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@@ -32,7 +32,7 @@
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<a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</small>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</small>
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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">
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</small>
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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">
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@@ -92,7 +92,7 @@
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website update since they are based on randomly created values and the
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page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
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Markdown</a>. However, the methodology remains unchanged. This page was
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generated on 08 April 2025.</p>
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generated on 12 April 2025.</p>
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<div class="section level2">
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<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
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</h2>
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@@ -148,21 +148,21 @@ make the structure of your data generally look like this:</p>
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</tr></thead>
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<tbody>
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<tr class="odd">
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<td align="center">2025-04-08</td>
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<td align="center">2025-04-12</td>
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<td align="center">abcd</td>
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<td align="center">Escherichia coli</td>
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<td align="center">S</td>
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<td align="center">S</td>
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</tr>
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<tr class="even">
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<td align="center">2025-04-08</td>
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<td align="center">2025-04-12</td>
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<td align="center">abcd</td>
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<td align="center">Escherichia coli</td>
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<td align="center">S</td>
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<td align="center">R</td>
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</tr>
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<tr class="odd">
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<td align="center">2025-04-08</td>
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<td align="center">2025-04-12</td>
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<td align="center">efgh</td>
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<td align="center">Escherichia coli</td>
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<td align="center">R</td>
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@@ -183,7 +183,7 @@ for cleaning data and creating frequency tables.</p>
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<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
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<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span>
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<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://www.amr-for-r.org/" class="external-link">AMR</a></span><span class="op">)</span></span>
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<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
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<span></span>
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<span><span class="co"># (if not yet installed, install with:)</span></span>
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<span><span class="co"># install.packages(c("dplyr", "ggplot2", "AMR"))</span></span></code></pre></div>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</small>
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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">
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@@ -31,7 +31,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</small>
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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">
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@@ -133,7 +133,7 @@ train, and evaluate the model.</li>
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package.</p>
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<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="co"># Load required libraries</span></span>
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<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://www.amr-for-r.org/" class="external-link">AMR</a></span><span class="op">)</span> <span class="co"># For AMR data analysis</span></span>
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<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span> <span class="co"># For AMR data analysis</span></span>
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<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://tidymodels.tidymodels.org" class="external-link">tidymodels</a></span><span class="op">)</span> <span class="co"># For machine learning workflows, and data manipulation (dplyr, tidyr, ...)</span></span></code></pre></div>
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<p>Prepare the data:</p>
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<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
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@@ -455,7 +455,7 @@ model.</li>
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into a structured time-series format.</p>
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<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="co"># Load required libraries</span></span>
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<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://www.amr-for-r.org/" class="external-link">AMR</a></span><span class="op">)</span></span>
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<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
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<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://tidymodels.tidymodels.org" class="external-link">tidymodels</a></span><span class="op">)</span></span>
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<span></span>
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<span><span class="co"># Transform dataset</span></span>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</small>
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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">
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
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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">
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+2
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</small>
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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">
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@@ -100,7 +100,7 @@ is currently being developed.</strong></p>
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<p>For PCA, we need to transform our AMR data first. This is what the
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<code>example_isolates</code> data set in this package looks like:</p>
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<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://www.amr-for-r.org/" class="external-link">AMR</a></span><span class="op">)</span></span>
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<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
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<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
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<span><span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span>
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<span><span class="co">#> Rows: 2,000</span></span>
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@@ -31,7 +31,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</small>
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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">
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@@ -113,7 +113,7 @@ yet, I suggest you read about it on their website: <a href="https://www.tidyvers
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<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span> <span class="co"># part of tidyverse</span></span>
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<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span> <span class="co"># part of tidyverse</span></span>
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<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://www.amr-for-r.org/" class="external-link">AMR</a></span><span class="op">)</span> <span class="co"># this package</span></span>
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<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span> <span class="co"># this package</span></span>
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<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/cleaner/" class="external-link">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></span></code></pre></div>
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<p>We will have to transform some variables to simplify and automate the
|
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analysis:</p>
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@@ -31,7 +31,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</small>
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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">
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@@ -81,7 +81,7 @@
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<main id="main" class="col-md-9"><div class="page-header">
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<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
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<h4 data-toc-skip class="date">08 April 2025</h4>
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<h4 data-toc-skip class="date">12 April 2025</h4>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
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<div class="d-none name"><code>datasets.Rmd</code></div>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</small>
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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">
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</small>
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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">
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@@ -91,19 +91,18 @@
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<p>Note: to keep the package size as small as possible, we only include
|
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this vignette on CRAN. You can read more vignettes on our website about
|
||||
how to conduct AMR data analysis, determine MDROs, find explanation of
|
||||
EUCAST and CLSI breakpoints, and much more: <a href="https://www.amr-for-r.org/articles/" class="external-link uri">https://www.amr-for-r.org/articles/</a>.</p>
|
||||
EUCAST and CLSI breakpoints, and much more: <a href="https://amr-for-r.org/articles/" class="uri">https://amr-for-r.org/articles/</a>.</p>
|
||||
<hr>
|
||||
<p>The <code>AMR</code> package is a <a href="https://www.amr-for-r.org/" class="external-link">free and open-source</a> R package
|
||||
with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero
|
||||
<p>The <code>AMR</code> package is a <a href="https://amr-for-r.org/">free and open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero
|
||||
dependencies</a> to simplify the analysis and prediction of
|
||||
Antimicrobial Resistance (AMR) and to work with microbial and
|
||||
antimicrobial data and properties, by using evidence-based methods.
