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404.html
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404.html
@ -30,7 +30,7 @@
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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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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@ -7,7 +7,7 @@
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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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="">2.1.1.9094</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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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@ -29,7 +29,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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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<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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@ -87,7 +87,7 @@
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website update since they are based on randomly created values and the
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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
|
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
|
Markdown</a>. However, the methodology remains unchanged. This page was
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||||||
generated on 10 October 2024.</p>
|
generated on 15 October 2024.</p>
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||||||
<div class="section level2">
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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 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
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</h2>
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</h2>
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@ -143,21 +143,21 @@ make the structure of your data generally look like this:</p>
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</tr></thead>
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</tr></thead>
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<tbody>
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<tbody>
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<tr class="odd">
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<tr class="odd">
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<td align="center">2024-10-10</td>
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<td align="center">2024-10-15</td>
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<td align="center">abcd</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">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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<td align="center">S</td>
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<td align="center">S</td>
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</tr>
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</tr>
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<tr class="even">
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<tr class="even">
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<td align="center">2024-10-10</td>
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<td align="center">2024-10-15</td>
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<td align="center">abcd</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">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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<td align="center">R</td>
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<td align="center">R</td>
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</tr>
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</tr>
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<tr class="odd">
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<tr class="odd">
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<td align="center">2024-10-10</td>
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<td align="center">2024-10-15</td>
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<td align="center">efgh</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">Escherichia coli</td>
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<td align="center">R</td>
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<td align="center">R</td>
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@ -29,7 +29,7 @@
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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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</small>
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||||||
|
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||||||
|
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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">
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@ -86,203 +86,562 @@
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<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>
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</h2>
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<p>The <code>AMR</code> package for R is an incredible tool for
|
<p>The <code>AMR</code> package for R is a powerful tool for
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antimicrobial resistance (AMR) data analysis, providing extensive
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antimicrobial resistance (AMR) analysis. It provides extensive features
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functionality for working with microbial and antimicrobial properties.
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for handling microbial and antimicrobial data. However, for those who
|
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But what if you’re working in Python and still want to benefit from the
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work primarily in Python, we now have a more intuitive option available:
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robust features of <code>AMR</code>?</p>
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the <code>AMR</code> Python package, which uses <code>rpy2</code>
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<p>The best way is to access R directly from Python with the help of
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internally. This package allows Python users to access all the functions
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<code>rpy2</code>, a simple yet powerful Python package. You can easily
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from the R <code>AMR</code> package without the need to set up
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call functions from the <code>AMR</code> package to process your own
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<code>rpy2</code> themselves. Since this Python package is not a true
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||||||
data in your own Python environment. This post will guide you through
|
‘port’ (which would require all R functions to be rewritten into
|
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setting up <code>rpy2</code> and show you how to use R functions from
|
Python), R and the AMR R package are still required to be installed.
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<code>AMR</code> in Python to supercharge your antimicrobial resistance
|
Yet, Python users can now easily work with AMR data directly through
|
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analysis.</p>
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Python code.</p>
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</div>
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<p>In this document, we explain how this works and provide simple
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<div class="section level2">
|
examples of using the <code>AMR</code> Python package.</p>
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<h2 id="what-is-rpy2">What is <code>rpy2</code>?<a class="anchor" aria-label="anchor" href="#what-is-rpy2"></a>
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||||||
</h2>
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<p><code>rpy2</code> is a Python library that allows Python users to run
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||||||
R code within their Python scripts. Essentially, it acts as a bridge
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between the two languages, allowing you to tap into the rich ecosystem
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of R libraries (like <code>AMR</code>) while maintaining the flexibility
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of Python.</p>
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<div class="section level3">
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<div class="section level3">
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||||||
<h3 id="key-features-of-rpy2">Key Features of <code>rpy2</code>:<a class="anchor" aria-label="anchor" href="#key-features-of-rpy2"></a>
|
<h3 id="how-it-works">How It Works<a class="anchor" aria-label="anchor" href="#how-it-works"></a>
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||||||
</h3>
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</h3>
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||||||
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<p>The <code>AMR</code> Python package acts as a wrapper around the
|
||||||
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functions in the <code>AMR</code> R package. The package simplifies the
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||||||
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process of calling R functions in Python, eliminating the need to
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||||||
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manually manage the <code>rpy2</code> setup, which Python uses
|
||||||
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internally to be able to work with the R package. By just using
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||||||
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<code>import AMR</code>, Python users can directly use the functions
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from the <code>AMR</code> R package as if they were native Python
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||||||
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functions.</p>
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||||||
|
<p>Internally, <code>rpy2</code> is still being used, but all complexity
|
||||||
|
is hidden from the user. This approach keeps the Python code clean and
|
||||||
|
Pythonic, while still leveraging the full power of the R
