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@@ -619,6 +619,59 @@ frames:</p>
</div> </div>
</div> </div>
<div class="section level2"> <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 id="conclusion">Conclusion<a class="anchor" aria-label="anchor" href="#conclusion"></a>
</h2> </h2>
<p>With the <code>AMR</code> Python package, Python users can now <p>With the <code>AMR</code> Python package, Python users can now
articles/AMR_for_Python.md
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| ZID | 77846445.0 | Zidebactam | Other antibacterials | NaN | None | NaN | None | | ZID | 77846445.0 | Zidebactam | Other antibacterials | NaN | None | NaN | None |
| ZFD | NaN | Zoliflodacin | None | 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 ## Conclusion
With the `AMR` Python package, Python users can now effortlessly call R With the `AMR` Python package, Python users can now effortlessly call R
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</div> </div>
<div class="section level2"> <div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.1.9075" id="amr-3019075">AMR 3.0.1.9075<a class="anchor" aria-label="anchor" href="#amr-3019075"></a></h2> <h2 class="pkg-version" data-toc-text="3.0.1.9076" id="amr-3019076">AMR 3.0.1.9076<a class="anchor" aria-label="anchor" href="#amr-3019076"></a></h2>
<p>Planned as v3.1.0, end of June 2026.</p> <p>Planned as v3.1.0, end of June 2026.</p>
<div class="section level4"> <div class="section level4">
<h4 id="breaking-changes-3-0-1-9075">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9075"></a></h4> <h4 id="breaking-changes-3-0-1-9076">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9076"></a></h4>
<ul><li>The former <em>kingdoms</em> Bacteria and Archaea are now each divided into four kingdoms with new top-level <em>domains</em> ‘Bacteria’ and ‘Archaea’ (Göker and Oren, 2024, DOI: 10.1099/ijsem.0.006242). Following this, a new <code>domain</code> column in the <code>microorganisms</code> data set was added, and more importantly, <code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now returns the formal kingdom (e.g. <code>"Pseudomonadati"</code> instead of <code>"Bacteria"</code>). Use <code><a href="../reference/mo_property.html">mo_domain()</a></code> for the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa, etc.), <code>kingdom</code> and <code>domain</code> are identical.</li> <ul><li>The former <em>kingdoms</em> Bacteria and Archaea are now each divided into four kingdoms with new top-level <em>domains</em> ‘Bacteria’ and ‘Archaea’ (Göker and Oren, 2024, DOI: 10.1099/ijsem.0.006242). Following this, a new <code>domain</code> column in the <code>microorganisms</code> data set was added, and more importantly, <code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now returns the formal kingdom (e.g. <code>"Pseudomonadati"</code> instead of <code>"Bacteria"</code>). Use <code><a href="../reference/mo_property.html">mo_domain()</a></code> for the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa, etc.), <code>kingdom</code> and <code>domain</code> are identical.</li>
<li>Faster parallel computing via the <code>future</code> package for <code><a href="../reference/as.sir.html">as.sir()</a></code> and <code><a href="../reference/antibiogram.html">wisca()</a></code>: a non-sequential plan (e.g. <code>future::plan(future::multisession)</code>) must be active before using <code>parallel = TRUE</code>.</li> <li>Faster parallel computing via the <code>future</code> package for <code><a href="../reference/as.sir.html">as.sir()</a></code> and <code><a href="../reference/antibiogram.html">wisca()</a></code>: a non-sequential plan (e.g. <code>future::plan(future::multisession)</code>) must be active before using <code>parallel = TRUE</code>.</li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="new-3-0-1-9075">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9075"></a></h4> <h4 id="new-3-0-1-9076">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9076"></a></h4>
<ul><li>EUCAST 2026 and CLSI 2026 breakpoints: over 5,700 new breakpoints added to the <code>clinical_breakpoints</code> data set; EUCAST 2026 is now the default for all MIC and disk diffusion interpretations</li> <ul><li>EUCAST 2026 and CLSI 2026 breakpoints: over 5,700 new breakpoints added to the <code>clinical_breakpoints</code> data set; EUCAST 2026 is now the default for all MIC and disk diffusion interpretations</li>