|
||||
<strong>Our aim is to provide a standard</strong> for clean and
|
||||
reproducible AMR data analysis, that can therefore empower
|
||||
epidemiological analyses to continuously enable surveillance and
|
||||
treatment evaluation in any setting. <a href="https://www.amr-for-r.org/authors.html" class="external-link">Many different
|
||||
researchers</a> from around the globe are continually helping us to make
|
||||
this a successful and durable project!</p>
|
||||
treatment evaluation in any setting. <a href="https://amr-for-r.org/authors.html">Many different researchers</a>
|
||||
from around the globe are continually helping us to make this a
|
||||
successful and durable project!</p>
|
||||
<p>This work was published in the Journal of Statistical Software
|
||||
(Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">DOI
|
||||
10.18637/jss.v104.i03</a>) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI
|
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@@ -165,25 +164,25 @@ interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are
|
||||
publicly and freely available. We continually export our data sets to
|
||||
formats for use in R, SPSS, Stata and Excel. We also supply flat files
|
||||
that are machine-readable and suitable for input in any software
|
||||
program, such as laboratory information systems. Please find <a href="https://www.amr-for-r.org/articles/datasets.html" class="external-link">all download
|
||||
links on our website</a>, which is automatically updated with every code
|
||||
program, such as laboratory information systems. Please find <a href="https://amr-for-r.org/articles/datasets.html">all download links
|
||||
on our website</a>, which is automatically updated with every code
|
||||
change.</p>
|
||||
<p>This R package was created for both routine data analysis and
|
||||
academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration
|
||||
with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe
|
||||
Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>, and
|
||||
is being <a href="https://www.amr-for-r.org/news/" class="external-link">actively and durably
|
||||
is being <a href="https://amr-for-r.org/news/">actively and durably
|
||||
maintained</a> by two public healthcare organisations in the
|
||||
Netherlands.</p>
|
||||
<hr>
|
||||
<p><small> This AMR package for R is free, open-source software and
|
||||
licensed under the <a href="https://www.amr-for-r.org/LICENSE-text.html" class="external-link">GNU General Public
|
||||
License v2.0 (GPL-2)</a>. These requirements are consequently legally
|
||||
binding: modifications must be released under the same license when
|
||||
distributing the package, changes made to the code must be documented,
|
||||
source code must be made available when the package is distributed, and
|
||||
a copy of the license and copyright notice must be included with the
|
||||
package. </small></p>
|
||||
licensed under the <a href="https://amr-for-r.org/LICENSE-text.html">GNU
|
||||
General Public License v2.0 (GPL-2)</a>. These requirements are
|
||||
consequently legally binding: modifications must be released under the
|
||||
same license when distributing the package, changes made to the code
|
||||
must be documented, source code must be made available when the package
|
||||
is distributed, and a copy of the license and copyright notice must be
|
||||
included with the package. </small></p>
|
||||
</main>
|
||||
</div>
|
||||
|
||||
|
||||
+1
-1
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</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">
|
||||
|
||||
@@ -25,7 +25,7 @@
|
||||
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||
# #
|
||||
# Visit our website for the full manual and a complete tutorial about #
|
||||
# how to conduct AMR data analysis: https://amr-for-r.org/ #
|
||||
# how to conduct AMR data analysis: https://amr-for-r.org #
|
||||
# ==================================================================== #
|
||||
*/
|
||||
|
||||
|
||||
@@ -25,7 +25,7 @@
|
||||
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||
# #
|
||||
# Visit our website for the full manual and a complete tutorial about #
|
||||
# how to conduct AMR data analysis: https://amr-for-r.org/ #
|
||||
# how to conduct AMR data analysis: https://amr-for-r.org #
|
||||
# ==================================================================== #
|
||||
*/
|
||||
|
||||
@@ -110,9 +110,9 @@ $(document).ready(function() {
|
||||
// add doctoral titles to authors
|
||||
function doct_tit(x) {
|
||||
if (typeof(x) != "undefined") {
|
||||
x = x.replace(/Author, maintainer/g, "Principal developer");
|
||||
x = x.replace(/Author, maintainer/g, "Project founder and lead developer");
|
||||
x = x.replace(/Author, contributor/g, "Package maintainer");
|
||||
x = x.replace(/Thesis advisor/g, "(former) Doctoral advisor");
|
||||
x = x.replace(/Thesis advisor/g, "Former doctoral advisor");
|
||||
// contributors
|
||||
x = x.replace("Alex", "Prof. Alex");
|
||||
x = x.replace("Andrew", "Dr. Andrew");
|
||||
|
||||
+13
-10
@@ -34,7 +34,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</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">
|
||||
@@ -132,7 +132,7 @@
|
||||