|
||||||
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<code>AMR</code> package.</p>
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||||||
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</div>
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||||||
|
<div class="section level3">
|
||||||
|
<h3 id="example-of-usage">Example of Usage<a class="anchor" aria-label="anchor" href="#example-of-usage"></a>
|
||||||
|
</h3>
|
||||||
|
<p>Here’s an example that demonstrates how to clean microorganism and
|
||||||
|
drug names using the <code>AMR</code> Python package:</p>
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||||||
|
<div class="sourceCode" id="cb1"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
|
||||||
|
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="im">import</span> AMR</span>
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||||||
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<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a></span>
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||||||
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<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="co"># Sample data</span></span>
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||||||
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<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a>data <span class="op">=</span> {</span>
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||||||
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<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a> <span class="st">"MOs"</span>: [<span class="st">'E. coli'</span>, <span class="st">'ESCCOL'</span>, <span class="st">'esco'</span>, <span class="st">'Esche coli'</span>],</span>
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||||||
|
<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a> <span class="st">"Drug"</span>: [<span class="st">'Cipro'</span>, <span class="st">'CIP'</span>, <span class="st">'J01MA02'</span>, <span class="st">'Ciproxin'</span>]</span>
|
||||||
|
<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a>}</span>
|
||||||
|
<span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a>df <span class="op">=</span> pd.DataFrame(data)</span>
|
||||||
|
<span id="cb1-10"><a href="#cb1-10" tabindex="-1"></a></span>
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||||||
|
<span id="cb1-11"><a href="#cb1-11" tabindex="-1"></a><span class="co"># Use AMR functions to clean microorganism and drug names</span></span>
|
||||||
|
<span id="cb1-12"><a href="#cb1-12" tabindex="-1"></a>df[<span class="st">'MO_clean'</span>] <span class="op">=</span> AMR.mo_name(df[<span class="st">'MOs'</span>])</span>
|
||||||
|
<span id="cb1-13"><a href="#cb1-13" tabindex="-1"></a>df[<span class="st">'Drug_clean'</span>] <span class="op">=</span> AMR.ab_name(df[<span class="st">'Drug'</span>])</span>
|
||||||
|
<span id="cb1-14"><a href="#cb1-14" tabindex="-1"></a></span>
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||||||
|
<span id="cb1-15"><a href="#cb1-15" tabindex="-1"></a><span class="co"># Display the results</span></span>
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||||||
|
<span id="cb1-16"><a href="#cb1-16" tabindex="-1"></a><span class="bu">print</span>(df)</span></code></pre></div>
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||||||
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<table class="table">
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||||||
|
<thead><tr class="header">
|
||||||
|
<th>MOs</th>
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||||||
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<th>Drug</th>
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||||||
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<th>MO_clean</th>
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||||||
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<th>Drug_clean</th>
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||||||
|
</tr></thead>
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||||||
|
<tbody>
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||||||
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<tr class="odd">
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||||||
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<td>E. coli</td>
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||||||
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<td>Cipro</td>
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||||||
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<td>Escherichia coli</td>
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||||||
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<td>Ciprofloxacin</td>
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||||||
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</tr>
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<tr class="even">
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||||||
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<td>ESCCOL</td>
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||||||
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<td>CIP</td>
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||||||
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<td>Escherichia coli</td>
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||||||
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<td>Ciprofloxacin</td>
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||||||
|
</tr>
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<tr class="odd">
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<td>esco</td>
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<td>J01MA02</td>
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<td>Escherichia coli</td>
|
||||||
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<td>Ciprofloxacin</td>
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||||||
|
</tr>
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||||||
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<tr class="even">
|
||||||
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<td>Esche coli</td>
|
||||||
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<td>Ciproxin</td>
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||||||
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<td>Escherichia coli</td>
|
||||||
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<td>Ciprofloxacin</td>
|
||||||
|
</tr>
|
||||||
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</tbody>
|
||||||
|
</table>
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||||||
|
<div class="section level4">
|
||||||
|
<h4 id="explanation">Explanation<a class="anchor" aria-label="anchor" href="#explanation"></a>
|
||||||
|
</h4>
|
||||||
<ul>
|
<ul>
|
||||||
<li>Seamlessly call R functions from Python.</li>
|
<li><p><strong>mo_name:</strong> This function standardises
|
||||||
<li>Convert R data structures into Python data structures like pandas
|
microorganism names. Here, different variations of <em>Escherichia
|
||||||
DataFrames.</li>
|
coli</em> (such as “E. coli”, “ESCCOL”, “esco”, and “Esche coli”) are
|
||||||
<li>Leverage the full power of R libraries without leaving your Python
|
all converted into the correct, standardised form, “Escherichia
|
||||||
environment.</li>
|
coli”.</p></li>
|
||||||
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<li><p><strong>ab_name</strong>: Similarly, this function standardises
|
||||||
|
antimicrobial names. The different representations of ciprofloxacin
|
||||||
|
(e.g., “Cipro”, “CIP”, “J01MA02”, and “Ciproxin”) are all converted to
|
||||||
|
the standard name, “Ciprofloxacin”.</p></li>
|
||||||
</ul>
|
</ul>
|
||||||
</div>
|
</div>
|
||||||
|
<div class="section level4">
|
||||||
|
<h4 id="taxonomic-data-sets-now-in-python">Taxonomic Data Sets Now in Python!<a class="anchor" aria-label="anchor" href="#taxonomic-data-sets-now-in-python"></a>
|
||||||
|
</h4>
|
||||||
|
<p>As a Python user, you might like that the most important data sets of
|
||||||
|
the <code>AMR</code> R package, <code>microorganisms</code>,
|
||||||
|
<code>antibiotics</code>, <code>clinical_breakpoints</code>, and
|
||||||
|
<code>example_isolates</code>, are now available as regular Python data
|
||||||
|
frames:</p>
|
||||||
|
<div class="sourceCode" id="cb2"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a>AMR.microorganisms</span></code></pre></div>
|
||||||
|
<table class="table">
|
||||||
|
<colgroup>
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||||||
|
<col width="11%">
|
||||||
|
<col width="29%">
|
||||||
|
<col width="8%">
|
||||||
|
<col width="8%">
|
||||||
|
<col width="8%">
|
||||||
|
<col width="10%">
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||||||
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<col width="13%">
|
||||||
|
<col width="9%">
|
||||||
|
</colgroup>
|
||||||
|
<thead><tr class="header">
|
||||||
|
<th>mo</th>
|
||||||
|
<th>fullname</th>
|
||||||
|
<th>status</th>
|
||||||
|
<th>kingdom</th>
|
||||||
|
<th>gbif</th>
|
||||||
|
<th>gbif_parent</th>
|
||||||
|
<th>gbif_renamed_to</th>
|
||||||
|
<th>prevalence</th>
|
||||||
|
</tr></thead>
|
||||||
|
<tbody>
|
||||||
|
<tr class="odd">
|
||||||
|
<td>B_GRAMN</td>
|
||||||
|
<td>(unknown Gram-negatives)</td>
|
||||||
|
<td>unknown</td>
|
||||||
|
<td>Bacteria</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>2.0</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td>B_GRAMP</td>
|
||||||
|
<td>(unknown Gram-positives)</td>
|
||||||
|
<td>unknown</td>
|
||||||
|
<td>Bacteria</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>2.0</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td>B_ANAER-NEG</td>
|
||||||
|
<td>(unknown anaerobic Gram-negatives)</td>
|
||||||
|
<td>unknown</td>
|
||||||
|
<td>Bacteria</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>2.0</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td>B_ANAER-POS</td>
|
||||||
|
<td>(unknown anaerobic Gram-positives)</td>
|
||||||
|
<td>unknown</td>
|
||||||
|
<td>Bacteria</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>2.0</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td>B_ANAER</td>
|
||||||
|
<td>(unknown anaerobic bacteria)</td>
|
||||||
|
<td>unknown</td>
|
||||||
|
<td>Bacteria</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>2.0</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td>…</td>
|
||||||
|
<td>…</td>
|
||||||
|
<td>…</td>
|
||||||
|
<td>…</td>
|
||||||
|
<td>…</td>
|
||||||
|
<td>…</td>
|
||||||
|
<td>…</td>
|
||||||
|
<td>…</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td>B_ZYMMN_POMC</td>
|
||||||
|
<td>Zymomonas pomaceae</td>
|
||||||
|
<td>accepted</td>
|
||||||
|
<td>Bacteria</td>
|
||||||
|
<td>10744418</td>
|
||||||
|
