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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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<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
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<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</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>AMR for Python</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/AMR_for_Python.Rmd" class="external-link"><code>vignettes/AMR_for_Python.Rmd</code></a></small>
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<div class="d-none name"><code>AMR_for_Python.Rmd</code></div>
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</div>
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<div class="section level2">
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<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
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</h2>
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<p>The <code>AMR</code> package for R is a powerful tool for
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antimicrobial resistance (AMR) analysis. It provides extensive features
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for handling microbial and antimicrobial data. However, for those who
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work primarily in Python, we now have a more intuitive option available:
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the <code>AMR</code> Python package, which uses <code>rpy2</code>
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internally. This package allows Python users to access all the functions
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from the R <code>AMR</code> package without the need to set up
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<code>rpy2</code> themselves. Since this Python package is not a true
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‘port’ (which would require all R functions to be rewritten into
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Python), R and the AMR R package are still required to be installed.
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Yet, Python users can now easily work with AMR data directly through
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Python code.</p>
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<p>In this document, we explain how this works and provide simple
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examples of using the <code>AMR</code> Python package.</p>
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<div class="section level3">
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<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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<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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process of calling R functions in Python, eliminating the need to
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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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<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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functions.</p>
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<p>Internally, <code>rpy2</code> is still being used, but all complexity
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is hidden from the user. This approach keeps the Python code clean and
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Pythonic, while still leveraging the full power of the R
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<code>AMR</code> package.</p>
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</div>
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<div class="section level3">
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<h3 id="example-of-usage">Example of Usage<a class="anchor" aria-label="anchor" href="#example-of-usage"></a>
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</h3>
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<p>Here’s an example that demonstrates how to clean microorganism and
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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>
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<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="im">import</span> AMR</span>
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<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a></span>
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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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<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a>data <span class="op">=</span> {</span>
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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>
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<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a>}</span>
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<span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a>df <span class="op">=</span> pd.DataFrame(data)</span>
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<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>
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<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>
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<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>
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<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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<table class="table">
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<thead><tr class="header">
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<th>MOs</th>
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<th>Drug</th>
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<th>MO_clean</th>
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<th>Drug_clean</th>
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</tr></thead>
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<tbody>
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<tr class="odd">
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<td>E. coli</td>
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<td>Cipro</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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<tr class="even">
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<td>ESCCOL</td>
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<td>CIP</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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<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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<tr class="even">
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<td>Esche coli</td>
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||
<td>Ciproxin</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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||
</tbody>
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||
</table>
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<div class="section level4">
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<h4 id="explanation">Explanation<a class="anchor" aria-label="anchor" href="#explanation"></a>
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</h4>
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<ul>
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<li><p><strong>mo_name:</strong> This function standardises
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microorganism names. Here, different variations of <em>Escherichia
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coli</em> (such as “E. coli”, “ESCCOL”, “esco”, and “Esche coli”) are
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all converted into the correct, standardised form, “Escherichia
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coli”.</p></li>
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<li><p><strong>ab_name</strong>: Similarly, this function standardises
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antimicrobial names. The different representations of ciprofloxacin
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(e.g., “Cipro”, “CIP”, “J01MA02”, and “Ciproxin”) are all converted to
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the standard name, “Ciprofloxacin”.</p></li>
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||
</ul>
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||
</div>
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||
<div class="section level4">
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<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>
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||
</h4>
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<p>As a Python user, you might like that the most important data sets of
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the <code>AMR</code> R package, <code>microorganisms</code>,
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<code>antibiotics</code>, <code>clinical_breakpoints</code>, and
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<code>example_isolates</code>, are now available as regular Python data
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frames:</p>
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<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>
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<table class="table">
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||
<colgroup>
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||
<col width="11%">
