Built site for AMR@3.0.1.9044: 6c24718

404.html

@@ -31,7 +31,7 @@
 
     <a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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LICENSE-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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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articles/AMR.html

@@ -30,7 +30,7 @@
 
     <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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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@@ -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 02 April 2026.</p>
+generated on 04 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">2026-04-02</td>
+<td align="center">2026-04-04</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">2026-04-02</td>
+<td align="center">2026-04-04</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">2026-04-02</td>
+<td align="center">2026-04-04</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 02 April 2026.
+methodology remains unchanged. This page was generated on 04 April 2026.
 
 ## Introduction
 
@@ -51,9 +51,9 @@ structure of your data generally look like this:
 
 |    date    | patient_id |        mo        | AMX | CIP |
 |:----------:|:----------:|:----------------:|:---:|:---:|
-| 2026-04-02 |    abcd    | Escherichia coli |  S  |  S  |
+| 2026-04-04 |    abcd    | Escherichia coli |  S  |  S  |
-| 2026-04-02 |    abcd    | Escherichia coli |  S  |  R  |
+| 2026-04-04 |    abcd    | Escherichia coli |  S  |  R  |
-| 2026-04-02 |    efgh    | Escherichia coli |  R  |  S  |
+| 2026-04-04 |    efgh    | Escherichia coli |  R  |  S  |
 
 ### Needed R packages
 

articles/AMR_for_Python.html

@@ -30,7 +30,7 @@
 
     <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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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articles/AMR_with_tidymodels.html

@@ -30,7 +30,7 @@
 
     <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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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articles/EUCAST.html

@@ -30,7 +30,7 @@
 
     <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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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">

articles/PCA.html

@@ -30,7 +30,7 @@
 
     <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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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">
@@ -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 1.232e-16</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; 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 1.232e-16
+#> Standard deviation     2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17
 #> 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/WHONET.html

@@ -30,7 +30,7 @@
 
     <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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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articles/WISCA.html

@@ -30,7 +30,7 @@
 
     <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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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articles/datasets.html

@@ -30,7 +30,7 @@
 
     <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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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">
@@ -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">02 April 2026</h4>
+            <h4 data-toc-skip class="date">04 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>
@@ -424,7 +424,7 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
 <em>iv_ddd</em>, <em>iv_units</em>, and <em>loinc</em>.</p>
 <p>This data set is in R available as <code>antimicrobials</code>, after
 you load the <code>AMR</code> package.</p>
-<p>It was last updated on 23 March 2026 09:38:28 UTC. Find more info
+<p>It was last updated on 4 April 2026 09:51:50 UTC. Find more info
 about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
 here</a>.</p>
 <p><strong>Direct download links:</strong></p>

articles/datasets.md

@@ -100,7 +100,7 @@ names:
 This data set is in R available as `antimicrobials`, after you load the
 `AMR` package.
 
-It was last updated on 23 March 2026 09:38:28 UTC. Find more info about
+It was last updated on 4 April 2026 09:51:50 UTC. Find more info about
 the contents, (scientific) source, and structure of this [data set
 here](https://amr-for-r.org/reference/antimicrobials.html).
 

articles/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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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authors.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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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index.html

@@ -33,7 +33,7 @@
 
     <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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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">
@@ -49,9 +49,9 @@
     </div>
 
