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articles/AMR_for_Python.html

@@ -30,7 +30,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
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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

articles/AMR_for_Python.md

@@ -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

articles/AMR_with_tidymodels.html

@@ -30,7 +30,7 @@
 
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@@ -30,7 +30,7 @@
 
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@@ -30,7 +30,7 @@
 
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@@ -30,7 +30,7 @@
 
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@@ -30,7 +30,7 @@
 
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@@ -7,7 +7,7 @@
 
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authors.html

@@ -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>
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index.html

@@ -33,7 +33,7 @@
 
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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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news/index.html

@@ -7,7 +7,7 @@
 
     <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="">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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@@ -49,15 +49,15 @@
     </div>
 
     <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>
 <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>
 <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>
 <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>
 <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>
@@ -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>
 </ul></div>
 <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>
 <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>
@@ -101,7 +101,7 @@
 </li>
 </ul></div>
 <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>
 <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>
 <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>
 </div>
     <div class="section level2">

news/index.md

@@ -1,6 +1,6 @@
 # Changelog
 
-## AMR 3.0.1.9075
+## AMR 3.0.1.9076
 
 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
   called from Python
   ([\#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
 

pkgdown.yml

@@ -10,7 +10,7 @@ articles:
   PCA: PCA.html
   WHONET: WHONET.html
   WISCA: WISCA.html
-last_built: 2026-06-26T10:08Z
+last_built: 2026-06-26T13:07Z
 urls:
   reference: https://amr-for-r.org/reference
   article: https://amr-for-r.org/articles

reference/AMR-deprecated.html

@@ -7,7 +7,7 @@
 
     <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="">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

@@ -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>
 
-    <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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reference/AMR.html

@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
 
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reference/WHOCC.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/WHONET.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/ab_from_text.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/ab_property.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/add_custom_antimicrobials.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/add_custom_microorganisms.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/age.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/age_groups.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/amr-tidymodels.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/amr_course.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/antibiogram.html

@@ -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>
 
-    <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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/antimicrobial_selectors.html

@@ -17,7 +17,7 @@ my_data_with_all_these_columns %>%
 
     <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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/antimicrobials.html

@@ -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>
 
-    <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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/as.ab.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/as.av.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/as.disk.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/as.mic.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/as.mo.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/as.sir.html

@@ -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>
 
-    <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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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>   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: #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;">#   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>

reference/as.sir.md

@@ -712,10 +712,10 @@ sir_interpretation_history()
 #> # A tibble: 4 × 18
 #>   datetime            index method ab_given    mo_given   host_given input_given
 #>   <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>,
 #> #   outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
 #> #   breakpoint_S_R <chr>, site <chr>

reference/atc_online.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/av_from_text.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/av_property.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/availability.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/bug_drug_combinations.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/clinical_breakpoints.html

@@ -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>
 
-    <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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/count.html

@@ -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>
 
-    <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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/custom_interpretive_rules.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/custom_mdro_guideline.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/dosage.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/esbl_isolates.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/example_isolates.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/example_isolates_unclean.html

@@ -7,7 +7,7 @@
 
     <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="">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>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/export_ncbi_biosample.html

@@ -7,7 +7,7 @@
 
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reference/first_isolate.html

@@ -9,7 +9,7 @@
 
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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>
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reference/g.test.html

@@ -7,7 +7,7 @@
 
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reference/get_episode.html

@@ -7,7 +7,7 @@
 
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reference/ggplot_pca.html

@@ -7,7 +7,7 @@
 
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reference/ggplot_sir.html

@@ -7,7 +7,7 @@
 
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reference/guess_ab_col.html

@@ -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>
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reference/index.html

@@ -7,7 +7,7 @@
 
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reference/interpretive_rules.html

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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>
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reference/intrinsic_resistant.html

@@ -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>
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reference/italicise_taxonomy.html

@@ -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>
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reference/join.html

@@ -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>
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reference/key_antimicrobials.html

@@ -7,7 +7,7 @@
 
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reference/kurtosis.html

@@ -7,7 +7,7 @@
 
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reference/like.html

@@ -7,7 +7,7 @@
 
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reference/mdro.html

@@ -7,7 +7,7 @@
 
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reference/mean_amr_distance.html

@@ -7,7 +7,7 @@
 
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reference/microorganisms.codes.html

@@ -7,7 +7,7 @@
 
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reference/microorganisms.groups.html

@@ -7,7 +7,7 @@
 
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reference/microorganisms.html

@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
 
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reference/mo_matching_score.html

@@ -7,7 +7,7 @@
 
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reference/mo_property.html

@@ -7,7 +7,7 @@
 
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reference/mo_source.html

@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
 
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reference/pca.html

@@ -7,7 +7,7 @@
 
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reference/plot.html

@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 
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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>
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reference/proportion.html

@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
 
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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>
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reference/random.html

@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
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reference/resistance_predict.html

@@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
 
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reference/skewness.html

@@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
 
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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>
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reference/top_n_microorganisms.html

@@ -7,7 +7,7 @@
 
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reference/translate.html

@@ -7,7 +7,7 @@
 
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