<td>3221412</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>2.0</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td>B_ZYMPH</td>
|
||||||
|
<td>Zymophilus</td>
|
||||||
|
<td>synonym</td>
|
||||||
|
<td>Bacteria</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>9475166</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>2.0</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td>B_ZYMPH_PCVR</td>
|
||||||
|
<td>Zymophilus paucivorans</td>
|
||||||
|
<td>synonym</td>
|
||||||
|
<td>Bacteria</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>2.0</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td>B_ZYMPH_RFFN</td>
|
||||||
|
<td>Zymophilus raffinosivorans</td>
|
||||||
|
<td>synonym</td>
|
||||||
|
<td>Bacteria</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>2.0</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td>F_ZYZYG</td>
|
||||||
|
<td>Zyzygomyces</td>
|
||||||
|
<td>unknown</td>
|
||||||
|
<td>Fungi</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>7581</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>2.0</td>
|
||||||
|
</tr>
|
||||||
|
</tbody>
|
||||||
|
</table>
|
||||||
|
<div class="sourceCode" id="cb3"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a>AMR.antibiotics</span></code></pre></div>
|
||||||
|
<table style="width:100%;" class="table">
|
||||||
|
<colgroup>
|
||||||
|
<col width="4%">
|
||||||
|
<col width="12%">
|
||||||
|
<col width="20%">
|
||||||
|
<col width="25%">
|
||||||
|
<col width="9%">
|
||||||
|
<col width="11%">
|
||||||
|
<col width="7%">
|
||||||
|
<col width="9%">
|
||||||
|
</colgroup>
|
||||||
|
<thead><tr class="header">
|
||||||
|
<th>ab</th>
|
||||||
|
<th>cid</th>
|
||||||
|
<th>name</th>
|
||||||
|
<th>group</th>
|
||||||
|
<th>oral_ddd</th>
|
||||||
|
<th>oral_units</th>
|
||||||
|
<th>iv_ddd</th>
|
||||||
|
<th>iv_units</th>
|
||||||
|
</tr></thead>
|
||||||
|
<tbody>
|
||||||
|
<tr class="odd">
|
||||||
|
<td>AMA</td>
|
||||||
|
<td>4649.0</td>
|
||||||
|
<td>4-aminosalicylic acid</td>
|
||||||
|
<td>Antimycobacterials</td>
|
||||||
|
<td>12.00</td>
|
||||||
|
<td>g</td>
|
||||||
|
<td>NaN</td>
|
||||||
|
<td>None</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td>ACM</td>
|
||||||
|
<td>6450012.0</td>
|
||||||
|
<td>Acetylmidecamycin</td>
|
||||||
|
<td>Macrolides/lincosamides</td>
|
||||||
|
<td>NaN</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>NaN</td>
|
||||||
|
<td>None</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td>ASP</td>
|
||||||
|
<td>49787020.0</td>
|
||||||
|
<td>Acetylspiramycin</td>
|
||||||
|
<td>Macrolides/lincosamides</td>
|
||||||
|
<td>NaN</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>NaN</td>
|
||||||
|
<td>None</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td>ALS</td>
|
||||||
|
<td>8954.0</td>
|
||||||
|
<td>Aldesulfone sodium</td>
|
||||||
|
<td>Other antibacterials</td>
|
||||||
|
<td>0.33</td>
|
||||||
|
<td>g</td>
|
||||||
|
<td>NaN</td>
|
||||||
|
<td>None</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td>AMK</td>
|
||||||
|
<td>37768.0</td>
|
||||||
|
<td>Amikacin</td>
|
||||||
|
<td>Aminoglycosides</td>
|
||||||
|
<td>NaN</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>1.0</td>
|
||||||
|
<td>g</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td>…</td>
|
||||||
|
<td>…</td>
|
||||||
|
<td>…</td>
|
||||||
|
<td>…</td>
|
||||||
|
<td>…</td>
|
||||||
|
<td>…</td>
|
||||||
|
<td>…</td>
|
||||||
|
<td>…</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td>VIR</td>
|
||||||
|
<td>11979535.0</td>
|
||||||
|
<td>Virginiamycine</td>
|
||||||
|
<td>Other antibacterials</td>
|
||||||
|
<td>NaN</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>NaN</td>
|
||||||
|
<td>None</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td>VOR</td>
|
||||||
|
<td>71616.0</td>
|
||||||
|
<td>Voriconazole</td>
|
||||||
|
<td>Antifungals/antimycotics</td>
|
||||||
|
<td>0.40</td>
|
||||||
|
<td>g</td>
|
||||||
|
<td>0.4</td>
|
||||||
|
<td>g</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td>XBR</td>
|
||||||
|
<td>72144.0</td>
|
||||||
|
<td>Xibornol</td>
|
||||||
|
<td>Other antibacterials</td>
|
||||||
|
<td>NaN</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>NaN</td>
|
||||||
|
<td>None</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td>ZID</td>
|
||||||
|
<td>77846445.0</td>
|
||||||
|
<td>Zidebactam</td>
|
||||||
|
<td>Other antibacterials</td>
|
||||||
|
<td>NaN</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>NaN</td>
|
||||||
|
<td>None</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td>ZFD</td>
|
||||||
|
<td>NaN</td>
|
||||||
|
<td>Zoliflodacin</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>NaN</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>NaN</td>
|
||||||
|
<td>None</td>
|
||||||
|
</tr>
|
||||||
|
</tbody>
|
||||||
|
</table>
|
||||||
|
</div>
|
||||||
|
</div>
|
||||||
</div>
|
</div>
|
||||||
<div class="section level2">
|
<div class="section level2">
|
||||||
<h2 id="setting-up-rpy2">Setting Up <code>rpy2</code><a class="anchor" aria-label="anchor" href="#setting-up-rpy2"></a>
|
<h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
|
||||||
</h2>
|
</h2>
|
||||||
<p>Before diving into the examples, you’ll need to install both R and
|
<p>To be able to use the <code>AMR</code> Python package, it is required
|
||||||
<code>rpy2</code>. Here’s a step-by-step guide on setting things up.</p>
|
to install both R and the <code>AMR</code> R package.</p>
|
||||||
<div class="section level3">
|
<div class="section level4">
|
||||||
<h3 id="step-1-install-r">Step 1: Install R<a class="anchor" aria-label="anchor" href="#step-1-install-r"></a>
|
<h4 id="preparation-install-r-and-amr-r-package">Preparation: Install R and <code>AMR</code> R package<a class="anchor" aria-label="anchor" href="#preparation-install-r-and-amr-r-package"></a>
|
||||||
</h3>
|
</h4>
|
||||||
<p>Ensure that R is installed on your system. R has minimal dependencies
|
<p>For Linux and macOS, this is just:</p>
|
||||||
and is very simple to install:</p>
|
<div class="sourceCode" id="cb4"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="co"># Ubuntu / Debian</span></span>
|
||||||
<ul>
|
<span id="cb4-2"><a href="#cb4-2" tabindex="-1"></a><span class="fu">sudo</span> apt install r-base <span class="kw">&&</span> <span class="ex">Rscript</span> <span class="at">-e</span> <span class="st">'install.packages("AMR")'</span></span>
|
||||||
<li>
|
<span id="cb4-3"><a href="#cb4-3" tabindex="-1"></a><span class="co"># Fedora:</span></span>
|
||||||
<strong>Linux</strong>
|
<span id="cb4-4"><a href="#cb4-4" tabindex="-1"></a><span class="fu">sudo</span> dnf install R <span class="kw">&&</span> <span class="ex">Rscript</span> <span class="at">-e</span> <span class="st">'install.packages("AMR")'</span></span>
|
||||||
<ul>
|
<span id="cb4-5"><a href="#cb4-5" tabindex="-1"></a><span class="co"># CentOS/RHEL</span></span>
|
||||||
<li>Ubuntu / Debian:<br><code>sudo apt install r-base</code>
|
<span id="cb4-6"><a href="#cb4-6" tabindex="-1"></a><span class="fu">sudo</span> yum install R <span class="kw">&&</span> <span class="ex">Rscript</span> <span class="at">-e</span> <span class="st">'install.packages("AMR")'</span></span>
|
||||||
</li>
|
<span id="cb4-7"><a href="#cb4-7" tabindex="-1"></a><span class="co"># Arch Linux</span></span>
|
||||||
<li>Fedora:<br><code>sudo dnf install R</code>
|
<span id="cb4-8"><a href="#cb4-8" tabindex="-1"></a><span class="fu">sudo</span> pacman <span class="at">-S</span> r <span class="kw">&&</span> <span class="ex">Rscript</span> <span class="at">-e</span> <span class="st">'install.packages("AMR")'</span></span>
|
||||||
</li>
|
<span id="cb4-9"><a href="#cb4-9" tabindex="-1"></a><span class="co"># macOS</span></span>
|
||||||
<li>CentOS/RHEL:<br><code>sudo yum install R</code>
|
<span id="cb4-10"><a href="#cb4-10" tabindex="-1"></a><span class="ex">brew</span> install r <span class="kw">&&</span> <span class="ex">Rscript</span> <span class="at">-e</span> <span class="st">'install.packages("AMR")'</span></span></code></pre></div>
|
||||||
</li>
|
<p>For Windows, visit the <a href="https://cran.r-project.org" class="external-link">CRAN
|
||||||
<li>Arch Linux:<br><code>sudo pacman -S r</code>
|
download page</a> in install R, then afterwards install the ‘AMR’
|
||||||
</li>
|
package manually.</p>
|
||||||
</ul>
|
|
||||||
</li>
|
|
||||||
<li>
|
|
||||||
<strong>macOS</strong> (with Homebrew):<br><code>brew install r</code>
|
|
||||||
</li>
|
|
||||||
<li>
|
|
||||||
<strong>Other Systems:</strong><br>
|
|
||||||
Visit the <a href="https://cran.r-project.org" class="external-link">CRAN download
|
|
||||||
page</a>.</li>
|
|
||||||
</ul>
|
|
||||||
</div>
|
</div>
|
||||||
<div class="section level3">
|
<div class="section level4">
|
||||||
<h3 id="step-2-install-the-amr-package-in-r">Step 2: Install the <code>AMR</code> package in R<a class="anchor" aria-label="anchor" href="#step-2-install-the-amr-package-in-r"></a>
|
<h4 id="install-amr-python-package">Install <code>AMR</code> Python Package<a class="anchor" aria-label="anchor" href="#install-amr-python-package"></a>
|
||||||
</h3>
|
</h4>
|
||||||
<p>On Linux and macOS, open Terminal and run:</p>
|
<p>Since the Python package is available on the official <a href="https://pypi.org/project/AMR/" class="external-link">Python Package Index</a>, you can
|
||||||
<div class="sourceCode" id="cb1"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="ex">Rscript</span> <span class="at">-e</span> <span class="st">'install.packages("AMR")'</span></span></code></pre></div>
|
just run:</p>
|
||||||
<p>For other systems, open your R console and install the
|
<div class="sourceCode" id="cb5"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="ex">pip</span> install AMR</span></code></pre></div>
|
||||||
<code>AMR</code> package by running:</p>
|
|
||||||
<div class="sourceCode" id="cb2"><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>On any system, you can also install the latest development version of
|
|
||||||
the <code>AMR</code> package by setting <code>repos</code> to our beta
|
|
||||||
channel:</p>
|
|
||||||
<div class="sourceCode" id="cb3"><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">"https://msberends.r-universe.dev"</span><span class="op">)</span></span></code></pre></div>
|
|
||||||
</div>
|
|
||||||
<div class="section level3">
|
|
||||||
<h3 id="step-3-install-rpy2-in-python">Step 3: Install <code>rpy2</code> in Python<a class="anchor" aria-label="anchor" href="#step-3-install-rpy2-in-python"></a>
|
|
||||||
</h3>
|
|
||||||
<p>To install <code>rpy2</code>, simply run the following command in
|
|
||||||
your terminal:</p>
|
|
||||||
<div class="sourceCode" id="cb4"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="ex">pip</span> install rpy2</span></code></pre></div>
|
|
||||||
</div>
|
|
||||||
<div class="section level3">
|
|
||||||