<p>One of the most powerful functions of this package, aside from calculating and plotting AMR, is selecting and filtering based on antimicrobial columns. This can be done using the so-called <a href="https://amr-for-r.org/reference/antimicrobial_selectors.html">antimicrobial selectors</a>, which work in base R, <code>dplyr</code> and <code>data.table</code>.</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span></span>
|
||||
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://www.amr-for-r.org/" class="external-link">AMR</a></span><span class="op">)</span></span>
|
||||
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
|
||||
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
@@ -441,7 +441,7 @@
|
||||
<p>The <code>AMR</code> package allows interpretation of MIC and disk diffusion values based on CLSI and EUCAST. Moreover, the <code>ggplot2</code> package is extended with new scale functions, to allow plotting of log2-distributed MIC values and SIR values.</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span>
|
||||
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://www.amr-for-r.org/" class="external-link">AMR</a></span><span class="op">)</span></span>
|
||||
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># generate some random values</span></span>
|
||||
<span><span class="va">some_mic_values</span> <span class="op"><-</span> <span class="fu"><a href="reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
|
||||
@@ -466,7 +466,7 @@
|
||||
<span> <span class="co"># NEW scale function: write out S/I/R in any of the 20 supported languages</span></span>
|
||||
<span> <span class="co"># and set colourblind-friendly colours</span></span>
|
||||
<span> <span class="fu"><a href="reference/plot.html">scale_colour_sir</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
|
||||
<p><a href="./reference/plotting.html" title="Plotting Helpers for AMR Data Analysis"> <img src="./plot_readme.png" style="max-width: 600px;"></a></p>
|
||||
<p><a href="./reference/plotting.html" title="Plotting Helpers for AMR Data Analysis"> <img src="./plot_readme.png" style="width: 600px; max-width: 100%;"></a></p>
|
||||
</div>
|
||||
<div class="section level4">
|
||||
<h4 id="calculating-resistance-per-group">Calculating resistance per group<a class="anchor" aria-label="anchor" href="#calculating-resistance-per-group"></a>
|
||||
@@ -515,7 +515,7 @@
|
||||
</table>
|
||||
<p>Or use <a href="https://amr-for-r.org/reference/antimicrobial_selectors.html">antimicrobial selectors</a> to select a series of antibiotic columns:</p>
|
||||
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://www.amr-for-r.org/" class="external-link">AMR</a></span><span class="op">)</span></span>
|
||||
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
|
||||
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="va">out</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
@@ -691,22 +691,25 @@
|
||||
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></span></code></pre></div>
|
||||
<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> > <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
|
||||
<p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
|
||||
<p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest beta version.</p>
|
||||
</div>
|
||||
<div class="section level4">
|
||||
<h4 id="latest-development-version">Latest development version<a class="anchor" aria-label="anchor" href="#latest-development-version"></a>
|
||||
<h4 id="latest-beta-version">Latest beta version<a class="anchor" aria-label="anchor" href="#latest-beta-version"></a>
|
||||
</h4>
|
||||
<p><a href="https://github.com/msberends/AMR/actions/workflows/check-old-tinytest.yaml" class="external-link"><img src="https://github.com/msberends/AMR/actions/workflows/check-old-tinytest.yaml/badge.svg?branch=main" alt="check-old"></a> <a href="https://github.com/msberends/AMR/actions/workflows/check-current-testthat.yaml" class="external-link"><img src="https://github.com/msberends/AMR/actions/workflows/check-current-testthat.yaml/badge.svg?branch=main" alt="check-recent"></a> <a href="https://www.codefactor.io/repository/github/msberends/amr" class="external-link"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://codecov.io/gh/msberends/AMR/branch/main/graph/badge.svg" alt="Codecov"></a></p>
|
||||
<p>Please read our <a href="https://github.com/msberends/AMR/wiki/Developer-Guideline" class="external-link">Developer Guideline here</a>.</p>
|
||||
<p>To install the latest and unpublished development version:</p>
|
||||
<p>To install the latest and unpublished beta version:</p>
|
||||
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span>, repos <span class="op">=</span> <span class="st">"beta.amr-for-r.org"</span><span class="op">)</span></span></code></pre></div>
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span>, repos <span class="op">=</span> <span class="st">"beta.amr-for-r.org"</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># if this does not work, try to install directly from GitHub using the 'remotes' package:</span></span>
|
||||
<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu">install_github</span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></span></code></pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="get-started">Get started<a class="anchor" aria-label="anchor" href="#get-started"></a>
|
||||
</h3>
|
||||
<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click a link in the <a href="https://amr-for-r.org/articles/">‘How to’ menu</a>.</p>
