494;">08:23:31</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-10-22 <span style="color: #949494;">08:23:31</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-10-22 <span style="color: #949494;">08:23:32</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-10-22 <span style="color: #949494;">08:23:32</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-10-22 <span style="color: #949494;">08:23:32</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-10-22 <span style="color: #949494;">08:23:32</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 6 more variables: ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S &lt;dbl&gt;, breakpoint_R &lt;dbl&gt;, input &lt;dbl&gt;, interpretation &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># and abbreviated variable names ¹​ab_considered, ²​mo_input, ³​mo_considered,</span></span>
reference/atc_online.html
+1 -1
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/availability.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/bug_drug_combinations.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/count.html
+1 -1
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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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/custom_eucast_rules.html
+1 -1
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/dosage.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/eucast_rules.html
+1 -1
View File
@@ -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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/example_isolates.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</small>
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reference/example_isolates_unclean.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/first_isolate.html
+1 -1
View File
@@ -12,7 +12,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/g.test.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/get_episode.html
+64 -67
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
@@ -177,43 +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></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] 30 12 7 57 9 44 25 31 3 56 6 43 38 46 39 12 53 24 46 60 48 28 31 8 29</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 41 38 35 37 17 38 58 35 56 18 65 31 32 28 56 37 30 51 17 62 34 30 2 21 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 12 62 1 48 63 20 27 22 37 10 47 5 13 23 38 65 15 21 12 59 32 57 20 41 64</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 26 12 38 44 42 55 20 57 45 8 29 19 5 8 48 19 61 55 7 49 2 57 20 18 63</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 3 26 55 22 37 62 38 54 58 60 18 15 18 15 4 40 20 47 42 60 18 7 38 3 51</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 8 24 33 11 46 16 63 58 7 21 48 50 22 29 4 40 25 13 43 48 9 36 14 10 5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 44 8 3 1 21 15 22 46 4 10 61 15 39 22 28 58 1 16 8 60 36 19 49 53 61</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 6 55 29 17 63 26 14 23 52 23 18 6 63 64 18 9 41 8 52 39 3 23 54 10 23</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 32 48 50 13 52 47 10 39 18 45 31 54 2 17 55 46 26 24 22 39 41 52 30 56 49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 51 26 61 52 53 13 57 15 16 52 57 48 63 6 45 13 63 60 20 27 47 56 9 39 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 31 8 53 17 5 61 67 64 40 3 35 27 31 32 13 67 17 37 4 53 67 58 19 28 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 8 49 14 46 59 63 2 58 40 28 2 42 3 1 7 48 16 63 19 5 1 25 32 52 45</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 17 46 12 44 6 62 24 11 66 33 63 13 22 43 62 48 32 27 19 23 4 54 8 57 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 65 65 45 17 64 33 55 24 64 40 28 67 18 40 35 12 66 60 57 22 37 29 43 63 9</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 22 57 58 9 57 9 22 4 7 31 25 67 26 37 59 41 23 36 10 59 22 1 43 31 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 39 10 11 4 62 66 16 34 9 44 66 9 34 34 20 37 11 29 9 53 45 38 21 50 4</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 FALSE TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE FALSE FALSE TRUE TRUE TRUE FALSE TRUE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] TRUE FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE TRUE FALSE FALSE TRUE TRUE TRUE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE FALSE FALSE TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] TRUE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE FALSE TRUE TRUE TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE</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="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: 5 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </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;chr&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 style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-11-14 058917 76 F ICU B_STPHY_HMNS R NA S NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-11-12 CF9318 29 M ICU B_STPHY_CONS R NA R R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-11-16 762305 87 F Clinical B_PROTS_MRBL R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2002-11-18 956065 89 F Clinical B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> 2002-11-18 956065 89 F Clinical B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-08-19 A49852 70 M Clinical B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-08-31 149442 80 F ICU B_STPHY_AURS R NA S R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 36 more variables: AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;, CZO &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FEP &lt;rsi&gt;, CXM &lt;rsi&gt;, FOX &lt;rsi&gt;, CTX &lt;rsi&gt;, CAZ &lt;rsi&gt;, CRO &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># GEN &lt;rsi&gt;, TOB &lt;rsi&gt;, AMK &lt;rsi&gt;, KAN &lt;rsi&gt;, TMP &lt;rsi&gt;, SXT &lt;rsi&gt;,</span></span>
@@ -249,16 +246,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: condition [3]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> F68330 2009-04-09 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> F35553 2004-12-29 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 218456 2003-09-26 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 438196 2016-02-16 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 386739 2004-04-15 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> C541BC 2012-09-03 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 192790 2008-02-15 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 008218 2009-04-27 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 058917 2002-11-14 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 375975 2015-11-19 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 668048 2009-06-29 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 964129 2013-09-11 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> C06794 2013-12-18 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> C21760 2004-12-28 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> E225B0 2014-07-22 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 970832 2013-07-09 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 05B00F 2004-05-11 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 690B42 2011-06-16 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 740354 2005-10-31 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 431647 2012-10-04 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</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">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -270,19 +267,19 @@