<h3 id="step-4-test-rpy2-installation">Step 4: Test <code>rpy2</code> Installation<a class="anchor" aria-label="anchor" href="#step-4-test-rpy2-installation"></a>
|
|
||||||
</h3>
|
|
||||||
<p>To ensure everything is set up correctly, you can test your
|
|
||||||
installation by running the following Python script, which essentially
|
|
||||||
runs R in the background:</p>
|
|
||||||
<div class="sourceCode" id="cb5"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="im">import</span> rpy2.robjects <span class="im">as</span> ro</span>
|
|
||||||
<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a></span>
|
|
||||||
<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a><span class="co"># Test a simple R function from Python</span></span>
|
|
||||||
<span id="cb5-4"><a href="#cb5-4" tabindex="-1"></a>ro.r(<span class="st">'1 + 1'</span>)</span></code></pre></div>
|
|
||||||
<p>If this returns <code>2</code>, you’re good to go!</p>
|
|
||||||
</div>
|
</div>
|
||||||
</div>
|
</div>
|
||||||
<div class="section level2">
|
<div class="section level2">
|
||||||
<h2 id="working-with-amr-in-python">Working with <code>AMR</code> in Python<a class="anchor" aria-label="anchor" href="#working-with-amr-in-python"></a>
|
<h2 id="working-with-amr-in-python">Working with <code>AMR</code> in Python<a class="anchor" aria-label="anchor" href="#working-with-amr-in-python"></a>
|
||||||
</h2>
|
</h2>
|
||||||
<p>Now that we have <code>rpy2</code> set up, let’s walk through some
|
<p>Now that we have everything set up, let’s walk through some practical
|
||||||
practical examples of using the <code>AMR</code> package within
|
examples of using the <code>AMR</code> package within Python.</p>
|
||||||
Python.</p>
|
|
||||||
<div class="section level3">
|
<div class="section level3">
|
||||||
<h3 id="example-1-converting-taxonomic-data">Example 1: Converting Taxonomic Data<a class="anchor" aria-label="anchor" href="#example-1-converting-taxonomic-data"></a>
|
<h3 id="example-1-calculating-amr">Example 1: Calculating AMR<a class="anchor" aria-label="anchor" href="#example-1-calculating-amr"></a>
|
||||||
</h3>
|
</h3>
|
||||||
<p>Let’s start by converting taxonomic user input to valid taxonomy
|
<div class="sourceCode" id="cb6"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="im">import</span> AMR</span>
|
||||||
using the <code>AMR</code> package, from within Python:</p>
|
<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
|
||||||
<div class="sourceCode" id="cb6"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
|
<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a></span>
|
||||||
<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="im">import</span> rpy2.robjects <span class="im">as</span> ro</span>
|
<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a>df <span class="op">=</span> AMR.example_isolates</span>
|
||||||
<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a><span class="im">from</span> rpy2.robjects.packages <span class="im">import</span> importr</span>
|
<span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a>result <span class="op">=</span> AMR.resistance(df[<span class="st">"AMX"</span>])</span>
|
||||||
<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="im">from</span> rpy2.robjects <span class="im">import</span> pandas2ri</span>
|
<span id="cb6-6"><a href="#cb6-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
|
||||||
<span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a></span>
|
<pre><code>[0.59555556]</code></pre>
|
||||||
<span id="cb6-6"><a href="#cb6-6" tabindex="-1"></a><span class="co"># Load the AMR package from R</span></span>
|
|
||||||
<span id="cb6-7"><a href="#cb6-7" tabindex="-1"></a>amr <span class="op">=</span> importr(<span class="st">'AMR'</span>)</span>
|
|
||||||
<span id="cb6-8"><a href="#cb6-8" tabindex="-1"></a></span>
|
|
||||||
<span id="cb6-9"><a href="#cb6-9" tabindex="-1"></a><span class="co"># Example user dataset in Python</span></span>
|
|
||||||
<span id="cb6-10"><a href="#cb6-10" tabindex="-1"></a>data <span class="op">=</span> pd.DataFrame({</span>
|
|
||||||
<span id="cb6-11"><a href="#cb6-11" tabindex="-1"></a> <span class="st">'microorganism'</span>: [<span class="st">'E. coli'</span>, <span class="st">'S. aureus'</span>, <span class="st">'P. aeruginosa'</span>, <span class="st">'K. pneumoniae'</span>]</span>
|
|
||||||
<span id="cb6-12"><a href="#cb6-12" tabindex="-1"></a>})</span>
|
|
||||||
<span id="cb6-13"><a href="#cb6-13" tabindex="-1"></a></span>
|
|
||||||
<span id="cb6-14"><a href="#cb6-14" tabindex="-1"></a><span class="co"># Apply mo_name() from the AMR package to the 'microorganism' column</span></span>
|
|
||||||
<span id="cb6-15"><a href="#cb6-15" tabindex="-1"></a>ro.globalenv[<span class="st">'r_data'</span>] <span class="op">=</span> data</span>
|
|
||||||
<span id="cb6-16"><a href="#cb6-16" tabindex="-1"></a>ro.r(<span class="st">'r_data$mo_name <- mo_name(r_data$microorganism)'</span>)</span>
|
|
||||||
<span id="cb6-17"><a href="#cb6-17" tabindex="-1"></a></span>
|
|
||||||
<span id="cb6-18"><a href="#cb6-18" tabindex="-1"></a><span class="co"># Retrieve and print the modified R DataFrame in Python</span></span>
|
|
||||||
<span id="cb6-19"><a href="#cb6-19" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'r_data'</span>)</span>
|
|
||||||
<span id="cb6-20"><a href="#cb6-20" tabindex="-1"></a>result <span class="op">=</span> pandas2ri.rpy2py(result)</span>
|
|
||||||
<span id="cb6-21"><a href="#cb6-21" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
|
|
||||||
<p>In this example, a Python dataset with microorganism names like
|
|
||||||
<em>E. coli</em> and <em>S. aureus</em> is passed to the R function
|
|
||||||
<code><a href="../reference/mo_property.html">mo_name()</a></code>. The result is an updated <code>DataFrame</code>
|
|
||||||
that includes the standardised microorganism names based on the
|
|
||||||
<code><a href="../reference/mo_property.html">mo_name()</a></code> function from the <code>AMR</code> package.</p>
|
|
||||||
</div>
|
</div>
|
||||||
<div class="section level3">
|
<div class="section level3">
|
||||||
<h3 id="example-2-generating-an-antibiogram">Example 2: Generating an Antibiogram<a class="anchor" aria-label="anchor" href="#example-2-generating-an-antibiogram"></a>
|
<h3 id="example-2-generating-antibiograms">Example 2: Generating Antibiograms<a class="anchor" aria-label="anchor" href="#example-2-generating-antibiograms"></a>
|
||||||
</h3>
|
</h3>
|
||||||
<p>One of the core functions of the <code>AMR</code> package is
|
<p>One of the core functions of the <code>AMR</code> package is
|
||||||
generating an antibiogram, a table that summarises the antimicrobial
|
generating an antibiogram, a table that summarises the antimicrobial
|
||||||
susceptibility of bacterial isolates. Here’s how you can generate an
|
susceptibility of bacterial isolates. Here’s how you can generate an
|
||||||
antibiogram from Python:</p>
|
antibiogram from Python:</p>
|
||||||
<div class="sourceCode" id="cb7"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="co"># Run an antibiogram in R from Python</span></span>
|
<div class="sourceCode" id="cb8"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a>result2a <span class="op">=</span> AMR.antibiogram(df[[<span class="st">"mo"</span>, <span class="st">"AMX"</span>, <span class="st">"CIP"</span>, <span class="st">"TZP"</span>]])</span>
|
||||||
<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a>ro.r(<span class="st">'result <- antibiogram(example_isolates, antibiotics = c(aminoglycosides(), carbapenems()))'</span>)</span>
|
<span id="cb8-2"><a href="#cb8-2" tabindex="-1"></a><span class="bu">print</span>(result2a)</span></code></pre></div>
|
||||||
<span id="cb7-3"><a href="#cb7-3" tabindex="-1"></a></span>
|
<table class="table">
|
||||||
<span id="cb7-4"><a href="#cb7-4" tabindex="-1"></a><span class="co"># Retrieve the result in Python</span></span>
|
<colgroup>
|
||||||
<span id="cb7-5"><a href="#cb7-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
|
<col width="22%">
|
||||||
<span id="cb7-6"><a href="#cb7-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
|
<col width="22%">
|
||||||
<p>In this example, we generate an antibiogram by selecting
|
<col width="22%">
|
||||||
aminoglycosides and carbapenems, two classes of antibiotics, and then
|
<col width="33%">
|
||||||
convert the resulting R data frame into a Python-readable format.</p>
|
</colgroup>
|
||||||
</div>
|
<thead><tr class="header">
|
||||||
<div class="section level3">
|
<th>Pathogen</th>
|
||||||
<h3 id="example-3-filtering-data-based-on-gram-negative-bacteria">Example 3: Filtering Data Based on Gram-Negative Bacteria<a class="anchor" aria-label="anchor" href="#example-3-filtering-data-based-on-gram-negative-bacteria"></a>
|
<th>Amoxicillin</th>
|
||||||
</h3>
|
<th>Ciprofloxacin</th>
|
||||||
<p>Let’s say you want to filter the dataset for Gram-negative bacteria
|
<th>Piperacillin/tazobactam</th>
|
||||||
and display their resistance to certain antibiotics:</p>
|
</tr></thead>
|
||||||
<div class="sourceCode" id="cb8"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a><span class="co"># Filter for Gram-negative bacteria with intrinsic resistance to cefotaxime</span></span>
|
<tbody>
|
||||||
<span id="cb8-2"><a href="#cb8-2" tabindex="-1"></a>ro.r(<span class="st">'result <- example_isolates[which(mo_is_gram_negative() & mo_is_intrinsic_resistant(ab = "cefotax")), c("bacteria", aminoglycosides(), carbapenems())]'</span>)</span>
|
<tr class="odd">
|
||||||
<span id="cb8-3"><a href="#cb8-3" tabindex="-1"></a></span>
|
<td>CoNS</td>
|
||||||
<span id="cb8-4"><a href="#cb8-4" tabindex="-1"></a><span class="co"># Retrieve the filtered result in Python</span></span>
|
<td>7% (10/142)</td>
|
||||||
<span id="cb8-5"><a href="#cb8-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
|
<td>73% (183/252)</td>
|
||||||
<span id="cb8-6"><a href="#cb8-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
|
<td>30% (10/33)</td>
|
||||||
<p>This example uses the AMR functions
|
</tr>
|
||||||
<code><a href="../reference/mo_property.html">mo_is_gram_negative()</a></code> and
|
<tr class="even">
|
||||||
<code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> to filter the dataset and
|
<td>E. coli</td>
|
||||||
returns a subset of bacteria with resistance data.</p>
|
<td>50% (196/392)</td>
|
||||||
</div>
|
<td>88% (399/456)</td>
|
||||||
<div class="section level3">
|
<td>94% (393/416)</td>
|
||||||
<h3 id="example-4-customising-the-antibiogram">Example 4: Customising the Antibiogram<a class="anchor" aria-label="anchor" href="#example-4-customising-the-antibiogram"></a>
|
</tr>
|
||||||
</h3>
|
<tr class="odd">
|
||||||
<p>You can easily customise the antibiogram by passing different
|
<td>K. pneumoniae</td>
|
||||||
antibiotics or microorganism transformations, as shown below:</p>
|
<td>0% (0/58)</td>
|
||||||