|
||||
<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click a link in the <a href="./articles/">‘How to’ menu</a>.</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="partners">Partners<a class="anchor" aria-label="anchor" href="#partners"></a>
|
||||
|
||||
+12
-12
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</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">
|
||||
@@ -49,24 +49,24 @@
|
||||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
<h2 class="pkg-version" data-toc-text="2.1.1.9235" id="amr-2119235">AMR 2.1.1.9235<a class="anchor" aria-label="anchor" href="#amr-2119235"></a></h2>
|
||||
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://www.amr-for-r.org/" class="external-link">the instructions here</a>.)</em></p>
|
||||
<h2 class="pkg-version" data-toc-text="2.1.1.9236" id="amr-2119236">AMR 2.1.1.9236<a class="anchor" aria-label="anchor" href="#amr-2119236"></a></h2>
|
||||
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://amr-for-r.org/#get-this-package">the instructions here</a>.)</em></p>
|
||||
<div class="section level5">
|
||||
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9235">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9235"></a></h5>
|
||||
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9236">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9236"></a></h5>
|
||||
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="breaking-2-1-1-9235">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9235"></a></h3>
|
||||
<h3 id="breaking-2-1-1-9236">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9236"></a></h3>
|
||||
<ul><li>Dataset <code>antibiotics</code> has been renamed to <code>antimicrobials</code> as the data set contains more than just antibiotics. Using <code>antibiotics</code> will still work, but now returns a warning.</li>
|
||||
<li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over two years ago.</li>
|
||||
<li>Function <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code> is now deprecated and will be removed in a future version. Use the <code>tidymodels</code> framework instead, for which we <a href="https://www.amr-for-r.org/articles/AMR_with_tidymodels.html" class="external-link">wrote a basic introduction</a>.</li>
|
||||
<li>Function <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code> is now deprecated and will be removed in a future version. Use the <code>tidymodels</code> framework instead, for which we <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">wrote a basic introduction</a>.</li>
|
||||
</ul></div>
|
||||
<div class="section level3">
|
||||
<h3 id="new-2-1-1-9235">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9235"></a></h3>
|
||||
<h3 id="new-2-1-1-9236">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9236"></a></h3>
|
||||
<ul><li>
|
||||
<strong>One Health implementation</strong>
|
||||
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
|
||||
<li>The <code>clinical_breakpoints</code> data set contains all these breakpoints, and can be downloaded on our <a href="https://www.amr-for-r.org/articles/datasets.html" class="external-link">download page</a>.</li>
|
||||
<li>The <code>clinical_breakpoints</code> data set contains all these breakpoints, and can be downloaded on our <a href="https://amr-for-r.org/articles/datasets.html">download page</a>.</li>
|
||||
<li>The (new) <code>antimicrobials</code> data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well.</li>
|
||||
<li>
|
||||
<code><a href="../reference/ab_property.html">ab_atc()</a></code> now supports ATC codes of veterinary antibiotics (that all start with “Q”)</li>
|
||||
@@ -106,7 +106,7 @@
|
||||
</ul></li>
|
||||
<li>
|
||||
<strong>Support for <code>tidymodels</code></strong>
|
||||
<ul><li>All antimicrobial selectors (such as <code><a href="../reference/antimicrobial_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antimicrobial_selectors.html">betalactams()</a></code>) are now supported in <code>tidymodels</code> packages such as <code>recipe</code> and <code>parsnip</code>. See for more info <a href="https://www.amr-for-r.org/articles/AMR_with_tidymodels.html" class="external-link">our tutorial</a> on using these AMR functions for predictive modelling.</li>
|
||||
<ul><li>All antimicrobial selectors (such as <code><a href="../reference/antimicrobial_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antimicrobial_selectors.html">betalactams()</a></code>) are now supported in <code>tidymodels</code> packages such as <code>recipe</code> and <code>parsnip</code>. See for more info <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">our tutorial</a> on using these AMR functions for predictive modelling.</li>
|
||||
</ul></li>
|
||||
<li>
|
||||
<strong>Other</strong>
|
||||
@@ -116,7 +116,7 @@
|
||||
</ul></li>
|
||||
</ul></div>
|
||||
<div class="section level3">
|
||||
<h3 id="changed-2-1-1-9235">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9235"></a></h3>
|
||||
<h3 id="changed-2-1-1-9236">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9236"></a></h3>
|
||||
<ul><li>SIR interpretation
|
||||
<ul><li>It is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
|
||||
<li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
|
||||
@@ -195,7 +195,7 @@
|
||||
<li>Added console colours support of <code>sir</code> class for Positron</li>
|
||||
</ul></div>
|
||||
