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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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">
@ -97,8 +97,8 @@ antimicrobial resistance (AMR) analysis. It provides extensive features
for handling microbial and antimicrobial data. However, for those who
work primarily in Python, we now have a more intuitive option available:
the <a href="https://pypi.org/project/AMR/" class="external-link"><code>AMR</code> Python
Package Index</a>.</p>
<p>This Python package is a wrapper round the <code>AMR</code> R
package</a>.</p>
<p>This Python package is a wrapper around the <code>AMR</code> R
package. It uses the <code>rpy2</code> package internally. Despite the
need to have R installed, Python users can now easily work with AMR data
directly through Python code.</p>
@ -106,15 +106,15 @@ directly through Python code.</p>
<div class="section level2">
<h2 id="prerequisites">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
</h2>
<p>This package was only tested with <a href="https://docs.python.org/3/library/venv.html" class="external-link"><code>venv</code></a>.
You can set up such a virtual environment by running:</p>
<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="co"># for linux and macOS:</span></span>
<p>This package was only tested with a <a href="https://docs.python.org/3/library/venv.html" class="external-link">virtual environment
(venv)</a>. You can set up such an environment by running:</p>
<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="co"># linux and macOS:</span></span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a>python <span class="op">-</span>m venv <span class="op">/</span>path<span class="op">/</span>to<span class="op">/</span>new<span class="op">/</span>virtual<span class="op">/</span>environment</span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="co"># for Windows:</span></span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a>python <span class="op">-</span>m venv C:\path\to\new\virtual\environment</span></code></pre></div>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a></span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="co"># Windows:</span></span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a>python <span class="op">-</span>m venv C:\path\to\new\virtual\environment</span></code></pre></div>
<p>Then you can <a href="https://docs.python.org/3/library/venv.html#how-venvs-work" class="external-link">activate
the environment</a>, after the which the virtual environment is ready to
work with.</p>
the environment</a>, after which the venv is ready to work with.</p>
</div>
<div class="section level2">
<h2 id="install-amr">Install AMR<a class="anchor" aria-label="anchor" href="#install-amr"></a>