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||
<col width="29%">
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||
<col width="8%">
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||
<col width="8%">
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||
<col width="8%">
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||
<col width="10%">
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<col width="13%">
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<col width="9%">
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</colgroup>
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<thead><tr class="header">
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<th>mo</th>
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<th>fullname</th>
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<th>status</th>
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<th>kingdom</th>
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<th>gbif</th>
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<th>gbif_parent</th>
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<th>gbif_renamed_to</th>
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<th>prevalence</th>
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</tr></thead>
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<tbody>
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||
<tr class="odd">
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<td>B_GRAMN</td>
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<td>(unknown Gram-negatives)</td>
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<td>unknown</td>
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<td>Bacteria</td>
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<td>None</td>
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||
<td>None</td>
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<td>None</td>
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<td>2.0</td>
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</tr>
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<tr class="even">
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<td>B_GRAMP</td>
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<td>(unknown Gram-positives)</td>
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<td>unknown</td>
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||
<td>Bacteria</td>
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||
<td>None</td>
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||
<td>None</td>
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||
<td>None</td>
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||
<td>2.0</td>
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||
</tr>
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||
<tr class="odd">
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||
<td>B_ANAER-NEG</td>
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<td>(unknown anaerobic Gram-negatives)</td>
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||
<td>unknown</td>
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||
<td>Bacteria</td>
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||
<td>None</td>
|
||
<td>None</td>
|
||
<td>None</td>
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||
<td>2.0</td>
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||
</tr>
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||
<tr class="even">
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||
<td>B_ANAER-POS</td>
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||
<td>(unknown anaerobic Gram-positives)</td>
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||
<td>unknown</td>
|
||
<td>Bacteria</td>
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||
<td>None</td>
|
||
<td>None</td>
|
||
<td>None</td>
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||
<td>2.0</td>
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||
</tr>
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||
<tr class="odd">
|
||
<td>B_ANAER</td>
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||
<td>(unknown anaerobic bacteria)</td>
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||
<td>unknown</td>
|
||
<td>Bacteria</td>
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||
<td>None</td>
|
||
<td>None</td>
|
||
<td>None</td>
|
||
<td>2.0</td>
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||
</tr>
|
||
<tr class="even">
|
||
<td>…</td>
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||
<td>…</td>
|
||
<td>…</td>
|
||
<td>…</td>
|
||
<td>…</td>
|
||
<td>…</td>
|
||
<td>…</td>
|
||
<td>…</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>B_ZYMMN_POMC</td>
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||
<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>
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||
<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 class="section level2">
|
||
<h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
|
||
</h2>
|
||
<p>To be able to use the <code>AMR</code> Python package, it is required
|
||
to install both R and the <code>AMR</code> R package.</p>
|
||
<div class="section level4">
|
||
<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>
|
||
</h4>
|
||
<p>For Linux and macOS, this is just:</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>
|
||
<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>
|
||
<span id="cb4-3"><a href="#cb4-3" tabindex="-1"></a><span class="co"># Fedora:</span></span>
|
||
<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>
|
||
<span id="cb4-5"><a href="#cb4-5" tabindex="-1"></a><span class="co"># CentOS/RHEL</span></span>
|
||
<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>
|
||
<span id="cb4-7"><a href="#cb4-7" tabindex="-1"></a><span class="co"># Arch Linux</span></span>
|
||
<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>
|
||
<span id="cb4-9"><a href="#cb4-9" tabindex="-1"></a><span class="co"># macOS</span></span>
|
||
<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>
|
||
<p>For Windows, visit the <a href="https://cran.r-project.org" class="external-link">CRAN
|
||
download page</a> in install R, then afterwards install the ‘AMR’
|
||
package manually.</p>
|
||
</div>
|
||
<div class="section level4">
|
||
<h4 id="install-amr-python-package">Install <code>AMR</code> Python Package<a class="anchor" aria-label="anchor" href="#install-amr-python-package"></a>
|
||
</h4>
|
||
<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
|
||
just run:</p>
|
||
<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>
|
||
</div>
|
||
</div>
|
||
<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>
|
||
<p>Now that we have everything set up, let’s walk through some practical
|
||
examples of using the <code>AMR</code> package within Python.</p>
|
||
<div class="section level3">
|
||
<h3 id="example-1-calculating-amr">Example 1: Calculating AMR<a class="anchor" aria-label="anchor" href="#example-1-calculating-amr"></a>
|
||
</h3>
|
||
<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>
|
||
<span id="cb6-2"><a href="#cb6-2" 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="cb6-4"><a href="#cb6-4" tabindex="-1"></a>df <span class="op">=</span> AMR.example_isolates</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="cb6-6"><a href="#cb6-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
|
||
<pre><code>[0.59555556]</code></pre>
|
||
</div>
|
||
<div class="section level3">
|
||
<h3 id="example-2-generating-antibiograms">Example 2: Generating Antibiograms<a class="anchor" aria-label="anchor" href="#example-2-generating-antibiograms"></a>
|
||
</h3>
|
||
<p>One of the core functions of the <code>AMR</code> package is
|
||
generating an antibiogram, a table that summarises the antimicrobial
|
||
susceptibility of bacterial isolates. Here’s how you can generate an
|
||
antibiogram from Python:</p>
|
||
<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="cb8-2"><a href="#cb8-2" tabindex="-1"></a><span class="bu">print</span>(result2a)</span></code></pre></div>
|
||
<table class="table">
|
||
<colgroup>
|
||
<col width="22%">
|
||
<col width="22%">
|
||
<col width="22%">
|
||
<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>CoNS</td>
|
||
<td>7% (10/142)</td>
|
||
<td>73% (183/252)</td>
|
||
<td>30% (10/33)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>E. coli</td>
|
||
<td>50% (196/392)</td>
|
||
<td>88% (399/456)</td>
|
||
<td>94% (393/416)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>K. pneumoniae</td>
|
||
<td>0% (0/58)</td>
|
||
<td>96% (53/55)</td>
|
||
<td>89% (47/53)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>P. aeruginosa</td>
|
||
<td>0% (0/30)</td>
|
||
<td>100% (30/30)</td>
|
||
<td>None</td>
|
||
</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 class="section level2">
|
||
<h2 id="conclusion">Conclusion<a class="anchor" aria-label="anchor" href="#conclusion"></a>
|
||
</h2>
|
||
<p>With the <code>AMR</code> Python package, Python users can now
|
||
effortlessly call R functions from the <code>AMR</code> R package. This
|
||
eliminates the need for complex <code>rpy2</code> configurations and
|
||
provides a clean, easy-to-use interface for antimicrobial resistance
|
||
analysis. The examples provided above demonstrate how this can be
|
||
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>
|
||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||
</nav></aside>
|
||
</div>
|
||
|
||
|
||
|
||
<footer><div class="pkgdown-footer-left">
|
||
<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>
|
||
</div>
|
||
|
||
<div class="pkgdown-footer-right">
|
||
<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>
|
||
</div>
|
||
|
||
</footer>
|
||
</div>
|
||
|
||
|
||
|
||
|
||
|
||
</body>
|
||
</html>
|