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@ -36,7 +36,7 @@
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@ -116,28 +116,28 @@
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@ -89,28 +89,28 @@
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@ -38,7 +38,7 @@
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@ -118,28 +118,28 @@
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AMR &amp; base R AMR &amp; base R
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@ -204,7 +204,7 @@
website update since they are based on randomly created values and the 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 page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was Markdown</a>. However, the methodology remains unchanged. This page was
generated on 26 May 2023.</p> generated on 27 May 2023.</p>
<div class="section level2"> <div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a> <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2> </h2>
@ -260,21 +260,21 @@ make the structure of your data generally look like this:</p>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">2023-05-26</td> <td align="center">2023-05-27</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2023-05-26</td> <td align="center">2023-05-27</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">2023-05-26</td> <td align="center">2023-05-27</td>
<td align="center">efgh</td> <td align="center">efgh</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">R</td> <td align="center">R</td>

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@ -38,7 +38,7 @@
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@ -118,28 +118,28 @@
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articles/MDR.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -118,28 +118,28 @@
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@ -402,17 +402,17 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co">#&gt; rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span> <span><span class="co">#&gt; rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co">#&gt; 1 R R R S S S</span></span> <span><span class="co">#&gt; 1 R S S R R S</span></span>
<span><span class="co">#&gt; 2 S R S S R S</span></span> <span><span class="co">#&gt; 2 R R I I S S</span></span>
<span><span class="co">#&gt; 3 S R I R I I</span></span> <span><span class="co">#&gt; 3 S R S S I S</span></span>
<span><span class="co">#&gt; 4 R I S I S R</span></span> <span><span class="co">#&gt; 4 R R S R R R</span></span>
<span><span class="co">#&gt; 5 S I R I I S</span></span> <span><span class="co">#&gt; 5 I I I S R R</span></span>
<span><span class="co">#&gt; 6 R R I S S I</span></span> <span><span class="co">#&gt; 6 S I R R S R</span></span>
<span><span class="co">#&gt; kanamycin</span></span> <span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 I</span></span> <span><span class="co">#&gt; 1 S</span></span>
<span><span class="co">#&gt; 2 I</span></span> <span><span class="co">#&gt; 2 S</span></span>
<span><span class="co">#&gt; 3 I</span></span> <span><span class="co">#&gt; 3 I</span></span>
<span><span class="co">#&gt; 4 S</span></span> <span><span class="co">#&gt; 4 R</span></span>
<span><span class="co">#&gt; 5 S</span></span> <span><span class="co">#&gt; 5 S</span></span>
<span><span class="co">#&gt; 6 R</span></span></code></pre></div> <span><span class="co">#&gt; 6 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can <p>We can now add the interpretation of MDR-TB to our data set. You can
@ -455,40 +455,40 @@ Unique: 5</p>
<tr class="odd"> <tr class="odd">
<td align="left">1</td> <td align="left">1</td>
<td align="left">Mono-resistant</td> <td align="left">Mono-resistant</td>
<td align="right">3180</td> <td align="right">3225</td>
<td align="right">63.60%</td> <td align="right">64.50%</td>
<td align="right">3180</td> <td align="right">3225</td>
<td align="right">63.60%</td> <td align="right">64.50%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">2</td> <td align="left">2</td>
<td align="left">Negative</td> <td align="left">Negative</td>
<td align="right">1032</td> <td align="right">963</td>
<td align="right">20.64%</td> <td align="right">19.26%</td>
<td align="right">4212</td> <td align="right">4188</td>
<td align="right">84.24%</td> <td align="right">83.76%</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">3</td> <td align="left">3</td>
<td align="left">Multi-drug-resistant</td> <td align="left">Multi-drug-resistant</td>
<td align="right">462</td> <td align="right">478</td>
<td align="right">9.24%</td> <td align="right">9.56%</td>
<td align="right">4674</td> <td align="right">4666</td>
<td align="right">93.48%</td> <td align="right">93.32%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">4</td> <td align="left">4</td>
<td align="left">Poly-resistant</td> <td align="left">Poly-resistant</td>
<td align="right">226</td> <td align="right">228</td>
<td align="right">4.52%</td> <td align="right">4.56%</td>
<td align="right">4900</td> <td align="right">4894</td>
<td align="right">98.00%</td> <td align="right">97.88%</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">5</td> <td align="left">5</td>
<td align="left">Extensively drug-resistant</td> <td align="left">Extensively drug-resistant</td>
<td align="right">100</td> <td align="right">106</td>
<td align="right">2.00%</td> <td align="right">2.12%</td>
<td align="right">5000</td> <td align="right">5000</td>
<td align="right">100.00%</td> <td align="right">100.00%</td>
</tr> </tr>