<div class="sourceCode" id="cb9"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a><span class="co"># Customise the antibiogram with different settings</span></span>
|
<td>96% (53/55)</td>
|
||||||
<span id="cb9-2"><a href="#cb9-2" tabindex="-1"></a>ro.r(<span class="st">'result <- antibiogram(example_isolates, antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"), mo_transform = "gramstain")'</span>)</span>
|
<td>89% (47/53)</td>
|
||||||
<span id="cb9-3"><a href="#cb9-3" tabindex="-1"></a></span>
|
</tr>
|
||||||
<span id="cb9-4"><a href="#cb9-4" tabindex="-1"></a><span class="co"># Retrieve and print the result</span></span>
|
<tr class="even">
|
||||||
<span id="cb9-5"><a href="#cb9-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
|
<td>P. aeruginosa</td>
|
||||||
<span id="cb9-6"><a href="#cb9-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
|
<td>0% (0/30)</td>
|
||||||
<p>Here, we use piperacillin/tazobactam (TZP) in combination with
|
<td>100% (30/30)</td>
|
||||||
tobramycin (TOB) and gentamicin (GEN) to see how they perform against
|
<td>None</td>
|
||||||
various Gram-negative bacteria.</p>
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td>P. mirabilis</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>94% (34/36)</td>
|
||||||
|
<td>None</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td>S. aureus</td>
|
||||||
|
<td>6% (8/131)</td>
|
||||||
|
<td>90% (171/191)</td>
|
||||||
|
<td>None</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td>S. epidermidis</td>
|
||||||
|
<td>1% (1/91)</td>
|
||||||
|
<td>64% (87/136)</td>
|
||||||
|
<td>None</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td>S. hominis</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>80% (56/70)</td>
|
||||||
|
<td>None</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td>S. pneumoniae</td>
|
||||||
|
<td>100% (112/112)</td>
|
||||||
|
<td>None</td>
|
||||||
|
<td>100% (112/112)</td>
|
||||||
|
</tr>
|
||||||
|
</tbody>
|
||||||
|
</table>
|
||||||
|
<div class="sourceCode" id="cb9"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a>result2b <span class="op">=</span> AMR.antibiogram(df[[<span class="st">"mo"</span>, <span class="st">"AMX"</span>, <span class="st">"CIP"</span>, <span class="st">"TZP"</span>]], mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>)</span>
|
||||||
|
<span id="cb9-2"><a href="#cb9-2" tabindex="-1"></a><span class="bu">print</span>(result2b)</span></code></pre></div>
|
||||||
|
<table class="table">
|
||||||
|
<colgroup>
|
||||||
|
<col width="20%">
|
||||||
|
<col width="22%">
|
||||||
|
<col width="23%">
|
||||||
|
<col width="33%">
|
||||||
|
</colgroup>
|
||||||
|
<thead><tr class="header">
|
||||||
|
<th>Pathogen</th>
|
||||||
|
<th>Amoxicillin</th>
|
||||||
|
<th>Ciprofloxacin</th>
|
||||||
|
<th>Piperacillin/tazobactam</th>
|
||||||
|
</tr></thead>
|
||||||
|
<tbody>
|
||||||
|
<tr class="odd">
|
||||||
|
<td>Gram-negative</td>
|
||||||
|
<td>36% (226/631)</td>
|
||||||
|
<td>91% (621/684)</td>
|
||||||
|
<td>88% (565/641)</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td>Gram-positive</td>
|
||||||
|
<td>43% (305/703)</td>
|
||||||
|
<td>77% (560/724)</td>
|
||||||
|
<td>86% (296/345)</td>
|
||||||
|
</tr>
|
||||||
|
</tbody>
|
||||||
|
</table>
|
||||||
|
<p>In this example, we generate an antibiogram by selecting various
|
||||||
|
antibiotics.</p>
|
||||||
</div>
|
</div>
|
||||||
</div>
|
</div>
|
||||||
<div class="section level2">
|
<div class="section level2">
|
||||||
<h2 id="conclusion">Conclusion<a class="anchor" aria-label="anchor" href="#conclusion"></a>
|
<h2 id="conclusion">Conclusion<a class="anchor" aria-label="anchor" href="#conclusion"></a>
|
||||||
</h2>
|
</h2>
|
||||||
<p>Using <code>rpy2</code>, you can easily integrate the power of R’s
|
<p>With the <code>AMR</code> Python package, Python users can now
|
||||||
<code>AMR</code> package into your Python workflows. Whether you are
|
effortlessly call R functions from the <code>AMR</code> R package. This
|
||||||
generating antibiograms, analyzing resistance data, or performing
|
eliminates the need for complex <code>rpy2</code> configurations and
|
||||||
complex filtering, <code>rpy2</code> gives you the flexibility to run R
|
provides a clean, easy-to-use interface for antimicrobial resistance
|
||||||
code without leaving the Python environment. This makes it a perfect
|
analysis. The examples provided above demonstrate how this can be
|
||||||
solution for teams working across both R and Python.</p>
|
applied to typical workflows, such as standardising microorganism and
|
||||||
|
antimicrobial names or calculating resistance.</p>
|
||||||
|
<p>By using <code>import AMR</code>, you can seamlessly integrate the
|
||||||
|
robust features of the R <code>AMR</code> package into your Python
|
||||||
|
workflows. Whether you’re cleaning data or analysing resistance
|
||||||
|
patterns, the <code>AMR</code> Python package makes it easy to work with
|
||||||
|
AMR data in Python.</p>
|
||||||
</div>
|
</div>
|
||||||
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|
||||||
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|
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|
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</small>
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@ -29,7 +29,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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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="">2.1.1.9094</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</small>
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@ -76,7 +76,7 @@
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<main id="main" class="col-md-9"><div class="page-header">
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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>
|
<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">10 October 2024</h4>
|
<h4 data-toc-skip class="date">15 October 2024</h4>
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||||||
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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>
|
<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>
|
||||||
<div class="d-none name"><code>datasets.Rmd</code></div>
|
<div class="d-none name"><code>datasets.Rmd</code></div>
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|
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@ -7,7 +7,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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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="">2.1.1.9094</small>
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@ -59,8 +59,6 @@
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<dd>
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<dd>
|
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</dd><dt><a href="MDR.html">How to determine multi-drug resistance (MDR)</a></dt>
|
</dd><dt><a href="MDR.html">How to determine multi-drug resistance (MDR)</a></dt>
|
||||||
<dd>
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<dd>
|
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</dd><dt><a href="other_pkg.html">Using AMR with other packages: AMR & dplyr/tidyverse</a></dt>
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<dd>
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</dd><dt><a href="PCA.html">How to conduct principal component analysis (PCA) for AMR</a></dt>
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</dd><dt><a href="PCA.html">How to conduct principal component analysis (PCA) for AMR</a></dt>
|
||||||
<dd>
|
<dd>
|
||||||
</dd><dt><a href="resistance_predict.html">How to predict antimicrobial resistance</a></dt>
|
</dd><dt><a href="resistance_predict.html">How to predict antimicrobial resistance</a></dt>
|
||||||
|
|||||||
@ -1,110 +0,0 @@
|
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<li><a class="dropdown-item" href="../articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
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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>Using AMR with other packages: AMR & dplyr/tidyverse</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/other_pkg.Rmd" class="external-link"><code>vignettes/other_pkg.Rmd</code></a></small>
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||||||
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<p>This page will be updated shortly, to give explicit examples of how
|
|
||||||
to work ideally with the <code>AMR</code> package, for those who are
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||||||
used to working in <code>dplyr</code> or other tidyverse packages.</p>
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</main>
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
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<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_umcg.svg" style="max-width: 150px;"></a></p>
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@ -29,7 +29,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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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="">2.1.1.9094</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</small>
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@ -29,7 +29,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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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="">2.1.1.9094</small>
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@ -7,7 +7,7 @@
|
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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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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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@ -32,7 +32,7 @@
|
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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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</small>
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@ -91,6 +91,9 @@
|
|||||||
<li>100% free of costs and dependencies, highly suitable for places with <strong>limited resources</strong>
|
<li>100% free of costs and dependencies, highly suitable for places with <strong>limited resources</strong>
|
||||||
</li>
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
|
<blockquote>
|
||||||
|
<p>Now available for Python too! <a href="./articles/AMR_for_Python.html">Click here</a> to read more.</p>
|
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|
</blockquote>
|
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<div style="display: flex; font-size: 0.8em;">
|
<div style="display: flex; font-size: 0.8em;">
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<p style="text-align:left; width: 50%;">
|
<p style="text-align:left; width: 50%;">
|
||||||
