Built site for AMR@3.0.1.9044: fb8758f

CLAUDE.html

@@ -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">package_coverage</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"><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>
 <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>
@@ -221,13 +221,18 @@ _pkgdown.yml    # pkgdown website configuration</code></pre>
 <p>All PRs are <strong>squash-merged</strong>, so each PR lands as exactly <strong>one commit</strong> on the default branch. Version numbers are kept in sync with the cumulative commit count since the last released tag. Therefore <strong>exactly one version bump is allowed per PR</strong>, regardless of how many intermediate commits are made on the branch.</p>
 <div class="section level4">
 <h4 id="computing-the-correct-version-number">Computing the correct version number<a class="anchor" aria-label="anchor" href="#computing-the-correct-version-number"></a></h4>
-<p>Run the following from the repo root to determine the version string to use:</p>
+<p><strong>First, ensure <code>git</code> and <code>gh</code> are installed</strong> — both are required for the version computation and for pushing changes. Install them if missing before doing anything else:</p>
-<div class="sourceCode" id="cb5"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="va">currenttag</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> describe <span class="at">--tags</span> <span class="at">--abbrev</span><span class="op">=</span>0 <span class="kw">|</span> <span class="fu">sed</span> <span class="st">'s/v//'</span><span class="va">)</span></span>
+<div class="sourceCode" id="cb5"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="fu">which</span> git <span class="kw">||</span> <span class="ex">apt-get</span> install <span class="at">-y</span> git</span>
-<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a><span class="va">currenttagfull</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> describe <span class="at">--tags</span> <span class="at">--abbrev</span><span class="op">=</span>0<span class="va">)</span></span>
+<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a><span class="fu">which</span> gh   <span class="kw">||</span> <span class="ex">apt-get</span> install <span class="at">-y</span> gh</span>
-<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a><span class="va">defaultbranch</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> branch <span class="kw">|</span> <span class="fu">cut</span> <span class="at">-c</span> 3- <span class="kw">|</span> <span class="fu">grep</span> <span class="at">-E</span> <span class="st">'^master$|^main$'</span><span class="va">)</span></span>
+<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a><span class="co"># Also ensure all tags are fetched so git describe works</span></span>
-<span id="cb5-4"><a href="#cb5-4" tabindex="-1"></a><span class="va">currentcommit</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> rev-list <span class="at">--count</span> <span class="va">${currenttagfull}</span>..<span class="va">${defaultbranch})</span></span>
+<span id="cb5-4"><a href="#cb5-4" tabindex="-1"></a><span class="fu">git</span> fetch <span class="at">--tags</span></span></code></pre></div>
-<span id="cb5-5"><a href="#cb5-5" tabindex="-1"></a><span class="va">currentversion</span><span class="op">=</span><span class="st">"</span><span class="va">${currenttag}</span><span class="st">.</span><span class="va">$((currentcommit</span> <span class="op">+</span> <span class="dv">9001</span> <span class="op">+</span> <span class="dv">1</span><span class="va">))</span><span class="st">"</span></span>
+<p>Then run the following from the repo root to determine the version string to use:</p>
-<span id="cb5-6"><a href="#cb5-6" tabindex="-1"></a><span class="bu">echo</span> <span class="st">"</span><span class="va">$currentversion</span><span class="st">"</span></span></code></pre></div>
+<div class="sourceCode" id="cb6"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="va">currenttag</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> describe <span class="at">--tags</span> <span class="at">--abbrev</span><span class="op">=</span>0 <span class="kw">|</span> <span class="fu">sed</span> <span class="st">'s/v//'</span><span class="va">)</span></span>
+<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="va">currenttagfull</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> describe <span class="at">--tags</span> <span class="at">--abbrev</span><span class="op">=</span>0<span class="va">)</span></span>
+<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a><span class="va">defaultbranch</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> branch <span class="kw">|</span> <span class="fu">cut</span> <span class="at">-c</span> 3- <span class="kw">|</span> <span class="fu">grep</span> <span class="at">-E</span> <span class="st">'^master$|^main$'</span><span class="va">)</span></span>
+<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="va">currentcommit</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> rev-list <span class="at">--count</span> <span class="va">${currenttagfull}</span>..<span class="va">${defaultbranch})</span></span>
+<span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a><span class="va">currentversion</span><span class="op">=</span><span class="st">"</span><span class="va">${currenttag}</span><span class="st">.</span><span class="va">$((currentcommit</span> <span class="op">+</span> <span class="dv">9001</span> <span class="op">+</span> <span class="dv">1</span><span class="va">))</span><span class="st">"</span></span>
+<span id="cb6-6"><a href="#cb6-6" tabindex="-1"></a><span class="bu">echo</span> <span class="st">"</span><span class="va">$currentversion</span><span class="st">"</span></span></code></pre></div>
 <p>The <code>+ 1</code> accounts for the fact that this PR’s squash commit is not yet on the default branch. Set <strong>both</strong> of these files to the resulting version string (and only once per PR, even across multiple commits):</p>
 <ol style="list-style-type: decimal"><li><p><strong><code>DESCRIPTION</code></strong> — the <code>Version:</code> field</p></li>
 <li>

CLAUDE.md

@@ -171,8 +171,19 @@ intermediate commits are made on the branch.
 