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articles/PCA.html
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@ -38,7 +38,7 @@
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@ -118,28 +118,28 @@
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -118,28 +118,28 @@
</li> </li>
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With other pkgs With other pkgs
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AMR &amp; data.table AMR &amp; data.table
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AMR &amp; base R AMR &amp; base R
</a> </a>

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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> <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="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -118,28 +118,28 @@
</li> </li>
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<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
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With other pkgs With other pkgs
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AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
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<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
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AMR &amp; tidymodels AMR &amp; tidymodels
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AMR &amp; base R AMR &amp; base R
</a> </a>
@ -193,7 +193,7 @@
<main id="main" class="col-md-9"><div class="page-header"> <main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1> <img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">26 May 2023</h4> <h4 data-toc-skip class="date">27 May 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small> <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div> <div class="d-none name"><code>datasets.Rmd</code></div>

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articles/index.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
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<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
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AMR &amp; data.table AMR &amp; data.table
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AMR &amp; tidymodels AMR &amp; tidymodels
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AMR &amp; base R AMR &amp; base R
</a> </a>

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articles/other_pkg.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -118,28 +118,28 @@
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With other pkgs With other pkgs
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AMR &amp; data.table AMR &amp; data.table
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AMR &amp; tidymodels AMR &amp; tidymodels
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AMR &amp; base R AMR &amp; base R
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articles/resistance_predict.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
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@ -118,28 +118,28 @@
</li> </li>
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With other pkgs With other pkgs
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AMR &amp; data.table AMR &amp; data.table
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AMR &amp; tidymodels AMR &amp; tidymodels
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AMR &amp; base R AMR &amp; base R
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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> <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="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -118,28 +118,28 @@
</li> </li>
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<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
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With other pkgs With other pkgs
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AMR &amp; data.table AMR &amp; data.table
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AMR &amp; tidymodels AMR &amp; tidymodels
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AMR &amp; base R AMR &amp; base R
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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> <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="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
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<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
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AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
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AMR &amp; data.table AMR &amp; data.table
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AMR &amp; tidymodels AMR &amp; tidymodels
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AMR &amp; base R AMR &amp; base R
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@ -10,7 +10,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
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@ -10,7 +10,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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index.html
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>
@ -159,9 +159,9 @@
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 class="pkg-version" data-toc-text="2.0.0.9022" id="amr-2009022">AMR 2.0.0.9022<a class="anchor" aria-label="anchor" href="#amr-2009022"></a></h2> <h2 class="pkg-version" data-toc-text="2.0.0.9023" id="amr-2009023">AMR 2.0.0.9023<a class="anchor" aria-label="anchor" href="#amr-2009023"></a></h2>
<div class="section level3"> <div class="section level3">
<h3 id="changed-2-0-0-9022">Changed<a class="anchor" aria-label="anchor" href="#changed-2-0-0-9022"></a></h3> <h3 id="changed-2-0-0-9023">Changed<a class="anchor" aria-label="anchor" href="#changed-2-0-0-9023"></a></h3>
<ul><li>Added oxygen tolerance from BacDive to over 25,000 bacteria in the <code>microorganisms</code> data set <ul><li>Added oxygen tolerance from BacDive to over 25,000 bacteria in the <code>microorganisms</code> data set
<ul><li>Added <code><a href="../reference/mo_property.html">mo_oxygen_tolerance()</a></code> to retrieve the values</li> <ul><li>Added <code><a href="../reference/mo_property.html">mo_oxygen_tolerance()</a></code> to retrieve the values</li>
<li>Added <code><a href="../reference/mo_property.html">mo_is_anaerobic()</a></code> to determine which genera/species are obligate anaerobic bacteria</li> <li>Added <code><a href="../reference/mo_property.html">mo_is_anaerobic()</a></code> to determine which genera/species are obligate anaerobic bacteria</li>

