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@@ -116,28 +116,28 @@
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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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@@ -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>
articles/EUCAST.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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@@ -118,28 +118,28 @@
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With other pkgs With other pkgs
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AMR &amp; base R AMR &amp; base R
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articles/MDR.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 @@
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AMR &amp; base R AMR &amp; base R
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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>
articles/PCA.html
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@@ -38,7 +38,7 @@
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@@ -118,28 +118,28 @@
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articles/WHONET.html
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<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>
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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@@ -89,28 +89,28 @@
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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
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@@ -159,9 +159,9 @@
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<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>
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
reference/AMR-deprecated.html
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reference/AMR-options.html
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AMR &amp; base R AMR &amp; base R
</a> </a>
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>
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@@ -103,28 +103,28 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
</li> </li>
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AMR &amp; dplyr/tidyverse AMR &amp; dplyr/tidyverse
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@@ -89,28 +89,28 @@
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@@ -10,7 +10,7 @@
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@@ -89,28 +89,28 @@
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@@ -89,28 +89,28 @@
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@@ -89,28 +89,28 @@
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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>
reference/add_custom_antimicrobials.html
+6 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/add_custom_microorganisms.html
+6 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/age.html
+16 -16
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>
reference/age_groups.html
+6 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/antibiogram.html
+6 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/antibiotic_class_selectors.html
+10 -10
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>
reference/antibiotics.html
+6 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/as.ab.html
+6 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/as.av.html
+6 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/as.disk.html
+6 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/as.mic.html
+6 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/as.mo.html
+6 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/as.sir.html
+16 -16
View File
@@ -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>
reference/atc_online.html
+6 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/av_from_text.html
+6 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/av_property.html
+6 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/availability.html
+6 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/bug_drug_combinations.html
+6 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/clinical_breakpoints.html
+6 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/count.html
+6 -6
View File
@@ -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>
reference/custom_eucast_rules.html
+6 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/dosage.html
+6 -6
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/eucast_rules.html
+6 -6
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>
reference/example_isolates.html
+6 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/example_isolates_unclean.html
+6 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/first_isolate.html
+6 -6
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>
reference/g.test.html
+6 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/get_episode.html
+56 -58
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>
@@ -405,18 +403,18 @@
<span class="r-in"><span><span class="op">}</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</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> <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>
reference/ggplot_pca.html
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<span class="fa fa-layer-plus"></span> <span class="fa fa-layer-group"></span>
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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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reference/ggplot_sir.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>
<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>
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<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
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AMR &amp; base R AMR &amp; base R
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reference/guess_ab_col.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 @@
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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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<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
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AMR &amp; base R AMR &amp; base R
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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>
<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
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<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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<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
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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
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reference/intrinsic_resistant.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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@@ -89,28 +89,28 @@
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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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<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 @@
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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">
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AMR &amp; base R AMR &amp; base R
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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 @@
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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">
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With other pkgs With other pkgs
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<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">