<small><a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR</a></small>
|
<small><a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR</a></small>
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|
|||||||
@ -7,7 +7,7 @@
|
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|
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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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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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@ -47,18 +47,18 @@
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</div>
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|
||||||
<div class="section level2">
|
<div class="section level2">
|
||||||
<h2 class="pkg-version" data-toc-text="2.1.1.9094" id="amr-2119094">AMR 2.1.1.9094<a class="anchor" aria-label="anchor" href="#amr-2119094"></a></h2>
|
<h2 class="pkg-version" data-toc-text="2.1.1.9095" id="amr-2119095">AMR 2.1.1.9095<a class="anchor" aria-label="anchor" href="#amr-2119095"></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://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p>
|
<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://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p>
|
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<div class="section level5">
|
<div class="section level5">
|
||||||
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9094">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-2-1-1-9094"></a></h5>
|
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9095">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-2-1-1-9095"></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>
|
<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>
|
||||||
<div class="section level3">
|
<div class="section level3">
|
||||||
<h3 id="breaking-2-1-1-9094">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9094"></a></h3>
|
<h3 id="breaking-2-1-1-9095">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9095"></a></h3>
|
||||||
<ul><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 a year ago</li>
|
<ul><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 a year ago</li>
|
||||||
</ul></div>
|
</ul></div>
|
||||||
<div class="section level3">
|
<div class="section level3">
|
||||||
<h3 id="new-2-1-1-9094">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9094"></a></h3>
|
<h3 id="new-2-1-1-9095">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9095"></a></h3>
|
||||||
<ul><li>
|
<ul><li>
|
||||||
<strong>One Health implementation</strong>
|
<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>
|
<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>
|
||||||
@ -90,12 +90,16 @@
|
|||||||
<li>New function <code><a href="../reference/as.mic.html">rescale_mic()</a></code>, which allows users to rescale MIC values to a manually set range. This is the powerhouse behind the <code>scale_*_mic()</code> functions, but it can be used independently to, for instance, compare equality in MIC distributions by rescaling them to the same range first.</li>
|
<li>New function <code><a href="../reference/as.mic.html">rescale_mic()</a></code>, which allows users to rescale MIC values to a manually set range. This is the powerhouse behind the <code>scale_*_mic()</code> functions, but it can be used independently to, for instance, compare equality in MIC distributions by rescaling them to the same range first.</li>
|
||||||
</ul></li>
|
</ul></li>
|
||||||
<li>
|
<li>
|
||||||
|
<strong>Support for Python</strong>
|
||||||
|
<ul><li>While using R for the heavy lifting, <a href="https://pypi.org/project/AMR/" class="external-link">our ‘AMR’ Python Package</a> was developed to run the AMR R package natively in Python. The Python package will always have the same version number as the R package, as it is built automatically with every code change.</li>
|
||||||
|
</ul></li>
|
||||||
|
<li>
|
||||||
<strong>Other</strong>
|
<strong>Other</strong>
|
||||||
<ul><li>New function <code><a href="../reference/mo_property.html">mo_group_members()</a></code> to retrieve the member microorganisms of a microorganism group. For example, <code>mo_group_members("Strep group C")</code> returns a vector of all microorganisms that belong to that group.</li>
|
<ul><li>New function <code><a href="../reference/mo_property.html">mo_group_members()</a></code> to retrieve the member microorganisms of a microorganism group. For example, <code>mo_group_members("Strep group C")</code> returns a vector of all microorganisms that belong to that group.</li>
|
||||||
</ul></li>
|
</ul></li>
|
||||||
</ul></div>
|
</ul></div>
|
||||||
<div class="section level3">
|
<div class="section level3">
|
||||||
<h3 id="changed-2-1-1-9094">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9094"></a></h3>
|
<h3 id="changed-2-1-1-9095">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9095"></a></h3>
|
||||||
<ul><li>SIR interpretation
|
<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>
|
<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>
|
<li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
|
||||||
@ -125,6 +129,7 @@
|
|||||||
<li>Sorting of MIC values (using <code><a href="https://rdrr.io/r/base/sort.html" class="external-link">sort()</a></code>) was fixed in the same manner; <code><0.001</code> now gets sorted before <code>0.001</code>, and <code>>0.001</code> gets sorted after <code>0.001</code>.</li>
|
<li>Sorting of MIC values (using <code><a href="https://rdrr.io/r/base/sort.html" class="external-link">sort()</a></code>) was fixed in the same manner; <code><0.001</code> now gets sorted before <code>0.001</code>, and <code>>0.001</code> gets sorted after <code>0.001</code>.</li>
|
||||||
<li>Intermediate log2 levels used for MIC plotting are now more common values instead of following a strict dilution range</li>
|
<li>Intermediate log2 levels used for MIC plotting are now more common values instead of following a strict dilution range</li>
|
||||||
</ul></li>
|
</ul></li>
|
||||||
|
<li>Disks of 0 to 5 mm are now allowed, the newly allowed range for disk diffusion (<code><a href="../reference/as.disk.html">as.disk()</a></code>) is now between 0 and 50 mm</li>
|
||||||
<li>Updated <code><a href="../reference/italicise_taxonomy.html">italicise_taxonomy()</a></code> to support HTML output</li>
|
<li>Updated <code><a href="../reference/italicise_taxonomy.html">italicise_taxonomy()</a></code> to support HTML output</li>
|
||||||
<li>
|
<li>
|
||||||
<code><a href="../reference/custom_eucast_rules.html">custom_eucast_rules()</a></code> now supports multiple antibiotics and antibiotic groups to be affected by a single rule</li>
|
<code><a href="../reference/custom_eucast_rules.html">custom_eucast_rules()</a></code> now supports multiple antibiotics and antibiotic groups to be affected by a single rule</li>
|
||||||
@ -147,14 +152,14 @@
|
|||||||
<li>Improved algorithm of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> when using the phenotype-based method, to prioritise records with the highest availability of SIR values</li>
|
<li>Improved algorithm of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> when using the phenotype-based method, to prioritise records with the highest availability of SIR values</li>
|
||||||
</ul></div>
|
</ul></div>
|
||||||
<div class="section level3">
|
<div class="section level3">
|
||||||
<h3 id="other-2-1-1-9094">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9094"></a></h3>
|
<h3 id="other-2-1-1-9095">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9095"></a></h3>
|
||||||
<ul><li>Greatly improved <code>vctrs</code> integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that functions such as <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/bind_rows.html" class="external-link">bind_rows()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/rowwise.html" class="external-link">rowwise()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/c_across.html" class="external-link">c_across()</a></code> are now supported for e.g. columns of class <code>mic</code>. Despite this, this <code>AMR</code> package is still zero-dependent on any other package, including <code>dplyr</code> and <code>vctrs</code>.</li>
|
<ul><li>Greatly improved <code>vctrs</code> integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that functions such as <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/bind_rows.html" class="external-link">bind_rows()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/rowwise.html" class="external-link">rowwise()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/c_across.html" class="external-link">c_across()</a></code> are now supported for e.g. columns of class <code>mic</code>. Despite this, this <code>AMR</code> package is still zero-dependent on any other package, including <code>dplyr</code> and <code>vctrs</code>.</li>
|
||||||
<li>Greatly updated and expanded documentation</li>
|
<li>Greatly updated and expanded documentation</li>
|
||||||
<li>Added Larisse Bolton, Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
|
<li>Added Larisse Bolton, Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
|
||||||
<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>
|
<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>
|
</ul></div>
|
||||||
<div class="section level3">
|
<div class="section level3">
|
||||||
<h3 id="older-versions-2-1-1-9094">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9094"></a></h3>
|
<h3 id="older-versions-2-1-1-9095">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9095"></a></h3>
|
||||||
<p>This changelog only contains changes from AMR v3.0 (October 2024) and later.</p>
|
<p>This changelog only contains changes from AMR v3.0 (October 2024) 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>
|
<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>
|
<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>
|
||||||
|
|||||||
@ -7,12 +7,11 @@ articles:
|
|||||||
datasets: datasets.html
|
datasets: datasets.html
|
||||||
EUCAST: EUCAST.html
|
EUCAST: EUCAST.html
|
||||||
MDR: MDR.html
|
MDR: MDR.html
|
||||||
other_pkg: other_pkg.html
|
|
||||||
PCA: PCA.html
|
PCA: PCA.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
|
||||||
WHONET: WHONET.html
|
WHONET: WHONET.html
|
||||||
last_built: 2024-10-10T14:41Z
|
last_built: 2024-10-15T15:34Z
|
||||||
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
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -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>
|
<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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<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="">2.1.1.9094</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
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|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