2
pkgdown.yml
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@ -11,7 +11,7 @@ articles:
other_pkg: other_pkg.html other_pkg: other_pkg.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2023-05-26T18:41Z last_built: 2023-05-27T08:50Z
urls: urls:
reference: https://msberends.github.io/AMR/reference reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles article: https://msberends.github.io/AMR/articles

12
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> <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="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/AMR-options.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/AMR.html
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@ -24,7 +24,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -103,28 +103,28 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

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reference/WHOCC.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/WHONET.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
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<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/ab_from_text.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
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AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
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<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/ab_property.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
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<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
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AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/add_custom_antimicrobials.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/add_custom_microorganisms.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

32
reference/age.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>
@ -222,16 +222,16 @@
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span> <span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span> <span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1931-09-23 91 91.67123 68</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 1989-07-11 33 33.87671 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1943-05-24 80 80.00548 56</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 1976-01-27 47 47.32877 23</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1940-06-21 82 82.92877 59</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 1952-06-04 70 70.97808 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1961-09-19 61 61.68219 38</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 1975-04-14 48 48.11781 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1950-09-30 72 72.65205 49</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 1980-05-09 43 43.04932 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1984-08-13 38 38.78356 15</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 1959-05-20 64 64.01918 40</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1942-06-08 80 80.96438 57</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 1956-11-01 66 66.56712 43</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1983-08-05 39 39.80548 16</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 1986-10-27 36 36.58082 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1985-01-31 38 38.31507 14</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 1989-06-17 33 33.94247 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1992-07-28 30 30.82740 7</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 1965-07-30 57 57.82466 34</span>
</code></pre></div> </code></pre></div>
</div> </div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

12
reference/age_groups.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/antibiogram.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

20
reference/antibiotic_class_selectors.html
View File

@ -12,7 +12,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -91,28 +91,28 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>
@ -626,11 +626,11 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 5 × 1</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 5 × 1</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> kefzol</span> <span class="r-out co"><span class="r-pr">#&gt;</span> kefzol</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> R </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> I </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> R </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> R </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> I </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> S </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> I </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> I </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> S </span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span> <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># get AMR for all aminoglycosides e.g., per ward:</span></span></span> <span class="r-in"><span> <span class="co"># get AMR for all aminoglycosides e.g., per ward:</span></span></span>

12
reference/antibiotics.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/as.ab.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/as.av.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/as.disk.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/as.mic.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/as.mo.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

32
reference/as.sir.html
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@ -12,7 +12,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -91,28 +91,28 @@ All breakpoints used for interpretation are publicly available in the clinical_b
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>
@ -551,16 +551,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 12</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 12</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_guideline mo_input mo_guideline </span> <span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_guideline mo_input mo_guideline </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> <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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-05-26 <span style="color: #949494;">18:42:01</span> 1 TOB TOB Escherichia… B_[ORD]_ENTRBCTR</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-05-27 <span style="color: #949494;">08:50:58</span> 1 TOB TOB Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-05-26 <span style="color: #949494;">18:42:01</span> 1 GEN GEN Escherichia… B_[ORD]_ENTRBCTR</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-05-27 <span style="color: #949494;">08:50:58</span> 1 GEN GEN Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-05-26 <span style="color: #949494;">18:42:00</span> 1 CIP CIP Escherichia… B_[ORD]_ENTRBCTR</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-05-27 <span style="color: #949494;">08:50:57</span> 1 CIP CIP Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-05-26 <span style="color: #949494;">18:42:00</span> 1 AMP AMP Escherichia… B_[ORD]_ENTRBCTR</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-05-27 <span style="color: #949494;">08:50:57</span> 1 AMP AMP Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-05-26 <span style="color: #949494;">18:41:54</span> 1 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-05-27 <span style="color: #949494;">08:50:52</span> 1 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-05-26 <span style="color: #949494;">18:41:54</span> 2 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-05-27 <span style="color: #949494;">08:50:52</span> 2 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-05-26 <span style="color: #949494;">18:41:54</span> 3 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-05-27 <span style="color: #949494;">08:50:52</span> 3 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-05-26 <span style="color: #949494;">18:41:54</span> 4 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-05-27 <span style="color: #949494;">08:50:52</span> 4 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-05-26 <span style="color: #949494;">18:41:54</span> 5 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-05-27 <span style="color: #949494;">08:50:52</span> 5 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-05-26 <span style="color: #949494;">18:41:54</span> 6 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-05-27 <span style="color: #949494;">08:50:52</span> 6 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 40 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 40 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 6 more variables: guideline &lt;chr&gt;, 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;"># ℹ 6 more variables: guideline &lt;chr&gt;, 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;"># input &lt;dbl&gt;, outcome &lt;sir&gt;, breakpoint_S_R &lt;chr&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># input &lt;dbl&gt;, outcome &lt;sir&gt;, breakpoint_S_R &lt;chr&gt;</span></span>