<li>Wildtype/Non-wildtype (WT/NWT) output when using ECOFF-based interpretation, by setting <code>breakpoint_type = "ECOFF"</code> in <code><a href="../reference/as.sir.html">as.sir()</a></code>; WT/NWT results are fully supported in all resistance/susceptibility functions and plots (<a href="https://github.com/msberends/AMR/issues/254" class="external-link">#254</a>)</li> <li>Wildtype/Non-wildtype (WT/NWT) output when using ECOFF-based interpretation, by setting <code>breakpoint_type = "ECOFF"</code> in <code><a href="../reference/as.sir.html">as.sir()</a></code>; WT/NWT results are fully supported in all resistance/susceptibility functions and plots (<a href="https://github.com/msberends/AMR/issues/254" class="external-link">#254</a>)</li>
<li> <li>
@@ -74,7 +74,7 @@
<li>New <code><a href="../reference/antibiogram.html">wisca_plot()</a></code> to assess the susceptibility and incidence distributions from the Monte Carlo simulations</li> <li>New <code><a href="../reference/antibiogram.html">wisca_plot()</a></code> to assess the susceptibility and incidence distributions from the Monte Carlo simulations</li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="fixed-3-0-1-9075">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9075"></a></h4> <h4 id="fixed-3-0-1-9076">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9076"></a></h4>
<ul><li> <ul><li>
<code><a href="../reference/as.sir.html">as.sir()</a></code> <code><a href="../reference/as.sir.html">as.sir()</a></code>
<ul><li>On data frames: already-converted SIR columns no longer dropped on re-run (<a href="https://github.com/msberends/AMR/issues/278" class="external-link">#278</a>)</li> <ul><li>On data frames: already-converted SIR columns no longer dropped on re-run (<a href="https://github.com/msberends/AMR/issues/278" class="external-link">#278</a>)</li>
@@ -101,7 +101,7 @@
</li> </li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="updated-3-0-1-9075">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9075"></a></h4> <h4 id="updated-3-0-1-9076">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9076"></a></h4>
<ul><li>Taxonomic update for all microorganisms, now updated to June 2026</li> <ul><li>Taxonomic update for all microorganisms, now updated to June 2026</li>
<li> <li>
<code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now returns the formal taxonomic kingdom; a one-time note per session explains the change when querying bacterial or archaeal records.</li> <code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now returns the formal taxonomic kingdom; a one-time note per session explains the change when querying bacterial or archaeal records.</li>
@@ -127,6 +127,8 @@
<code><a href="../reference/as.disk.html">as.disk()</a></code>: input validation is now more strict, rejecting values that are not recognisable as a numeric disk zone diameter</li> <code><a href="../reference/as.disk.html">as.disk()</a></code>: input validation is now more strict, rejecting values that are not recognisable as a numeric disk zone diameter</li>
<li> <li>
<code><a href="../reference/as.sir.html">as.sir()</a></code> gains an <code>enforce_method</code> argument (<code>"auto"</code>, <code>"mic"</code>, or <code>"disk"</code>) to force the interpretation method when S3 class information is lost, e.g. when called from Python (<a href="https://github.com/msberends/AMR/issues/291" class="external-link">#291</a>)</li> <code><a href="../reference/as.sir.html">as.sir()</a></code> gains an <code>enforce_method</code> argument (<code>"auto"</code>, <code>"mic"</code>, or <code>"disk"</code>) to force the interpretation method when S3 class information is lost, e.g. when called from Python (<a href="https://github.com/msberends/AMR/issues/291" class="external-link">#291</a>)</li>
<li>
<code>AMR for Python</code> vignette: added sections on installation channels (stable CRAN vs. development GitHub via <code>AMR.beta</code>) and on using <code>enforce_method</code> in <code>as_sir()</code> from Python</li>
</ul></div> </ul></div>
</div> </div>
<div class="section level2"> <div class="section level2">
news/index.md
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@@ -1,6 +1,6 @@
# Changelog # Changelog
## AMR 3.0.1.9075 ## AMR 3.0.1.9076
Planned as v3.1.0, end of June 2026. Planned as v3.1.0, end of June 2026.
@@ -180,6 +180,9 @@ Planned as v3.1.0, end of June 2026.