@ -110,16 +110,16 @@
|
|||||||
<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">#></span> birth_date age age_exact age_at_y2k</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 1965-12-05 58 58.84699 34</span>
|
<span class="r-out co"><span class="r-pr">#></span> 1 1965-12-05 58 58.86066 34</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 2 1980-03-01 44 44.60929 19</span>
|
<span class="r-out co"><span class="r-pr">#></span> 2 1980-03-01 44 44.62295 19</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 3 1949-11-01 74 74.93989 50</span>
|
<span class="r-out co"><span class="r-pr">#></span> 3 1949-11-01 74 74.95355 50</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 4 1947-02-14 77 77.65301 52</span>
|
<span class="r-out co"><span class="r-pr">#></span> 4 1947-02-14 77 77.66667 52</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 5 1940-02-19 84 84.63934 59</span>
|
<span class="r-out co"><span class="r-pr">#></span> 5 1940-02-19 84 84.65301 59</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 6 1988-01-10 36 36.74863 11</span>
|
<span class="r-out co"><span class="r-pr">#></span> 6 1988-01-10 36 36.76230 11</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 7 1997-08-27 27 27.12022 2</span>
|
<span class="r-out co"><span class="r-pr">#></span> 7 1997-08-27 27 27.13388 2</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 8 1978-01-26 46 46.70492 21</span>
|
<span class="r-out co"><span class="r-pr">#></span> 8 1978-01-26 46 46.71858 21</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 9 1972-06-17 52 52.31421 27</span>
|
<span class="r-out co"><span class="r-pr">#></span> 9 1972-06-17 52 52.32787 27</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 10 1986-08-10 38 38.16667 13</span>
|
<span class="r-out co"><span class="r-pr">#></span> 10 1986-08-10 38 38.18033 13</span>
|
||||||
</code></pre></div>
|
</code></pre></div>
|
||||||
</div>
|
</div>
|
||||||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
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|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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|
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -9,7 +9,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
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@ -7,7 +7,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -7,7 +7,7 @@
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|
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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|
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@ -1,5 +1,5 @@
|
|||||||
<!DOCTYPE html>
|
<!DOCTYPE html>
|
||||||
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Transform Input to Disk Diffusion Diameters — as.disk • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Transform Input to Disk Diffusion Diameters — as.disk"><meta name="description" content="This transforms a vector to a new class disk, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 6 and 50."><meta property="og:description" content="This transforms a vector to a new class disk, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 6 and 50."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"></head><body>
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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Transform Input to Disk Diffusion Diameters — as.disk • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Transform Input to Disk Diffusion Diameters — as.disk"><meta name="description" content="This transforms a vector to a new class disk, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 0 and 50."><meta property="og:description" content="This transforms a vector to a new class disk, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 0 and 50."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"></head><body>
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||||||
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
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|
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||||||
@ -7,7 +7,7 @@
|
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|
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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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||||||
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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||||||
@ -48,7 +48,7 @@
|
|||||||
</div>
|
</div>
|
||||||
|
|
||||||
<div class="ref-description section level2">
|
<div class="ref-description section level2">
|
||||||
<p>This transforms a vector to a new class <code>disk</code>, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 6 and 50.</p>
|
<p>This transforms a vector to a new class <code>disk</code>, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 0 and 50.</p>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
<div class="section level2">
|
<div class="section level2">
|
||||||
@ -83,7 +83,7 @@
|
|||||||
<div class="section level2">
|
<div class="section level2">
|
||||||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||||||
<p>Interpret disk values as SIR values with <code><a href="as.sir.html">as.sir()</a></code>. It supports guidelines from EUCAST and CLSI.</p>
|
<p>Interpret disk values as SIR values with <code><a href="as.sir.html">as.sir()</a></code>. It supports guidelines from EUCAST and CLSI.</p>
|
||||||
<p>Disk diffusion growth zone sizes must be between 6 and 50 millimetres. Values higher than 50 but lower than 100 will be maximised to 50. All others input values outside the 6-50 range will return <code>NA</code>.</p>
|
<p>Disk diffusion growth zone sizes must be between 0 and 50 millimetres. Values higher than 50 but lower than 100 will be maximised to 50. All others input values outside the 0-50 range will return <code>NA</code>.</p>
|
||||||
<p><code>NA_disk_</code> is a missing value of the new <code>disk</code> class.</p>
|
<p><code>NA_disk_</code> is a missing value of the new <code>disk</code> class.</p>
|
||||||
</div>
|
</div>
|
||||||
<div class="section level2">
|
<div class="section level2">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||||
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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@ -7,7 +7,7 @@
|
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|
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
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||||||
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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|
||||||
|
|||||||
@ -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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||||||
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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||||||
@ -727,8 +727,8 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
|||||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations.</span>
|
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations.</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column 'nitrofuratoin' (NIT, nitrofurantoin),</span>
|
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: column 'nitrofuratoin' (NIT,</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024...</span>
|
<span class="r-msg co"><span class="r-pr">#></span> nitrofurantoin), EUCAST 2024...</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Assuming value "urine" in column 'specimen' reflects a urinary tract</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Assuming value "urine" in column 'specimen' reflects a urinary tract</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> infection.</span>
|
<span class="r-msg co"><span class="r-pr">#></span> infection.</span>
|
||||||
@ -736,8 +736,8 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
|||||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations.</span>
|
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations.</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column 'nitrofuratoin' (NIT, nitrofurantoin),</span>
|
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: column 'nitrofuratoin' (NIT,</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024...</span>
|
<span class="r-msg co"><span class="r-pr">#></span> nitrofurantoin), EUCAST 2024...</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||||
@ -785,16 +785,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
|||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 57 × 16</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 57 × 16</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> datetime index ab_given mo_given host_given ab mo </span>
|
<span class="r-out co"><span class="r-pr">#></span> datetime index ab_given mo_given host_given ab mo </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</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;"><ab></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</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;"><ab></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2024-10-10 <span style="color: #949494;">14:42:40</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2024-10-15 <span style="color: #949494;">15:35:01</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2024-10-10 <span style="color: #949494;">14:42:47</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2024-10-15 <span style="color: #949494;">15:35:08</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2024-10-10 <span style="color: #949494;">14:42:47</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2024-10-15 <span style="color: #949494;">15:35:09</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2024-10-10 <span style="color: #949494;">14:42:48</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2024-10-15 <span style="color: #949494;">15:35:09</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2024-10-10 <span style="color: #949494;">14:42:48</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2024-10-15 <span style="color: #949494;">15:35:10</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2024-10-10 <span style="color: #949494;">14:42:40</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2024-10-15 <span style="color: #949494;">15:35:01</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2024-10-10 <span style="color: #949494;">14:42:47</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2024-10-15 <span style="color: #949494;">15:35:08</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2024-10-10 <span style="color: #949494;">14:42:47</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2024-10-15 <span style="color: #949494;">15:35:08</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2024-10-10 <span style="color: #949494;">14:42:48</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2024-10-15 <span style="color: #949494;">15:35:09</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2024-10-10 <span style="color: #949494;">14:42:48</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2024-10-15 <span style="color: #949494;">15:35:10</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 47 more rows</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 47 more rows</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 9 more variables: host <chr>, method <chr>, input <dbl>, outcome <sir>,</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 9 more variables: host <chr>, method <chr>, input <dbl>, outcome <sir>,</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