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [184]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [188]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2009-04-09 F68330 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU 2004-12-29 F35553 4 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2003-09-26 218456 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU 2016-02-16 438196 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2004-04-15 386739 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2012-09-03 C541BC 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Outpatient 2008-02-15 192790 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2009-04-27 008218 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU 2002-11-14 058917 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2015-11-19 375975 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2009-06-29 668048 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2013-09-11 964129 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2013-12-18 C06794 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU 2004-12-28 C21760 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Outpatient 2014-07-22 E225B0 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2013-07-09 970832 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2004-05-11 05B00F 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2011-06-16 690B42 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Outpatient 2005-10-31 740354 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2012-10-04 431647 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</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">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -297,9 +294,9 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 118 15 55 72</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 54 12 35 40</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 12 7 10 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 117 14 54 77</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 61 12 35 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 10 7 9 9</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></span>
<span class="r-in"><span> <span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
@@ -329,19 +326,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [192]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [191]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&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 style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> F68330 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> F35553 B_SERRT_MRCS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 218456 B_PROTS_MRBL Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 438196 B_STPHY_AURS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 386739 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> C541BC B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 192790 B_STPHY_CONS Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 008218 B_STRPT_GRPA Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 058917 B_STPHY_HMNS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 375975 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 668048 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 964129 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> C06794 B_STPHY_HMNS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> C21760 B_STPHY_EPDR ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> E225B0 B_ESCHR_COLI Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 970832 B_STRPT_DYSG Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 05B00F F_CANDD_ALBC ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 690B42 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 740354 B_STPHY_CONS Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 431647 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
reference/ggplot_pca.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/ggplot_rsi.html
+1 -1
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/guess_ab_col.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/index.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/intrinsic_resistant.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/italicise_taxonomy.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/join.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/key_antimicrobials.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/kurtosis.html
+3 -3
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
@@ -167,9 +167,9 @@
<div class="section level2">
<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>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.90906</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.041992</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] -0.02213884</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01855637</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
reference/like.html
+1 -1
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/mdro.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/mean_amr_distance.html
+37 -36
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
@@ -195,10 +195,11 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &gt;=128 0.005 0.001 &gt;=128 0.5 0.002 0.125 &gt;=128 0.001 0.001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5 0.005 0.025 0.25 0.5 4 2 256 0.005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &lt;=0.001</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.326173081 -0.625477475 -0.934930955 1.326173081 0.259978204</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [6] -0.801656595 -0.006570515 1.326173081 -0.934930955 -0.934930955</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.25069240 -0.97620422 -0.54742225 0.06602606 0.25069240 0.80469143</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.62002509 1.91268949 -0.97620422 -1.40498619</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@@ -209,37 +210,37 @@
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A &lt;=2 &lt;=0.0625 0.5 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B &lt;=2 &lt;=0.0625 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &lt;=2 0.25 1 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D &lt;=2 0.25 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 &lt;=0.0625 0.5 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 4 1 1 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &lt;=2 &lt;=0.0625 1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 16 1 0.5 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 4 &lt;=0.0625 1 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 8 0.25 0.5 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 16 2 &lt;=1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 4 0.5 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 8 1 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 2 0.125 4 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 2 4 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 1 0.025 &lt;=1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 0.025 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 1 2 &lt;=1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 16 0.125 &lt;=1 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 0.25 &gt;=8 1</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "id" and "tobr"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.63247597 0.12172575 0.13909708 0.17399130 -0.60692086 0.03530561</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.38107540 0.48453431 0.07749241 0.58832578</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.4941954 0.1411173 0.4018372 -0.4928375 0.8875875 -1.0556736</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.3568509 -0.1439580 -0.4546376 0.5792202</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A &lt;=2 &lt;=0.0625 0.5 2 -0.63247597</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 &lt;=0.0625 0.5 1 -0.60692086</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &lt;=2 &lt;=0.0625 1 2 -0.38107540</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 4 1 1 0.5 0.03530561</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 4 &lt;=0.0625 1 4 0.07749241</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B &lt;=2 &lt;=0.0625 4 2 0.12172575</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &lt;=2 0.25 1 4 0.13909708</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D &lt;=2 0.25 2 2 0.17399130</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 16 1 0.5 1 0.48453431</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 8 0.25 0.5 &gt;=8 0.58832578</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 1 0.025 &lt;=1 1 -1.0556736</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 2 0.125 4 0.5 -0.4928375</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 16 0.125 &lt;=1 0.5 -0.4546376</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 