12
reference/atc_online.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/av_from_text.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/av_property.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/availability.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/bug_drug_combinations.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/clinical_breakpoints.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/count.html
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@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -91,28 +91,28 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/custom_eucast_rules.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/dosage.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/eucast_rules.html
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> <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="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -91,28 +91,28 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/example_isolates.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/example_isolates_unclean.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/first_isolate.html
View File

@ -12,7 +12,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -91,28 +91,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/g.test.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

110
reference/get_episode.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>
@ -263,29 +263,27 @@
<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">100</span><span class="op">)</span>, <span class="op">]</span></span></span> <span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span> <span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3 16 36 32 3 13 40 10 35 39 8 16 32 29 8 38 21 11 15 30 5 20 45 9 12</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 34 32 18 15 11 8 45 29 7 7 46 31 27 44 20 38 47 11 42 3 46 4 13 37 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 8 34 14 31 38 26 10 43 36 11 17 38 39 35 42 17 8 19 43 25 38 6 24 7 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [26] 9 35 5 46 26 44 40 16 20 21 20 24 27 14 41 20 41 28 27 42 24 22 35 30 22</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 17 34 6 10 1 33 9 41 17 7 14 21 11 36 29 25 10 21 36 23 28 18 12 20 41</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [51] 16 44 25 35 30 6 12 13 38 8 33 46 29 6 23 6 34 47 11 1 16 40 27 46 5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 28 22 4 21 37 38 37 42 36 35 3 20 44 22 2 10 16 6 7 1 37 28 31 27 33</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [76] 10 2 39 48 4 23 46 25 36 19 12 43 17 22 9 47 11 2 45 17 15 42 37 28 8</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span> <span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE FALSE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE FALSE TRUE TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [85] TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE FALSE FALSE</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span> <span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span> <span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 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> 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;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;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;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-07-23 F35553 51 M ICU B_STPHY_AURS R NA S R </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> 2002-07-15 C42193 84 M ICU B_STPHY_HMNS R NA R R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-06-05 24D393 20 F Clinical B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;,</span></span>
@ -322,16 +320,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [99]</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [99]</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> 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: #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> 023456 2012-11-24 A TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 006827 2009-07-24 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 035268 2011-05-31 A TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 021648 2004-08-21 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 060287 2007-03-11 B TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 023456 2011-04-25 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 065133 2011-12-19 C TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 032343 2003-06-09 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 067927 2002-02-14 C TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 074321 2015-09-20 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 078381 2014-07-17 C TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 0D7D34 2011-03-19 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 082622 2014-02-08 C TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 0E2483 2007-08-10 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 092034 2016-08-07 B TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 164466 2009-10-07 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 097186 2015-10-28 C TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 16DC39 2015-11-19 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 0C0688 2014-09-05 C TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 189564 2009-12-22 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span> <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@ -348,16 +346,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [97]</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [97]</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> 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;int&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: #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;int&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 2012-11-24 023456 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2009-07-24 006827 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU 2011-05-31 035268 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2004-08-21 021648 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2007-03-11 060287 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2011-04-25 023456 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2011-12-19 065133 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2003-06-09 032343 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2002-02-14 067927 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2015-09-20 074321 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU 2014-07-17 078381 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU 2011-03-19 0D7D34 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2014-02-08 082622 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2007-08-10 0E2483 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2016-08-07 092034 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2009-10-07 164466 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2015-10-28 097186 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU 2015-11-19 16DC39 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2014-09-05 0C0688 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> ICU 2009-12-22 189564 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span> <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@ -373,9 +371,9 @@
<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> <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> 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: #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 61 13 41 46</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 60 13 37 45</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 32 10 21 26</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 31 12 22 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 4 3 3 4</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 6 3 5 5</span>
<span class="r-in"><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> <span class="r-in"><span><span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
<span class="r-in"><span><span class="co"># results as first_isolate() when using 'episode-based':</span></span></span> <span class="r-in"><span><span class="co"># results as first_isolate() when using 'episode-based':</span></span></span>
@ -407,16 +405,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [98]</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [98]</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> 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: #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> F35553 B_STPHY_AURS ICU TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 451000 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> F37316 B_STRPT_PNMN ICU TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 741413 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 375220 B_ENTRC_FCLS Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 8BBC46 B_ENTRC_FACM Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 082622 B_PSDMN_AERG ICU TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> F09078 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> C42193 B_STPHY_HMNS ICU TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> C56827 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> D43733 B_ESCHR_COLI ICU TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> D27410 B_BCTRD_FRGL Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 092034 B_ESCHR_COLI Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> D38469 UNKNOWN ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> F58364 B_STPHY_CONS Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 023456 B_PROTS_MRBL Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 438196 B_STPHY_COHN Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2FC253 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 534816 B_STPHY_AURS Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> EB1709 B_STRPT_PNMN ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div> </code></pre></div>