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="3.0.1.9043" id="amr-3019043">AMR 3.0.1.9043<a class="anchor" aria-label="anchor" href="#amr-3019043"></a></h2>
+<h2 class="pkg-version" data-toc-text="3.0.1.9044" id="amr-3019044">AMR 3.0.1.9044<a class="anchor" aria-label="anchor" href="#amr-3019044"></a></h2>
 <div class="section level4">
-<h4 id="new-3-0-1-9043">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9043"></a></h4>
+<h4 id="new-3-0-1-9044">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9044"></a></h4>
 <ul><li>Support for clinical breakpoints of 2026 of both CLSI and EUCAST, by adding all of their over 5,700 new clinical breakpoints to the <code>clinical_breakpoints</code> data set for usage in <code><a href="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2026 is now the new default guideline for all MIC and disk diffusion interpretations.</li>
 <li>Integration with the <strong>tidymodels</strong> framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via <code>recipes</code>
 <ul><li>
@@ -84,7 +84,7 @@
 <li>Function <code><a href="../reference/amr_course.html">amr_course()</a></code>, which allows for automated download and unpacking of a GitHub repository for e.g. webinar use</li>
 </ul></div>
 <div class="section level4">
-<h4 id="fixes-3-0-1-9043">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9043"></a></h4>
+<h4 id="fixes-3-0-1-9044">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9044"></a></h4>
 <ul><li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where values that were purely numeric (e.g., <code>"1"</code>) and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter</li>
 <li>Fixed a bug in <code><a href="../reference/as.mic.html">as.mic()</a></code> where MIC values in scientific notation (e.g., <code>"1e-3"</code>) were incorrectly handled because the letter <code>e</code> was removed along with other Unicode letters; scientific notation <code>e</code> is now preserved</li>
 <li>Fixed a bug in <code><a href="../reference/as.ab.html">as.ab()</a></code> where certain AB codes containing “PH” or “TH” (such as <code>ETH</code>, <code>MTH</code>, <code>PHE</code>, <code>PHN</code>, <code>STH</code>, <code>THA</code>, <code>THI1</code>) would incorrectly return <code>NA</code> when combined in a vector with any untranslatable value (<a href="https://github.com/msberends/AMR/issues/245" class="external-link">#245</a>)</li>
@@ -99,7 +99,7 @@
 <li>Fixed SIR and MIC coercion of combined values, e.g. <code>as.sir("&lt;= 0.002; S")</code> or <code>as.mic("S; 0.002")</code> (<a href="https://github.com/msberends/AMR/issues/252" class="external-link">#252</a>)</li>
 </ul></div>
 <div class="section level4">
-<h4 id="updates-3-0-1-9043">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9043"></a></h4>
+<h4 id="updates-3-0-1-9044">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9044"></a></h4>
 <ul><li>Extensive <code>cli</code> integration for better message handling and clickable links in messages and warnings (<a href="https://github.com/msberends/AMR/issues/191" class="external-link">#191</a>, <a href="https://github.com/msberends/AMR/issues/265" class="external-link">#265</a>)</li>
 <li>
 <code><a href="../reference/mdro.html">mdro()</a></code> now infers resistance for a <em>missing</em> base drug column from an <em>available</em> corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument <code>infer_from_combinations</code>, which defaults to <code>TRUE</code> (<a href="https://github.com/msberends/AMR/issues/209" class="external-link">#209</a>). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).</li>

news/index.md

@@ -1,6 +1,6 @@
 # Changelog
 
-## AMR 3.0.1.9043
+## AMR 3.0.1.9044
 
 #### New
 

pkgdown.yml

@@ -10,7 +10,7 @@ articles:
   PCA: PCA.html
   WHONET: WHONET.html
   WISCA: WISCA.html
-last_built: 2026-04-02T10:27Z
+last_built: 2026-04-04T09:58Z
 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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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-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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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.html