<div class="section level3">
|
||||
<h3 id="other-2-1-1-9235">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9235"></a></h3>
|
||||
<h3 id="other-2-1-1-9236">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9236"></a></h3>
|
||||
<ul><li>Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way</li>
|
||||
<li>Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations</li>
|
||||
<li>Added Prof. Kat Holt, Dr. Jane Hawkey, and Dr. Natacha Couto as contributors for their many suggestions, ideas and bugfixes</li>
|
||||
@@ -204,7 +204,7 @@
|
||||
<li>Stopped support for SAS (<code>.xpt</code>) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.</li>
|
||||
</ul></div>
|
||||
<div class="section level3">
|
||||
<h3 id="older-versions-2-1-1-9235">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9235"></a></h3>
|
||||
<h3 id="older-versions-2-1-1-9236">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9236"></a></h3>
|
||||
<p>This changelog only contains changes from AMR v3.0 (March 2025) and later.</p>
|
||||
<ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li>
|
||||
<li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li>
|
||||
|
||||
+1
-1
@@ -11,7 +11,7 @@ articles:
|
||||
PCA: PCA.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
WHONET: WHONET.html
|
||||
last_built: 2025-04-08T15:07Z
|
||||
last_built: 2025-04-12T15:54Z
|
||||
urls:
|
||||
reference: https://amr-for-r.org/reference
|
||||
article: https://amr-for-r.org/articles
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</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">
|
||||
|
||||
+2
-2
@@ -21,7 +21,7 @@ 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>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</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">
|
||||
@@ -104,7 +104,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
|
||||
<div class="dont-index"><p>Useful links:</p><ul><li><p><a href="https://www.amr-for-r.org/" class="external-link">https://www.amr-for-r.org/</a></p></li>
|
||||
<div class="dont-index"><p>Useful links:</p><ul><li><p><a href="https://amr-for-r.org">https://amr-for-r.org</a></p></li>
|
||||
<li><p><a href="https://github.com/msberends/AMR" class="external-link">https://github.com/msberends/AMR</a></p></li>
|
||||
<li><p>Report bugs at <a href="https://github.com/msberends/AMR/issues" class="external-link">https://github.com/msberends/AMR/issues</a></p></li>
|
||||
</ul></div>
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</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">
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</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">
|
||||
|
||||
+11
-11
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</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">
|
||||
@@ -112,16 +112,16 @@
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> birth_date age age_exact age_at_y2k</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1999-06-30 25 25.77260 0</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1968-01-29 57 57.18904 31</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1965-12-05 59 59.33973 34</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1980-03-01 45 45.10411 19</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1949-11-01 75 75.43288 50</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1947-02-14 78 78.14521 52</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1940-02-19 85 85.13151 59</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1988-01-10 37 37.24110 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1997-08-27 27 27.61370 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1978-01-26 47 47.19726 21</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1999-06-30 25 25.78356 0</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1968-01-29 57 57.20000 31</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1965-12-05 59 59.35068 34</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1980-03-01 45 45.11507 19</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1949-11-01 75 75.44384 50</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1947-02-14 78 78.15616 52</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1940-02-19 85 85.14247 59</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1988-01-10 37 37.25205 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1997-08-27 27 27.62466 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1978-01-26 47 47.20822 21</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9235</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9236</small>
|
||||
|
||||
|
||||
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||||
|
||||
@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
|
||||
|
||||
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|
||||
|
||||
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||||
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||||
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||||
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||||
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||||
@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&gt;%
|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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|
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|
||||