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With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>
@ -199,9 +199,9 @@
<div class="section level2"> <div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.899176</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.010824</span>
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.01410279</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.1430003</span>
</code></pre></div> </code></pre></div>
</div> </div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

12
reference/like.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/mdro.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

78
reference/mean_amr_distance.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>
@ -218,30 +218,30 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</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">sir</span></span></span> <span class="r-in"><span><span class="va">sir</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S R S I I I R S R S</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] I I R R I S I I S S</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.621059 1.449138 -0.621059 -0.621059 -0.621059 -0.621059 1.449138</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.4743416 -0.4743416 1.8973666 1.8973666 -0.4743416 -0.4743416</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [8] -0.621059 1.449138 -0.621059</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.4743416 -0.4743416 -0.4743416 -0.4743416</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">mic</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">mic</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">mic</span></span></span> <span class="r-in"><span><span class="va">mic</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> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5 4 1 0.001 32 0.125 0.25 0.125 0.125 64 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 &gt;=16 0.002 &gt;=16 0.025 &gt;=16 0.002 2 2 2 </span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.02261165 0.63329547 0.19602406 -1.98285222 1.28920259 -0.45988306</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.6738475 0.8649910 -1.6133339 0.8649910 -0.9168346 0.8649910</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.24124735 -0.45988306 -0.45988306 1.50783829</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.6133339 0.2915606 0.2915606 0.2915606</span>
<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span> <span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.02261165 0.63329547 0.19602406 -1.98285222 1.28920259 -0.45988306</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.6738475 0.8649910 -1.6133339 0.8649910 -0.9168346 0.8649910</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.24124735 -0.45988306 -0.45988306 1.50783829</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.6133339 0.2915606 0.2915606 0.2915606</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">disk</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_disk</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">disk</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_disk</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">disk</span></span></span> <span class="r-in"><span><span class="va">disk</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> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 12 39 10 7 40 39 30 44 18 39</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 39 15 22 38 19 50 29 46 40 18</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.0909965 0.7733646 -1.2290973 -1.4362486 0.8424150 0.7733646</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5869812 -1.3167417 -0.7614892 0.5076595 -0.9994545 1.4595209</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.1519109 1.1186167 -0.6766940 0.7733646</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.2062367 1.1422338 0.6663030 -1.0787763</span>
<span class="r-in"><span></span></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><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> <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>
@ -252,21 +252,21 @@
<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-in"><span><span class="va">y</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> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A S 27 1 0.5</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 A I 17 8 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B I 28 2 &gt;=4</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 B S 31 2 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C S 28 &gt;=4 &gt;=4</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 C R 19 16 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D S 18 &gt;=4 1</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 D S 18 8 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 19 &gt;=4 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 19 16 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F S 30 &gt;=4 1</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 F I 31 16 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 28 1 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 24 &lt;=1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H S 26 2 &gt;=4</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 H S 24 &lt;=1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I R 21 &gt;=4 1</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 I R 22 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 18 2 0.5</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 20 2 0.5</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-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> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and "tobr"</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> and "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.7116852 0.2836947 0.5873608 -0.3661781 -0.1004357 0.2669030</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.06628516 0.31654289 0.46727798 -0.49122694 -0.05027119 0.77969806</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.2329571 0.1781812 0.3850192 -0.2899029</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.42081207 -0.65798290 0.54387830 -0.42081897</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">y</span><span class="op">$</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"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span> <span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</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">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span> <span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
@ -283,16 +283,16 @@
<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> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and "tobr"</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> and "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> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C S 28 &gt;=4 &gt;=4 0.5873608 0.0000000</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 C R 19 16 2 0.46727798 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 I R 21 &gt;=4 1 0.3850192 0.2023416</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 I R 22 4 4 0.54387830 0.07660032</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 B I 28 2 &gt;=4 0.2836947 0.3036661</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 B S 31 2 4 0.31654289 0.15073509</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 F S 30 &gt;=4 1 0.2669030 0.3204579</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 F I 31 16 4 0.77969806 0.31242008</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 H S 26 2 &gt;=4 0.1781812 0.4091796</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 19 16 2 -0.05027119 0.51754917</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 E S 19 &gt;=4 2 -0.1004357 0.6877965</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 A I 17 8 4 -0.06628516 0.53356314</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 28 1 2 -0.2329571 0.8203179</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 24 &lt;=1 2 -0.42081207 0.88809005</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 J R 18 2 0.5 -0.2899029 0.8772637</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 J R 20 2 0.5 -0.42081897 0.88809695</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 D S 18 &gt;=4 1 -0.3661781 0.9535390</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 D S 18 8 1 -0.49122694 0.95850492</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 A S 27 1 0.5 -0.7116852 1.2990461</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 H S 24 &lt;=1 1 -0.65798290 1.12526088</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span> <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># support for groups</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> <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>