@@ -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>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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">
@@ -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  26.75616          0</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> 2  1968-01-29  58  58.17260         31</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> 3  1965-12-05  60  60.32329         34</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> 4  1980-03-01  46  46.08767         19</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> 5  1949-11-01  76  76.41644         50</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> 6  1947-02-14  79  79.12877         52</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> 7  1940-02-19  86  86.11507         59</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> 8  1988-01-10  38  38.22466         11</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> 9  1997-08-27  28  28.59726          2</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> 10 1978-01-26  48  48.18082         21</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26  48  48.18630         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  26.75616          0
+#> 1  1999-06-30  26  26.76164          0
-#> 2  1968-01-29  58  58.17260         31
+#> 2  1968-01-29  58  58.17808         31
-#> 3  1965-12-05  60  60.32329         34
+#> 3  1965-12-05  60  60.32877         34
-#> 4  1980-03-01  46  46.08767         19
+#> 4  1980-03-01  46  46.09315         19
-#> 5  1949-11-01  76  76.41644         50
+#> 5  1949-11-01  76  76.42192         50
-#> 6  1947-02-14  79  79.12877         52
+#> 6  1947-02-14  79  79.13425         52
-#> 7  1940-02-19  86  86.11507         59
+#> 7  1940-02-19  86  86.12055         59
-#> 8  1988-01-10  38  38.22466         11
+#> 8  1988-01-10  38  38.23014         11
-#> 9  1997-08-27  28  28.59726          2
+#> 9  1997-08-27  28  28.60274          2
-#> 10 1978-01-26  48  48.18082         21
+#> 10 1978-01-26  48  48.18630         21
 ```

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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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">
@@ -193,7 +193,7 @@ may affect the computations for subsequent operations.</p></dd>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">modeldata   </span> 1.5.1      <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tune        </span> 2.0.1 </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">parsnip     </span> 1.4.1      <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflows   </span> 1.3.0 </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">purrr       </span> 1.2.1      <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflowsets</span> 1.1.1 </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">recipes     </span> 1.3.1      <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">yardstick   </span> 1.3.2 </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">recipes     </span> 1.3.2      <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">yardstick   </span> 1.3.2 </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="font-weight: bold;">Conflicts</span> ───────────────────────────────────────── tidymodels_conflicts() ──</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">purrr</span>::<span style="color: #00BB00;">discard()</span> masks <span style="color: #0000BB;">scales</span>::discard()</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">dplyr</span>::<span style="color: #00BB00;">filter()</span>  masks <span style="color: #0000BB;">stats</span>::filter()</span>

reference/amr-tidymodels.md

@@ -172,7 +172,7 @@ if (require("tidymodels")) {
 #> ✔ modeldata    1.5.1      ✔ tune         2.0.1 
 #> ✔ parsnip      1.4.1      ✔ workflows    1.3.0 
 #> ✔ purrr        1.2.1      ✔ workflowsets 1.1.1 
-#> ✔ recipes      1.3.1      ✔ yardstick    1.3.2 
+#> ✔ recipes      1.3.2      ✔ yardstick    1.3.2 
 #> ── Conflicts ───────────────────────────────────────── tidymodels_conflicts() ──
 #> ✖ purrr::discard() masks scales::discard()
 #> ✖ dplyr::filter()  masks stats::filter()

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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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

@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
 
     <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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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">
@@ -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> 2026-04-02 <span style="color: #949494;">10:28:11</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> 2026-04-04 <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;">2</span> 2026-04-02 <span style="color: #949494;">10:28:11</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> 2026-04-04 <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;">3</span> 2026-04-02 <span style="color: #949494;">10:28:11</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> 2026-04-04 <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;">4</span> 2026-04-02 <span style="color: #949494;">10:28:12</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> 2026-04-04 <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: #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 2026-04-02 10:28:11     1 MIC    amoxicillin Escherich… human      8          
+#> 1 2026-04-04 09:59:50     1 MIC    amoxicillin Escherich… human      8          
-#> 2 2026-04-02 10:28:11     1 MIC    cipro       Escherich… human      0.256      
+#> 2 2026-04-04 09:59:50     1 MIC    cipro       Escherich… human      0.256      
-#> 3 2026-04-02 10:28:11     1 DISK   tobra       Escherich… human      16         
+#> 3 2026-04-04 09:59:50     1 DISK   tobra       Escherich… human      16         
-#> 4 2026-04-02 10:28:12     1 DISK   genta       Escherich… human      18         
+#> 4 2026-04-04 09:59:51     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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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_eucast_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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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reference/export_ncbi_biosample.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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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/first_isolate.html

@@ -9,7 +9,7 @@
 
     <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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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reference/g.test.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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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reference/get_episode.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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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reference/ggplot_pca.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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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/ggplot_sir.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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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/guess_ab_col.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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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reference/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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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reference/interpretive_rules.html

@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
 
     <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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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/intrinsic_resistant.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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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/italicise_taxonomy.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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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reference/join.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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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/key_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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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reference/kurtosis.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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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reference/like.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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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reference/mdro.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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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reference/mean_amr_distance.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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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reference/microorganisms.codes.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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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reference/microorganisms.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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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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
 
     <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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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reference/mo_matching_score.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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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reference/mo_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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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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
 
     <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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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reference/pca.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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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reference/plot.html

@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 
     <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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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reference/proportion.html

@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
 
     <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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</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>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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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
 
     <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="">3.0.1.9043</small>
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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
 
     <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="">3.0.1.9043</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9044</small>
 
 
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reference/top_n_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="">3.0.1.9043</small>
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reference/translate.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="">3.0.1.9043</small>
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