cli-147-2226

404.html

@@ -37,7 +37,7 @@
     
     <a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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">

LICENSE-text.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/AMR.html

@@ -39,7 +39,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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">
@@ -205,7 +205,7 @@
 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 24 May 2024.</p>
+generated on 30 May 2024.</p>
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
@@ -261,21 +261,21 @@ make the structure of your data generally look like this:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2024-05-24</td>
+<td align="center">2024-05-30</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">2024-05-24</td>
+<td align="center">2024-05-30</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">2024-05-24</td>
+<td align="center">2024-05-30</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>

articles/EUCAST.html

@@ -39,7 +39,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/MDR.html

@@ -39,7 +39,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -39,7 +39,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/WHONET.html

@@ -39,7 +39,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/datasets.html

@@ -39,7 +39,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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">
@@ -194,7 +194,7 @@
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
             
-            <h4 data-toc-skip class="date">24 May 2024</h4>
+            <h4 data-toc-skip class="date">30 May 2024</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
       <div class="d-none name"><code>datasets.Rmd</code></div>

articles/index.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/other_pkg.html

@@ -39,7 +39,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/resistance_predict.html

@@ -39,7 +39,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/welcome_to_AMR.html

@@ -39,7 +39,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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">

authors.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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">

index.html

@@ -39,7 +39,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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">

news/index.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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">
@@ -159,18 +159,18 @@
     </div>
 
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="2.1.1.9033" id="amr-2119033">AMR 2.1.1.9033<a class="anchor" aria-label="anchor" href="#amr-2119033"></a></h2>
+<h2 class="pkg-version" data-toc-text="2.1.1.9034" id="amr-2119034">AMR 2.1.1.9034<a class="anchor" aria-label="anchor" href="#amr-2119034"></a></h2>
 <p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support!)</em></p>
 <div class="section level5">
-<h5 id="a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9033">A New Milestone: One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9033"></a></h5>
+<h5 id="a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9034">A New Milestone: One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9034"></a></h5>
 <p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
 </div>
 <div class="section level3">
-<h3 id="breaking-2-1-1-9033">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9033"></a></h3>
+<h3 id="breaking-2-1-1-9034">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9034"></a></h3>
 <ul><li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over a year ago</li>
 </ul></div>
 <div class="section level3">
-<h3 id="new-2-1-1-9033">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9033"></a></h3>
+<h3 id="new-2-1-1-9034">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9034"></a></h3>
 <ul><li>One Health implementation
 <ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for animal breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
 <li>The <code>clinical_breakpoints</code> data set contains all these breakpoints, and can be downloaded on our <a href="https://msberends.github.io/AMR/articles/datasets.html">download page</a>.</li>
@@ -187,12 +187,13 @@
 <li>Function <code><a href="../reference/mo_property.html">mo_group_members()</a></code> to retrieve the member microorganisms of a microorganism group. For example, <code>mo_group_members("Strep group C")</code> returns a vector of all microorganisms that are in that group.</li>
 </ul></div>
 <div class="section level3">
-<h3 id="changed-2-1-1-9033">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9033"></a></h3>
+<h3 id="changed-2-1-1-9034">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9034"></a></h3>
 <ul><li>For SIR interpretation, it is now possible to use column names for argument <code>ab</code> and <code>mo</code>: <code>as.sir(..., ab = "column1", mo = "column2")</code>. This greatly improves the flexibility for users.</li>
 <li>For MICs:
 <ul><li>Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960)</li>
 <li>Added new argument <code>keep_operators</code> to <code><a href="../reference/as.mic.html">as.mic()</a></code>. This can be <code>"all"</code> (default), <code>"none"</code>, or <code>"edges"</code>. This argument is also available in the new <code><a href="../reference/as.mic.html">rescale_mic()</a></code> and <code>scale_*_mic()</code> functions.</li>
 <li>Comparisons of MIC values are now more strict. For example, <code>&gt;32</code> is higher than (and never equal to) <code>32</code>. Thus, <code>as.mic("&gt;32") == as.mic(32)</code> now returns <code>FALSE</code>, and <code>as.mic("&gt;32") &gt; as.mic(32)</code> now returns <code>TRUE</code>.</li>
+<li>Sorting of MIC values (using <code><a href="https://rdrr.io/r/base/sort.html" class="external-link">sort()</a></code>) was fixed in the same manner; <code>&lt;0.001</code> now gets sorted before <code>0.001</code>, and <code>&gt;0.001</code> gets sorted after <code>0.001</code>.</li>
 </ul></li>
 <li>Updated <code><a href="../reference/italicise_taxonomy.html">italicise_taxonomy()</a></code> to support HTML output</li>
 <li>
@@ -206,7 +207,7 @@
 <li>Improved overall algorithm of <code><a href="../reference/as.ab.html">as.ab()</a></code> for better performance and accuracy</li>
 </ul></div>
 <div class="section level3">
-<h3 id="other-2-1-1-9033">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9033"></a></h3>
+<h3 id="other-2-1-1-9034">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9034"></a></h3>
 <ul><li>Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
 </ul></div>
 </div>

