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<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="">3.0.1.9075</small>
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<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="">3.0.1.9075</small>
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@@ -619,6 +619,59 @@ frames:</p>
</div>
</div>
<div class="section level2">
<h2 id="installation-channels">Installation Channels<a class="anchor" aria-label="anchor" href="#installation-channels"></a>
</h2>
<div class="section level3">
<h3 id="stable-release-cran">Stable Release (CRAN)<a class="anchor" aria-label="anchor" href="#stable-release-cran"></a>
</h3>
<p>The default <code>AMR</code> Python package uses the latest stable
version of the <code>AMR</code> R package, published on CRAN. After
running <code>pip install AMR</code>, import it as usual:</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb12-1"><a href="#cb12-1" tabindex="-1"></a><span class="im">import</span> AMR</span>
<span id="cb12-2"><a href="#cb12-2" tabindex="-1"></a></span>
<span id="cb12-3"><a href="#cb12-3" tabindex="-1"></a>AMR.example_isolates</span></code></pre></div>
</div>
<div class="section level3">
<h3 id="development-version-github">Development Version (GitHub)<a class="anchor" aria-label="anchor" href="#development-version-github"></a>
</h3>
<p>To use the latest development version of the <code>AMR</code> R
package (sourced directly from GitHub), import the <code>beta</code>
sub-package and alias it as <code>AMR</code>:</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb13-1"><a href="#cb13-1" tabindex="-1"></a><span class="im">import</span> AMR.beta <span class="im">as</span> AMR</span>
<span id="cb13-2"><a href="#cb13-2" tabindex="-1"></a></span>
<span id="cb13-3"><a href="#cb13-3" tabindex="-1"></a>AMR.example_isolates</span></code></pre></div>
<p>Aliasing with <code>as AMR</code> keeps all downstream code identical
to the stable import. Switching between the stable release and the
development version requires changing only the import line — nothing
else in your script needs to change.</p>
</div>
</div>
<div class="section level2">
<h2 id="sir-classification-with-as_sir">SIR Classification with <code>as_sir()</code><a class="anchor" aria-label="anchor" href="#sir-classification-with-as_sir"></a>
</h2>
<div class="section level3">
<h3 id="using-enforce_method">Using <code>enforce_method</code><a class="anchor" aria-label="anchor" href="#using-enforce_method"></a>
</h3>
<p>The <code>as_sir()</code> function in R uses S3 method dispatch to
select the correct calculation method based on the input class:
<code>&lt;mic&gt;</code> for MIC values and <code>&lt;disk&gt;</code>
for disk diffusion values. Because Python objects do not carry R class
attributes through the <code>rpy2</code> bridge, this automatic dispatch
may not resolve correctly.</p>
<p>To explicitly specify the input type, use the
<code>enforce_method</code> argument:</p>
<div class="sourceCode" id="cb14"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb14-1"><a href="#cb14-1" tabindex="-1"></a><span class="co"># Treat the column as MIC values — maps to R's as.sir.mic()</span></span>
<span id="cb14-2"><a href="#cb14-2" tabindex="-1"></a>AMR.as_sir(df[<span class="st">"MIC_col"</span>], mo<span class="op">=</span><span class="st">"E. coli"</span>, ab<span class="op">=</span><span class="st">"AMX"</span>, guideline<span class="op">=</span><span class="st">"EUCAST"</span>, enforce_method<span class="op">=</span><span class="st">"mic"</span>)</span>
<span id="cb14-3"><a href="#cb14-3" tabindex="-1"></a></span>
<span id="cb14-4"><a href="#cb14-4" tabindex="-1"></a><span class="co"># Treat the column as disk diffusion values — maps to R's as.sir.disk()</span></span>
<span id="cb14-5"><a href="#cb14-5" tabindex="-1"></a>AMR.as_sir(df[<span class="st">"disk_col"</span>], mo<span class="op">=</span><span class="st">"E. coli"</span>, ab<span class="op">=</span><span class="st">"AMX"</span>, guideline<span class="op">=</span><span class="st">"EUCAST"</span>, enforce_method<span class="op">=</span><span class="st">"disk"</span>)</span></code></pre></div>
<p>Without <code>enforce_method</code>, R falls back to class-based
dispatch on the raw Python input, which may fail or return unexpected
results. Always supply <code>enforce_method</code> when calling
<code>as_sir()</code> from Python.</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

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articles/AMR_for_Python.md
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@@ -200,6 +200,61 @@ AMR.antimicrobials
| ZID | 77846445.0 | Zidebactam | Other antibacterials | NaN | None | NaN | None |
| ZFD | NaN | Zoliflodacin | None | NaN | None | NaN | None |
## Installation Channels
### Stable Release (CRAN)
The default `AMR` Python package uses the latest stable version of the
`AMR` R package, published on CRAN. After running `pip install AMR`,
import it as usual:
``` python
import AMR
AMR.example_isolates
```
### Development Version (GitHub)
To use the latest development version of the `AMR` R package (sourced
directly from GitHub), import the `beta` sub-package and alias it as
`AMR`:
``` python
import AMR.beta as AMR
AMR.example_isolates
```
Aliasing with `as AMR` keeps all downstream code identical to the stable
import. Switching between the stable release and the development version
requires changing only the import line — nothing else in your script
needs to change.
## SIR Classification with `as_sir()`
### Using `enforce_method`
The `as_sir()` function in R uses S3 method dispatch to select the
correct calculation method based on the input class: `<mic>` for MIC
values and `<disk>` for disk diffusion values. Because Python objects do
not carry R class attributes through the `rpy2` bridge, this automatic
dispatch may not resolve correctly.
To explicitly specify the input type, use the `enforce_method` argument:
``` python
# Treat the column as MIC values — maps to R's as.sir.mic()
AMR.as_sir(df["MIC_col"], mo="E. coli", ab="AMX", guideline="EUCAST", enforce_method="mic")
# Treat the column as disk diffusion values — maps to R's as.sir.disk()
AMR.as_sir(df["disk_col"], mo="E. coli", ab="AMX", guideline="EUCAST", enforce_method="disk")
```
Without `enforce_method`, R falls back to class-based dispatch on the
raw Python input, which may fail or return unexpected results. Always
supply `enforce_method` when calling `as_sir()` from Python.
## Conclusion
With the `AMR` Python package, Python users can now effortlessly call R

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