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<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
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<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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<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../articles/other_pkg.html">
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AMR &amp; base R AMR &amp; base R
</a> </a>
reference/key_antimicrobials.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">
@@ -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">
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<a class="dropdown-item" href="../articles/other_pkg.html"> <a class="dropdown-item" href="../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">
@@ -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>
@@ -199,9 +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>
reference/like.html
+6 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/mdro.html
+6 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/mean_amr_distance.html
+39 -39
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>
reference/microorganisms.codes.html
+81 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
reference/microorganisms.html
+6 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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>
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AMR &amp; base R AMR &amp; base R
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@@ -89,28 +89,28 @@
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@@ -89,28 +89,28 @@
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@@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@@ -89,28 +89,28 @@
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@@ -89,28 +89,28 @@
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AMR &amp; base R AMR &amp; base R
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reference/proportion.html
+6 -6
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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>
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@@ -91,28 +91,28 @@ resistance() should be used to calculate resistance, susceptibility() should be
</li> </li>
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reference/random.html
+22 -22
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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>
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@@ -89,28 +89,28 @@
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@@ -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>
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+6 -6
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@@ -10,7 +10,7 @@
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@@ -89,28 +89,28 @@
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+7 -7
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@@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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@@ -91,28 +91,28 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
</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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@@ -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>
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search.json
+1 -1
View File
@@ -1 +1 @@
[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) reliable data thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations SIR values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables. AMR package contains data set example_isolates_unclean, might look data users extracted laboratory systems: AMR data analysis, like microorganism column contain valid, --date taxonomy, antibiotic columns cleaned SIR values well.","code":"library(dplyr) library(ggplot2) library(AMR) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\")) example_isolates_unclean #> # A tibble: 3,000 × 8 #> patient_id hospital date bacteria AMX AMC CIP GEN #> <chr> <chr> <date> <chr> <chr> <chr> <chr> <chr> #> 1 J3 A 2012-11-21 E. coli R I S S #> 2 R7 A 2018-04-03 K. pneumoniae R I S S #> 3 P3 A 2014-09-19 E. coli R S S S #> 4 P10 A 2015-12-10 E. coli S I S S #> 5 B7 A 2015-03-02 E. coli S S S S #> 6 W3 A 2018-03-31 S. aureus R S R S #> 7 J8 A 2016-06-14 E. coli R S S S #> 8 M3 A 2015-10-25 E. coli R S S S #> 9 J3 A 2019-06-19 E. coli S S S S #> 10 G6 A 2015-04-27 S. aureus S S S S #> # ℹ 2,990 more rows # we will use 'our_data' as the data set name for this tutorial our_data <- example_isolates_unclean"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"taxonomy-of-microorganisms","dir":"Articles","previous_headings":"Preparation","what":"Taxonomy of microorganisms","title":"How to conduct AMR data analysis","text":".mo(), users can transform arbitrary microorganism names codes current taxonomy. AMR package contains --date taxonomic data. specific, currently included data retrieved 11 Dec 2022. codes AMR packages come .mo() short, still human readable. importantly, .mo() supports kinds input: first character codes denote taxonomic kingdom, Bacteria (B), Fungi (F), Protozoa (P). AMR package also contain functions directly retrieve taxonomic properties, name, genus, species, family, order, even Gram-stain. start mo_ use .mo() internally, still arbitrary user input can used: Now can thus clean data: Apparently, uncertainty translation taxonomic codes. Let’s check : ’s good.","code":"as.mo(\"Klebsiella pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"K. pneumoniae\") #> ClLine truncated [{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) reliable data thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations SIR values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables. AMR package contains data set example_isolates_unclean, might look data users extracted laboratory systems: AMR data analysis, like microorganism column contain valid, --date taxonomy, antibiotic columns cleaned SIR values well.","code":"library(dplyr) library(ggplot2) library(AMR) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\")) example_isolates_unclean #> # A tibble: 3,000 × 8 #> patient_id hospital date bacteria AMX AMC CIP GEN #> <chr> <chr> <date> <chr> <chr> <chr> <chr> <chr> #> 1 J3 A 2012-11-21 E. coli R I S S #> 2 R7 A 2018-04-03 K. pneumoniae R I S S #> 3 P3 A 2014-09-19 E. coli R S S S #> 4 P10 A 2015-12-10 E. coli S I S S #> 5 B7 A 2015-03-02 E. coli S S S S #> 6 W3 A 2018-03-31 S. aureus R S R S #> 7 J8 A 2016-06-14 E. coli R S S S #> 8 M3 A 2015-10-25 E. coli R S S S #> 9 J3 A 2019-06-19 E. coli S S S S #> 10 G6 A 2015-04-27 S. aureus S S S S #> # ℹ 2,990 more rows # we will use 'our_data' as the data set name for this tutorial our_data <- example_isolates_unclean"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"taxonomy-of-microorganisms","dir":"Articles","previous_headings":"Preparation","what":"Taxonomy of microorganisms","title":"How to conduct AMR data analysis","text":".mo(), users can transform arbitrary microorganism names codes current taxonomy. AMR package contains --date taxonomic data. specific, currently included data retrieved 11 Dec 2022. codes AMR packages come .mo() short, still human readable. importantly, .mo() supports kinds input: first character codes denote taxonomic kingdom, Bacteria (B), Fungi (F), Protozoa (P). AMR package also contain functions directly retrieve taxonomic properties, name, genus, species, family, order, even Gram-stain. start mo_ use .mo() internally, still arbitrary user input can used: Now can thus clean data: Apparently, uncertainty translation taxonomic codes. Let’s check : ’s good.","code":"as.mo(\"Klebsiella pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"K. pneumoniae\") #> ClLine truncated