87
reference/microorganisms.codes.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>
@ -199,6 +199,81 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 1101 B_STRPT_VIRI</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 1101 B_STRPT_VIRI</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 1102 B_STRPT_HAEM</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 1102 B_STRPT_HAEM</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 4,899 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 4,899 more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># 'ECO' or 'eco' is the WHONET code for E. coli:</span></span></span>
<span class="r-in"><span><span class="va">microorganisms.codes</span><span class="op">[</span><span class="va">microorganisms.codes</span><span class="op">$</span><span class="va">code</span> <span class="op">==</span> <span class="st">"ECO"</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> code mo </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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> ECO B_ESCHR_COLI</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># and therefore, 'eco' will be understood as E. coli in this package:</span></span></span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_info</a></span><span class="op">(</span><span class="st">"eco"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $mo</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "B_ESCHR_COLI"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $kingdom</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteria"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $phylum</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Pseudomonadota"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $class</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gammaproteobacteria"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $order</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Enterobacterales"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $family</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Enterobacteriaceae"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $genus</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Escherichia"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $species</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "coli"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $subspecies</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ""</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $status</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "accepted"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $synonyms</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> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $gramstain</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gram-negative"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $oxygen_tolerance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "facultative anaerobe"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $url</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "https://lpsn.dsmz.de/species/escherichia-coli"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $ref</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Castellani et al., 1919"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $snomed</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "1095001000112106" "715307006" "737528008" "416989002" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [5] "116397003" "414097009" "414098004" "414099007" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] "414100004" "116395006" "735270003" "116396007" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "83285000" "116394005" "112283007" "710886005" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [17] "710887001" "710888006" "710889003" "414132004" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] "721892009" "416812001" "416740004" "417216001" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "457541006" "710253004" "416530004" "417189006" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [29] "409800005" "713925008" "444771000124108" "838549008" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $lpsn</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "776057"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $gbif</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "11286021"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># works for all AMR functions:</span></span></span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"eco"</span>, ab <span class="op">=</span> <span class="st">"vancomycin"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
</code></pre></div> </code></pre></div>
</div> </div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

12
reference/microorganisms.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/mo_matching_score.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/mo_property.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
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With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/mo_source.html
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@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -91,28 +91,28 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/pca.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

