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CLAUDE.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="">3.0.1.9052</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9053</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">
@@ -73,7 +73,7 @@
 <span><span class="fu">pkgdown</span><span class="fu">::</span><span class="fu"><a href="https://pkgdown.r-lib.org/reference/build_site.html" class="external-link">build_site</a></span><span class="op">(</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># Code coverage report</span></span>
-<span><span class="fu">covr</span><span class="fu">::</span><span class="fu"><a href="http://covr.r-lib.org/reference/package_coverage.html" class="external-link">package_coverage</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
+<span><span class="fu">covr</span><span class="fu">::</span><span class="fu">package_coverage</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
 <p>From the shell:</p>
 <div class="sourceCode" id="cb2"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="co"># CRAN check from parent directory</span></span>
 <span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a><span class="ex">R</span> CMD check AMR</span></code></pre></div>
@@ -92,13 +92,13 @@ _pkgdown.yml    # pkgdown website configuration</code></pre>
 <div class="section level2">
 <h2 id="r-source-file-conventions">R Source File Conventions<a class="anchor" aria-label="anchor" href="#r-source-file-conventions"></a></h2>
 <p><strong>Naming conventions in <code>R/</code>:</strong></p>
-<table class="table"><thead><tr class="header"><th>Prefix/Name</th>
+<table class="table"><thead><tr><th>Prefix/Name</th>
 <th>Purpose</th>
-</tr></thead><tbody><tr class="odd"><td><code>aa_*.R</code></td>
+</tr></thead><tbody><tr><td><code>aa_*.R</code></td>
 <td>Loaded first (helpers, globals, options, package docs)</td>
-</tr><tr class="even"><td><code>zz_deprecated.R</code></td>
+</tr><tr><td><code>zz_deprecated.R</code></td>
 <td>Deprecated function wrappers</td>
-</tr><tr class="odd"><td><code>zzz.R</code></td>
+</tr><tr><td><code>zzz.R</code></td>
 <td>
 <code>.onLoad</code> / <code>.onAttach</code> initialization</td>
 </tr></tbody></table><p><strong>Key source files:</strong></p>
@@ -136,46 +136,46 @@ _pkgdown.yml    # pkgdown website configuration</code></pre>
 <div class="section level2">
 <h2 id="custom-s3-classes">Custom S3 Classes<a class="anchor" aria-label="anchor" href="#custom-s3-classes"></a></h2>
 <p>The package defines five S3 classes with full print/format/plot/vctrs support:</p>
-<table class="table"><thead><tr class="header"><th>Class</th>
+<table class="table"><thead><tr><th>Class</th>
 <th>Created by</th>
 <th>Represents</th>
-</tr></thead><tbody><tr class="odd"><td><code>&lt;mo&gt;</code></td>
+</tr></thead><tbody><tr><td><code>&lt;mo&gt;</code></td>
 <td><code><a href="reference/as.mo.html">as.mo()</a></code></td>
 <td>Microorganism code</td>
-</tr><tr class="even"><td><code>&lt;ab&gt;</code></td>
+</tr><tr><td><code>&lt;ab&gt;</code></td>
 <td><code><a href="reference/as.ab.html">as.ab()</a></code></td>
 <td>Antimicrobial drug code</td>
-</tr><tr class="odd"><td><code>&lt;av&gt;</code></td>
+</tr><tr><td><code>&lt;av&gt;</code></td>
 <td><code><a href="reference/as.av.html">as.av()</a></code></td>
 <td>Antiviral drug code</td>
-</tr><tr class="even"><td><code>&lt;sir&gt;</code></td>
+</tr><tr><td><code>&lt;sir&gt;</code></td>
 <td><code><a href="reference/as.sir.html">as.sir()</a></code></td>
 <td>SIR value (S/I/R/SDD)</td>
-</tr><tr class="odd"><td><code>&lt;mic&gt;</code></td>
+</tr><tr><td><code>&lt;mic&gt;</code></td>
 <td><code><a href="reference/as.mic.html">as.mic()</a></code></td>
 <td>Minimum inhibitory concentration</td>
-</tr><tr class="even"><td><code>&lt;disk&gt;</code></td>
+</tr><tr><td><code>&lt;disk&gt;</code></td>
 <td><code><a href="reference/as.disk.html">as.disk()</a></code></td>
 <td>Disk diffusion diameter</td>
 </tr></tbody></table></div>
 <div class="section level2">
 <h2 id="data-files">Data Files<a class="anchor" aria-label="anchor" href="#data-files"></a></h2>
 <p>Pre-compiled in <code>data/</code> (do not edit directly; regenerate via <code>data-raw/</code> scripts):</p>
-<table class="table"><colgroup><col width="50%"><col width="50%"></colgroup><thead><tr class="header"><th>File</th>
+<table class="table"><colgroup><col width="50%"><col width="50%"></colgroup><thead><tr><th>File</th>
 <th>Contents</th>
-</tr></thead><tbody><tr class="odd"><td><code>microorganisms.rda</code></td>
+</tr></thead><tbody><tr><td><code>microorganisms.rda</code></td>
 <td>~79,000 microbial species with full taxonomy</td>
-</tr><tr class="even"><td><code>antimicrobials.rda</code></td>
+</tr><tr><td><code>antimicrobials.rda</code></td>
 <td>~620 antimicrobial drugs with ATC codes</td>
-</tr><tr class="odd"><td><code>antivirals.rda</code></td>
+</tr><tr><td><code>antivirals.rda</code></td>
 <td>Antiviral drugs</td>
-</tr><tr class="even"><td><code>clinical_breakpoints.rda</code></td>
+</tr><tr><td><code>clinical_breakpoints.rda</code></td>
 <td>EUCAST + CLSI breakpoints (2011–2025)</td>
-</tr><tr class="odd"><td><code>intrinsic_resistant.rda</code></td>
+</tr><tr><td><code>intrinsic_resistant.rda</code></td>
 <td>Intrinsic resistance patterns</td>
-</tr><tr class="even"><td><code>example_isolates.rda</code></td>
+</tr><tr><td><code>example_isolates.rda</code></td>
 <td>Example AMR dataset for documentation/testing</td>
-</tr><tr class="odd"><td><code>WHONET.rda</code></td>
+</tr><tr><td><code>WHONET.rda</code></td>
 <td>Example WHONET-format dataset</td>
 </tr></tbody></table></div>
 <div class="section level2">