the interpretation method when S3 class information is lost, e.g. when the interpretation method when S3 class information is lost, e.g. when
called from Python called from Python
([\#291](https://github.com/msberends/AMR/issues/291)) ([\#291](https://github.com/msberends/AMR/issues/291))
- `AMR for Python` vignette: added sections on installation channels
(stable CRAN vs. development GitHub via `AMR.beta`) and on using
`enforce_method` in `as_sir()` from Python
## AMR 3.0.1 ## AMR 3.0.1
pkgdown.yml
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@@ -10,7 +10,7 @@ articles:
PCA: PCA.html PCA: PCA.html
WHONET: WHONET.html WHONET: WHONET.html
WISCA: WISCA.html WISCA: WISCA.html
last_built: 2026-06-26T10:08Z last_built: 2026-06-26T13:07Z
urls: urls:
reference: https://amr-for-r.org/reference reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles article: https://amr-for-r.org/articles
reference/AMR-deprecated.html
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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="">3.0.1.9075</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9076</small>
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reference/AMR-options.html
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@@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
<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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reference/AMR.html
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@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<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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reference/WHOCC.html
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@@ -7,7 +7,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9075</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9076</small>
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reference/WHONET.html
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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="">3.0.1.9075</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9076</small>
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reference/ab_from_text.html
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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="">3.0.1.9075</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9076</small>
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reference/ab_property.html
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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="">3.0.1.9075</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9076</small>
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reference/add_custom_antimicrobials.html
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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="">3.0.1.9075</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9076</small>
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reference/add_custom_microorganisms.html
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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="">3.0.1.9075</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9076</small>
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reference/age.html
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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="">3.0.1.9075</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9076</small>
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reference/age_groups.html
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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="">3.0.1.9075</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9076</small>
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reference/amr-tidymodels.html
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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="">3.0.1.9075</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9076</small>
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reference/amr_course.html
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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="">3.0.1.9075</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9076</small>
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reference/antibiogram.html
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@@ -13,7 +13,7 @@ All antibiogram types adhere to previously described approaches (see Source), an
<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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reference/antimicrobial_selectors.html
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@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
<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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reference/antimicrobials.html
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@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
<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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reference/as.ab.html
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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>
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reference/as.av.html
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@@ -7,7 +7,7 @@
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reference/as.disk.html
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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="">3.0.1.9075</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9076</small>
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reference/as.mic.html
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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="">3.0.1.9075</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9076</small>
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reference/as.mo.html
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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="">3.0.1.9075</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9076</small>
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reference/as.sir.html
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@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<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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@@ -462,10 +462,10 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span> <span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-06-26 <span style="color: #949494;">10:11:05</span> 1 MIC amoxicillin Escherich… human 8 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-06-26 <span style="color: #949494;">13:09:56</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-06-26 <span style="color: #949494;">10:11:06</span> 1 MIC cipro Escherich… human 0.256 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-06-26 <span style="color: #949494;">13:09:56</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-06-26 <span style="color: #949494;">10:11:06</span> 1 DISK tobra Escherich… human 16 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-06-26 <span style="color: #949494;">13:09:56</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-06-26 <span style="color: #949494;">10:11:06</span> 1 DISK genta Escherich… human 18 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-06-26 <span style="color: #949494;">13:09:56</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>