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|
||||
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||||
@@ -7,7 +7,7 @@
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||||
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||||
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||||
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||||
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||||
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||||
@@ -7,7 +7,7 @@
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||||
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||||
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||||
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||||
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@@ -7,7 +7,7 @@
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||||
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|
||||
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||||
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|
||||
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@@ -7,7 +7,7 @@
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||||
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||||
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||||
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||||
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||||
|
||||
+10
-10
@@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
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||||
@@ -842,16 +842,16 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 65 × 17</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> datetime index method ab_given mo_given host_given input_given</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2025-04-08 <span style="color: #949494;">15:07:44</span> 1 DISK ampicillin Strep pneu human 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2025-04-08 <span style="color: #949494;">15:07:44</span> 1 DISK AMP Escherich… human 20 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2025-04-08 <span style="color: #949494;">15:07:44</span> 1 DISK AMP Escherich… human 20 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2025-04-12 <span style="color: #949494;">15:55:26</span> 1 DISK ampicillin Strep pneu human 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2025-04-12 <span style="color: #949494;">15:55:26</span> 1 DISK AMP Escherich… human 20 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2025-04-12 <span style="color: #949494;">15:55:26</span> 1 DISK AMP Escherich… human 20 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2025-04-08 <span style="color: #949494;">15:07:45</span> 1 DISK GEN Escherich… human 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2025-04-08 <span style="color: #949494;">15:07:45</span> 1 DISK TOB Escherich… human 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2025-04-08 <span style="color: #949494;">15:07:45</span> 1 MIC AMX B_STRPT_P… human 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2025-04-08 <span style="color: #949494;">15:07:46</span> 1 MIC AMX B_STRPT_P… human 0.01 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2025-04-08 <span style="color: #949494;">15:07:46</span> 2 MIC AMX B_STRPT_P… human 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2025-04-08 <span style="color: #949494;">15:07:46</span> 3 MIC AMX B_STRPT_P… human 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2025-04-12 <span style="color: #949494;">15:55:27</span> 1 DISK GEN Escherich… human 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2025-04-12 <span style="color: #949494;">15:55:27</span> 1 DISK TOB Escherich… human 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2025-04-12 <span style="color: #949494;">15:55:27</span> 1 MIC AMX B_STRPT_P… human 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2025-04-12 <span style="color: #949494;">15:55:28</span> 1 MIC AMX B_STRPT_P… human 0.01 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2025-04-12 <span style="color: #949494;">15:55:28</span> 2 MIC AMX B_STRPT_P… human 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2025-04-12 <span style="color: #949494;">15:55:28</span> 3 MIC AMX B_STRPT_P… human 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 55 more rows</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 10 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
|
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[{"path":"https://amr-for-r.org/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://amr-for-r.org/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://amr-for-r.org/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://amr-for-r.org/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 24 Jun 2024. 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\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"KLELine truncated
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[{"path":"https://amr-for-r.org/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://amr-for-r.org/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://amr-for-r.org/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://amr-for-r.org/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 24 Jun 2024. 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\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"KLELine truncated
|
||||
Reference in new issue
Block a user