 #### Computing the correct version number
 
-Run the following from the repo root to determine the version string to
+**First, ensure `git` and `gh` are installed** — both are required for
-use:
+the version computation and for pushing changes. Install them if missing
+before doing anything else:
+
+``` bash
+which git || apt-get install -y git
+which gh   || apt-get install -y gh
+# Also ensure all tags are fetched so git describe works
+git fetch --tags
+```
+
+Then run the following from the repo root to determine the version
+string to use:
 
 ``` bash
 currenttag=$(git describe --tags --abbrev=0 | sed 's/v//')

articles/AMR.html

@@ -91,7 +91,7 @@
 website update since they are based on randomly created values and the
 page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
 Markdown</a>. However, the methodology remains unchanged. This page was
-generated on 04 April 2026.</p>
+generated on 05 April 2026.</p>
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
@@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2026-04-04</td>
+<td align="center">2026-04-05</td>
 <td align="center">abcd</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">S</td>
 </tr>
 <tr class="even">
-<td align="center">2026-04-04</td>
+<td align="center">2026-04-05</td>
 <td align="center">abcd</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">R</td>
 </tr>
 <tr class="odd">
-<td align="center">2026-04-04</td>
+<td align="center">2026-04-05</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>

articles/AMR.md

@@ -3,7 +3,7 @@
 **Note:** values on this page will change with every website update
 since they are based on randomly created values and the page was written
 in [R Markdown](https://rmarkdown.rstudio.com/). However, the
-methodology remains unchanged. This page was generated on 04 April 2026.
+methodology remains unchanged. This page was generated on 05 April 2026.
 
 ## Introduction
 
@@ -51,9 +51,9 @@ structure of your data generally look like this:
 
 |    date    | patient_id |        mo        | AMX | CIP |
 |:----------:|:----------:|:----------------:|:---:|:---:|
-| 2026-04-04 |    abcd    | Escherichia coli |  S  |  S  |
+| 2026-04-05 |    abcd    | Escherichia coli |  S  |  S  |
-| 2026-04-04 |    abcd    | Escherichia coli |  S  |  R  |
+| 2026-04-05 |    abcd    | Escherichia coli |  S  |  R  |
-| 2026-04-04 |    efgh    | Escherichia coli |  R  |  S  |
+| 2026-04-05 |    efgh    | Escherichia coli |  R  |  S  |
 
 ### Needed R packages
 

articles/PCA.html

@@ -200,7 +200,7 @@ function:</p>
 <span><span class="co">#&gt; [1] "Caryophanales"    "Enterobacterales" "Lactobacillales"  "Pseudomonadales"</span></span>
 <span><span class="co">#&gt; Importance of components:</span></span>
 <span><span class="co">#&gt;                           PC1    PC2    PC3     PC4     PC5     PC6       PC7</span></span>
-<span><span class="co">#&gt; Standard deviation     2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17</span></span>
+<span><span class="co">#&gt; Standard deviation     2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16</span></span>
 <span><span class="co">#&gt; Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span></span>
 <span><span class="co">#&gt; Cumulative Proportion  0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></span></code></pre></div>
 <pre><code><span><span class="co">#&gt; Groups (n=4, named as 'order'):</span></span>

articles/PCA.md

@@ -119,7 +119,7 @@ summary(pca_result)
 #> [1] "Caryophanales"    "Enterobacterales" "Lactobacillales"  "Pseudomonadales"
 #> Importance of components:
 #>                           PC1    PC2    PC3     PC4     PC5     PC6       PC7
-#> Standard deviation     2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17
+#> Standard deviation     2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16
 #> Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00
 #> Cumulative Proportion  0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00
 ```

articles/datasets.html

@@ -80,7 +80,7 @@
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
             
-            <h4 data-toc-skip class="date">04 April 2026</h4>
+            <h4 data-toc-skip class="date">05 April 2026</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
       <div class="d-none name"><code>datasets.Rmd</code></div>