0.025 2 1 -0.3568509</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 1 2 &lt;=1 2 -0.1439580</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 4 0.5 4 1 0.1411173</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 8 1 4 1 0.4018372</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 16 2 &lt;=1 2 0.4941954</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 0.25 &gt;=8 1 0.5792202</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 2 4 &gt;=4 0.8875875</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="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -252,16 +253,16 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C &lt;=2 0.25 1 4 0.13909708 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B &lt;=2 &lt;=0.0625 4 2 0.12172575 0.01737133</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 D &lt;=2 0.25 2 2 0.17399130 0.03489422</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 I 4 &lt;=0.0625 1 4 0.07749241 0.06160466</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 F 4 1 1 0.5 0.03530561 0.10379147</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 H 16 1 0.5 1 0.48453431 0.34543723</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 J 8 0.25 0.5 &gt;=8 0.58832578 0.44922870</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 G &lt;=2 &lt;=0.0625 1 2 -0.38107540 0.52017247</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 E 4 &lt;=0.0625 0.5 1 -0.60692086 0.74601794</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 A &lt;=2 &lt;=0.0625 0.5 2 -0.63247597 0.77157305</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C 8 1 4 1 0.4018372 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 A 16 2 &lt;=1 2 0.4941954 0.09235825</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 J 16 0.25 &gt;=8 1 0.5792202 0.17738302</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 B 4 0.5 4 1 0.1411173 0.26071983</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 2 4 &gt;=4 0.8875875 0.48575029</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 H 1 2 &lt;=1 2 -0.1439580 0.54579519</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 0.025 2 1 -0.3568509 0.75868806</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 I 16 0.125 &lt;=1 0.5 -0.4546376 0.85647479</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 D 2 0.125 4 0.5 -0.4928375 0.89467471</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 F 1 0.025 &lt;=1 1 -1.0556736 1.45751072</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"># support for groups</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>
reference/microorganisms.codes.html
+1 -1
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/microorganisms.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/mo_matching_score.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/mo_property.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/mo_source.html
+1 -1
View File
@@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/pca.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/plot-1.png
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reference/plot.html
+1 -1
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/proportion.html
+1 -1
View File
@@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
reference/random.html
+16 -19
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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">
@@ -178,44 +178,41 @@
<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>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 0.002 64 0.002 0.002 0.025 32 256 4 0.005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.005 0.125 16 0.01 8 16 0.001 0.001 4 0.0625</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 16 0.01 0.25 1 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 128 32 128 0.01 0.005 0.125 32 256 64 256 0.001 0.001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 4 0.025 32 1 0.5 32 1 0.001 0.5 0.5 0.005 0.001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 8 </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 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 46 14 7 43 47 45 46 44 10 23 43 50 26 36 9 41 8 11 30 7 30 40 44 29 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 18 41 42 38 50 47 45 30 44 7 22 24 47 42 41 7 40 39 6 35 9 23 9 48 45</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 'rsi'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S R S I S S I I I I R R I R R I S I S I I I S R S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I R I S S I R I I R S R S I S I R S S I R S R R I</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"># 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-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.002 32 &lt;=0.001 0.0625 4 0.01 4 0.125 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.005 0.005 64 64 32 2 64 0.0625 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 1 0.025 0.002 0.125 16 32 0.002 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 0.025 16 0.0625 2 4 4 4 0.001 0.002 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.001 64 0.005 0.005 0.025 32 8 0.001 0.25 0.005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 2 32 16 0.005 0.5 </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 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 8 16 1 1 16 &lt;=0.25 4 8 &lt;=0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 1 0.5 16 4 8 0.5 &lt;=0.25 8 2 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.5 2 4 0.5 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5 0.5 2 4 4 0.5 2 16 8 &gt;=64 32 0.5 4 2 &gt;=64</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] 0.5 4 8 32 &gt;=64 32 4 0.5 16 32 </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 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=0.0625 0.5 8 4 0.125 &lt;=0.0625 4 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] 0.5 4 8 0.125 0.125 4 &lt;=0.0625 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [17] &lt;=0.0625 1 8 &lt;=0.0625 8 2 8 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.25 8 8 4 8 8 4 4 1 1 0.5 2 4 2 0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] 0.25 0.5 8 4 2 0.5 4 1 4 8 </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-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 14 19 49 39 22 34 20 9 32 43 45 8 47 37 20 49 49 37 48 19 21 44 44 28 43</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 43 50 49 46 32 47 35 39 31 14 46 50 37 15 39 40 33 24 26 40 44 31 31 46</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 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 15 13 15 14 14 11 12 15 16 11 16 11 13 16 12 17 13 16 11 12 11 11 13 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 12 11 15 13 16 16 12 17 12 12 16 16 15 16 11 14 15 11 15 12 17 12 12 16</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 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 26 23 24 15 26 15 22 18 15 16 16 23 19 24 20 17 25 16 27 21 16 23 18 19 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 24 19 21 27 21 25 22 18 25 17 25 20 27 25 16 17 16 24 18 17 20 17 18 20 25</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>
reference/resistance_predict.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
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reference/rsi_translation.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</small>
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reference/skewness.html
+2 -2
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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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</small>
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@@ -166,7 +166,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<div class="section level2">
<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>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.0436877</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01934547</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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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-everything-together","dir":"Articles","previous_headings":"CreatLine 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-everything-together","dir":"Articles","previous_headings":"CreatLine truncated