reference/as.sir.md
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@@ -712,10 +712,10 @@ sir_interpretation_history()
#> # A tibble: 4 × 18 #> # A tibble: 4 × 18
#> datetime index method ab_given mo_given host_given input_given #> datetime index method ab_given mo_given host_given input_given
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr> #> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 2026-06-26 10:11:05 1 MIC amoxicillin Escherich… human 8 #> 1 2026-06-26 13:09:56 1 MIC amoxicillin Escherich… human 8
#> 2 2026-06-26 10:11:06 1 MIC cipro Escherich… human 0.256 #> 2 2026-06-26 13:09:56 1 MIC cipro Escherich… human 0.256
#> 3 2026-06-26 10:11:06 1 DISK tobra Escherich… human 16 #> 3 2026-06-26 13:09:56 1 DISK tobra Escherich… human 16
#> 4 2026-06-26 10:11:06 1 DISK genta Escherich… human 18 #> 4 2026-06-26 13:09:56 1 DISK genta Escherich… human 18
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>, #> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>, #> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
#> # breakpoint_S_R <chr>, site <chr> #> # breakpoint_S_R <chr>, site <chr>
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@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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reference/intrinsic_resistant.html
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reference/italicise_taxonomy.html
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reference/join.html
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reference/key_antimicrobials.html
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reference/kurtosis.html
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reference/like.html
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reference/mdro.html
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reference/mean_amr_distance.html
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reference/microorganisms.codes.html
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reference/microorganisms.groups.html
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reference/microorganisms.html
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reference/mo_matching_score.html
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reference/mo_source.html
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reference/pca.html
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reference/plot.html
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reference/proportion.html
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reference/random.html
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reference/resistance_predict.html
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reference/skewness.html
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reference/top_n_microorganisms.html
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reference/translate.html
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search.json
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Key capabilities: - SIR (Susceptible/Intermediate/Resistant) classification using EUCAST 2011–2025 CLSI 2011–2025 breakpoints - Antibiogram generation: traditional, combined, syndromic, WISCA - Microorganism taxonomy database (~79,000 species) - Antimicrobial drug database (~620 drugs) - Multi-drug resistant organism (MDRO) classification - First-isolate identification - Minimum Inhibitory Concentration (MIC) disk diffusion handling - Multilingual output (28 languages)","code":""},{"path":"https://amr-for-r.org/CLAUDE.html","id":"common-commands","dir":"","previous_headings":"","what":"Common Commands","title":"CLAUDE.md — AMR R Package","text":"commands run inside R session: shell:","code":"# Rebuild documentation (roxygen2 → .Rd files + NAMESPACE) devtools::document() # Run all tests devtools::test() # Full package check (CRAN-level: docs + tests + checks) devtools::check() # Build pkgdown website locally pkgdown::build_site() # Code coverage report covr::package_coverage() # CRAN check from parent directory R CMD check AMR"},{"path":"https://amr-for-r.org/CLAUDE.html","id":"repository-structure","dir":"","previous_headings":"","what":"Repository Structure","title":"CLAUDE.md — AMR R Package","text":"","code":"R/ # All R source files (62 files, ~28,000 lines) man/ # Auto-generated .Rd documentation (do not edit manually) tests/testthat/ # testthat test files (test-*.R) and helper-functions.R data/ # Pre-compiled .rda datasets data-raw/ # Scripts used to generate data/ files vignettes/ # Rmd vignette articles inst/ # Installed files (translations, etc.) _pkgdown.yml # pkgdown website configuration"},{"path":"https://amr-for-r.org/CLAUDE.html","id":"r-source-file-conventions","dir":"","previous_headings":"","what":"R Source File Conventions","title":"CLAUDE.md — AMR R Package","text":"Naming conventions R/: Key source files: aa_helper_functions.R / aa_helper_pm_functions.R — internal utility functions (large; ~63 KB ~37 KB) aa_globals.R — global constants breakpoint lookup structures aa_options.R — amr_options() / get_AMR_option() system mo.R / mo_property.R — microorganism lookup properties ab.R / ab_property.R — antimicrobial drug functions av.R / av_property.R — antiviral drug functions sir.R / sir_calc.R / sir_df.R — SIR classification engine mic.R / disk.R — MIC disk diffusion classes antibiogram.R — antibiogram generation (traditional, combined, syndromic, WISCA) first_isolate.R — first-isolate identification algorithms mdro.R — MDRO classification (EUCAST, CLSI, CDC, custom guidelines) amr_selectors.R — tidyselect helpers selecting AMR columns interpretive_rules.R / custom_eucast_rules.R — clinical interpretation rules translate.R — 28-language translation system ggplot_sir.R / ggplot_pca.R / plotting.R — visualisation functions","code":""},{"path":"https://amr-for-r.org/CLAUDE.html","id":"custom-s3-classes","dir":"","previous_headings":"","what":"Custom S3 Classes","title":"CLAUDE.md — AMR R Package","text":"package defines five S3 classes full print/format/plot/vctrs support:","code":""},{"path":"https://amr-for-r.org/CLAUDE.html","id":"data-files","dir":"","previous_headings":"","what":"Data Files","title":"CLAUDE.md — AMR R Package","text":"Pre-compiled data/ (edit directly; regenerate via data-raw/ scripts):","code":""},{"path":"https://amr-for-r.org/CLAUDE.html","id":"zero-dependency-design","dir":"","previous_headings":"","what":"Zero-Dependency Design","title":"CLAUDE.md — AMR R Package","text":"package Imports DESCRIPTION. optional integrations (ggplot2, dplyr, data.table, tidymodels, cli, crayon, etc.) listed Suggests guarded : Never add packages Imports. new functionality requires external package, add Suggests guard usage appropriately.","code":"if (requireNamespace(\"pkg\", quietly = TRUE)) { ... }"},{"path":"https://amr-for-r.org/CLAUDE.html","id":"testing","dir":"","previous_headings":"","what":"Testing","title":"CLAUDE.md — AMR R Package","text":"Framework: testthat (R ≥ 3.1); legacy tinytest used R 3.0–3.6 CI Test files: tests/testthat/test-*.R Helpers: tests/testthat/helper-functions.R CI matrix: GitHub Actions across Windows / macOS / Linux × R devel / release / oldrel-1 oldrel-4 Coverage: covr (files excluded: atc_online.R, mo_source.R, translate.R, resistance_predict.R, zz_deprecated.R, helper files, zzz.RLine truncated