pkgdown.yml

@@ -10,7 +10,7 @@ articles:
   PCA: PCA.html
   WHONET: WHONET.html
   WISCA: WISCA.html
-last_built: 2026-04-04T09:58Z
+last_built: 2026-04-05T15:31Z
 urls:
   reference: https://amr-for-r.org/reference
   article: https://amr-for-r.org/articles

reference/age.html

@@ -112,16 +112,16 @@
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">df</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    birth_date age age_exact age_at_y2k</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1999-06-30  26  26.76164          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1999-06-30  26  26.76438          0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1968-01-29  58  58.17808         31</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1968-01-29  58  58.18082         31</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1965-12-05  60  60.32877         34</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1965-12-05  60  60.33151         34</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1980-03-01  46  46.09315         19</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1980-03-01  46  46.09589         19</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1949-11-01  76  76.42192         50</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1949-11-01  76  76.42466         50</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1947-02-14  79  79.13425         52</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1947-02-14  79  79.13699         52</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1940-02-19  86  86.12055         59</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1940-02-19  86  86.12329         59</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1988-01-10  38  38.23014         11</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1988-01-10  38  38.23288         11</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1997-08-27  28  28.60274          2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1997-08-27  28  28.60548          2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26  48  48.18630         21</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26  48  48.18904         21</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

reference/age.md

@@ -81,14 +81,14 @@ df$age_at_y2k <- age(df$birth_date, "2000-01-01")
 
 df
 #>    birth_date age age_exact age_at_y2k
-#> 1  1999-06-30  26  26.76164          0
+#> 1  1999-06-30  26  26.76438          0
-#> 2  1968-01-29  58  58.17808         31
+#> 2  1968-01-29  58  58.18082         31
-#> 3  1965-12-05  60  60.32877         34
+#> 3  1965-12-05  60  60.33151         34
-#> 4  1980-03-01  46  46.09315         19
+#> 4  1980-03-01  46  46.09589         19
-#> 5  1949-11-01  76  76.42192         50
+#> 5  1949-11-01  76  76.42466         50
-#> 6  1947-02-14  79  79.13425         52
+#> 6  1947-02-14  79  79.13699         52
-#> 7  1940-02-19  86  86.12055         59
+#> 7  1940-02-19  86  86.12329         59
-#> 8  1988-01-10  38  38.23014         11
+#> 8  1988-01-10  38  38.23288         11
-#> 9  1997-08-27  28  28.60274          2
+#> 9  1997-08-27  28  28.60548          2
-#> 10 1978-01-26  48  48.18630         21
+#> 10 1978-01-26  48  48.18904         21
 ```

reference/as.sir.html

@@ -424,10 +424,10 @@ 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> 2026-04-04 <span style="color: #949494;">09:59:50</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> 2026-04-05 <span style="color: #949494;">15:32:33</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> 2026-04-04 <span style="color: #949494;">09:59:50</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> 2026-04-05 <span style="color: #949494;">15:32:33</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> 2026-04-04 <span style="color: #949494;">09:59:50</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> 2026-04-05 <span style="color: #949494;">15:32:33</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> 2026-04-04 <span style="color: #949494;">09:59:51</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> 2026-04-05 <span style="color: #949494;">15:32:33</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

@@ -660,10 +660,10 @@ 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 2026-04-04 09:59:50     1 MIC    amoxicillin Escherich… human      8          
+#> 1 2026-04-05 15:32:33     1 MIC    amoxicillin Escherich… human      8          
-#> 2 2026-04-04 09:59:50     1 MIC    cipro       Escherich… human      0.256      
+#> 2 2026-04-05 15:32:33     1 MIC    cipro       Escherich… human      0.256      
-#> 3 2026-04-04 09:59:50     1 DISK   tobra       Escherich… human      16         
+#> 3 2026-04-05 15:32:33     1 DISK   tobra       Escherich… human      16         
-#> 4 2026-04-04 09:59:51     1 DISK   genta       Escherich… human      18         
+#> 4 2026-04-05 15:32:33     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>

search.json

@@ -1 +1 @@
-[{"path":"https://amr-for-r.org/CLAUDE.html","id":null,"dir":"","previous_headings":"","what":"CLAUDE.md — AMR R Package","title":"CLAUDE.md — AMR R Package","text":"file provides context Claude Code working repository.","code":""},{"path":"https://amr-for-r.org/CLAUDE.html","id":"project-overview","dir":"","previous_headings":"","what":"Project Overview","title":"CLAUDE.md — AMR R Package","text":"AMR zero-dependency R package antimicrobial resistance (AMR) data analysis using One Health approach. peer-reviewed, used 175+ countries, supports 28 languages. 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
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