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12
reference/plot.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

12
reference/proportion.html
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@ -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> <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="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -91,28 +91,28 @@ resistance() should be used to calculate resistance, susceptibility() should be
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

44
reference/random.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>
@ -210,42 +210,42 @@
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</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] 1 128 0.01 0.25 256 0.002 &lt;=0.001 0.025 0.005 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.005 64 0.001 1 2 0.005 0.025 0.0625 0.005 0.0625</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 2 256 0.01 4 8 64 4 0.002 0.01 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [11] &gt;=128 2 8 8 16 0.001 0.125 32 0.01 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.0625 128 0.025 2 1 &lt;=0.001 &lt;=0.001</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [21] 2 0.5 0.0625 64 &gt;=128 </span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</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] 34 24 46 29 29 7 27 50 49 28 49 6 14 35 40 14 33 47 37 25 28 41 6 48 47</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 7 49 8 41 20 28 40 16 41 42 41 45 36 11 50 25 44 9 24 42 38 49 41 45 9</span>
<span class="r-in"><span><span class="fu">random_sir</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">random_sir</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 'sir'</span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R I R S S R I R I S I I S R R I I R S I S I R S I</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] R R S S R I R I I R S S I I I I I I I S I I S I S</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span> <span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span> <span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span> <span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</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 0.25 0.25 4 0.025 8 128 0.025 32 0.002 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.002 64 0.005 0.001 0.5 0.025 2 0.005 0.0625 0.005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.005 64 0.002 4 0.01 4 0.001 0.01 4 0.0625</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.125 8 2 0.125 16 0.0625 0.001 0.005 0.005 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.005 4 2 1 128 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.005 64 0.005 0.025 0.0625</span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span> <span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</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] 8 4 4 2 &gt;=16 &gt;=16 2 4 8 8 &gt;=16 8 2 2 4 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 1 &gt;=32 2 8 1 4 16 1 8 1 1 &gt;=32 16 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] 2 4 2 &gt;=16 2 2 &gt;=16 &lt;=1 2 4 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [16] 16 2 &gt;=32 1 8 8 1 4 1 16 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span> <span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</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] 0.25 2 1 0.25 4 1 0.25 &lt;=0.125 &lt;=0.125</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 &gt;=8 0.5 2 1 1 0.25 0.125 4 &gt;=8 &gt;=8 0.125</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.25 4 4 &lt;=0.125 4 0.25 1 &lt;=0.125 1 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [13] &gt;=8 &gt;=8 4 2 0.25 &gt;=8 &gt;=8 4 &gt;=8 4 0.125 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 2 2 0.25 0.25 4 &lt;=0.125 1 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [25] 2 </span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span> <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</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] 44 39 37 49 11 40 17 49 10 37 15 20 22 47 41 29 39 15 35 49 11 37 40 41 44</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 46 14 10 45 47 37 40 15 19 44 16 20 26 46 43 12 10 22 43 49 48 47 13 15 35</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span> <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</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] 16 15 15 12 14 17 16 15 11 14 16 15 14 14 12 12 12 15 13 16 12 15 12 14 15</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 11 17 14 15 13 17 17 12 17 14 16 16 11 12 16 12 13 11 15 12 17 15 11 14 11</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span> <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</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] 24 15 15 22 27 15 20 17 22 22 15 18 21 17 21 25 20 24 17 17 27 19 19 26 16</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 24 20 20 23 24 25 21 16 27 16 21 21 27 23 23 23 20 15 23 25 21 17 21 16 20</span>
<span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div> </code></pre></div>
</div> </div>

12
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> <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="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

14
reference/skewness.html
View File

@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -91,28 +91,28 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>
@ -198,7 +198,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<div class="section level2"> <div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.04805572</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.03385563</span>
</code></pre></div> </code></pre></div>
</div> </div>
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12
reference/translate.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9022</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9023</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,28 +89,28 @@
</li> </li>
<li class="nav-item dropdown"> <li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs"> <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
With other pkgs With other pkgs
</a> </a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs"> <div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; data.table AMR &amp; data.table
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; tidymodels AMR &amp; tidymodels
</a> </a>
<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
AMR &amp; base R AMR &amp; base R
</a> </a>

2
search.json
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