|
|||||||
|
|
||||||
<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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -9,7 +9,7 @@ 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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -9,7 +9,7 @@ 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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -9,7 +9,7 @@
|
|||||||
|
|
||||||
<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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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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|||||||
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||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</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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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</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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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</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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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</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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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</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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||||||
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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</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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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</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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||||||
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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</small>
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||||||
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||||||
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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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||||||
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|||||||
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||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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|
||||||
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|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</small>
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||||||
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||||||
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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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||||||
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|||||||
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||||||
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|
||||||
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|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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||||||
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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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||||||
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||||||
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|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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||||||
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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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|||||||
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||||||
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|
||||||
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|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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||||||
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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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|||||||
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||||||
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|
||||||
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|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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||||||
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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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||||||
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|
||||||
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|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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||||||
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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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||||||
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|||||||
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|||||||
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||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
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|
||||||
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|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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||||||
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||||||
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|||||||
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||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
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|
||||||
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|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</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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||||||
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|||||||
@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
|
|||||||
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||||||
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||||||
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||||||
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||||||
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|||||||
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||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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|
||||||
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|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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||||||
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||||||
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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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||||||
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||||||
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|||||||
@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
|||||||
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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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||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</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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||||||
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|||||||
@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
|
|||||||
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||||||
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|
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||||||
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||||||
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||||||
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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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||||||
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|||||||
@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
|||||||
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||||||
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|
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
<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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|||||||
@ -7,7 +7,7 @@
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|||||||
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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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<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="">2.1.1.9094</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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">
|
||||||
|
|||||||
File diff suppressed because one or more lines are too long
@ -9,7 +9,6 @@
|
|||||||
<url><loc>https://msberends.github.io/AMR/articles/WHONET.html</loc></url>
|
<url><loc>https://msberends.github.io/AMR/articles/WHONET.html</loc></url>
|
||||||
<url><loc>https://msberends.github.io/AMR/articles/datasets.html</loc></url>
|
<url><loc>https://msberends.github.io/AMR/articles/datasets.html</loc></url>
|
||||||
<url><loc>https://msberends.github.io/AMR/articles/index.html</loc></url>
|
<url><loc>https://msberends.github.io/AMR/articles/index.html</loc></url>
|
||||||
<url><loc>https://msberends.github.io/AMR/articles/other_pkg.html</loc></url>
|
|
||||||
<url><loc>https://msberends.github.io/AMR/articles/resistance_predict.html</loc></url>
|
<url><loc>https://msberends.github.io/AMR/articles/resistance_predict.html</loc></url>
|
||||||
<url><loc>https://msberends.github.io/AMR/articles/welcome_to_AMR.html</loc></url>
|
<url><loc>https://msberends.github.io/AMR/articles/welcome_to_AMR.html</loc></url>
|
||||||
<url><loc>https://msberends.github.io/AMR/authors.html</loc></url>
|
<url><loc>https://msberends.github.io/AMR/authors.html</loc></url>
|
||||||
|
|||||||
Loading…
Reference in New Issue
Block a user