pkgdown.yml

@@ -11,7 +11,7 @@ articles:
   resistance_predict: resistance_predict.html
   welcome_to_AMR: welcome_to_AMR.html
   WHONET: WHONET.html
-last_built: 2024-05-24T13:10Z
+last_built: 2024-05-30T14:04Z
 urls:
   reference: https://msberends.github.io/AMR/reference
   article: https://msberends.github.io/AMR/articles

reference/AMR-options.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -24,7 +24,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/WHOCC.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/WHONET.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/ab_from_text.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/ab_property.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/add_custom_antimicrobials.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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">
@@ -222,16 +222,16 @@
 <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  1965-12-05  58  58.46721         34</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1965-12-05  58  58.48361         34</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1980-03-01  44  44.22951         19</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1980-03-01  44  44.24590         19</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1949-11-01  74  74.56011         50</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1949-11-01  74  74.57650         50</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1947-02-14  77  77.27322         52</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1947-02-14  77  77.28962         52</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1940-02-19  84  84.25956         59</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1940-02-19  84  84.27596         59</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1988-01-10  36  36.36885         11</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1988-01-10  36  36.38525         11</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1997-08-27  26  26.74044          2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1997-08-27  26  26.75683          2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1978-01-26  46  46.32514         21</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1978-01-26  46  46.34153         21</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1972-06-17  51  51.93443         27</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1972-06-17  51  51.95082         27</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10  37  37.78689         13</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10  37  37.80328         13</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

reference/age_groups.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/antibiotic_class_selectors.html

@@ -12,7 +12,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/antibiotics.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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">
@@ -307,23 +307,27 @@
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   all the details of the breakpoint interpretations. Note that some</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   microorganisms might not have breakpoints for each antimicrobial drug in</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   EUCAST 2023.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMX', EUCAST 2023...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: , EUCAST 2023...</span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in data.frame(values = x, mo = mo, ab = ab, result = NA_sir_, uti = uti,     host = host, stringsAsFactors = FALSE):</span> arguments imply differing number of rows: 4, 1</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  NOTE </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   • Multiple breakpoints available for amoxicillin (AMX) in Streptococcus</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      pneumoniae - assuming body site 'Meningitis'.</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S R R R</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># plot MIC values, see ?plot</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">mic_data</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="as.mic-1.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in data.frame(values = x, mo = mo, ab = ab, result = NA_sir_, uti = uti,     host = host, stringsAsFactors = FALSE):</span> arguments imply differing number of rows: 9, 1</span>
+<span class="r-plt img"><img src="as.mic-2.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in data.frame(values = x, mo = mo, ab = ab, result = NA_sir_, uti = uti,     host = host, stringsAsFactors = FALSE):</span> arguments imply differing number of rows: 9, 1</span>
+<span class="r-plt img"><img src="as.mic-3.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span> <span class="co"># Dutch</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in data.frame(values = x, mo = mo, ab = ab, result = NA_sir_, uti = uti,     host = host, stringsAsFactors = FALSE):</span> arguments imply differing number of rows: 9, 1</span>
+<span class="r-plt img"><img src="as.mic-4.png" alt="" width="700" height="433"></span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

reference/as.mo.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -24,7 +24,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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">
@@ -602,13 +602,22 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># return a 'logbook' about the results:</span></span></span>
 <span class="r-in"><span><span class="fu">sir_interpretation_history</span><span class="op">(</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 14</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 13 × 14</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   datetime            index ab_user mo_user        ab   mo                input</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    datetime            index ab_user    mo_user    ab   mo                input</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;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>              <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span>              <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>              <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2024-05-24 <span style="color: #949494;">13:11:09</span>     1 TOB     Escherichia c… TOB  B_[ORD]_ENTRBCTR 16    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-05-30 <span style="color: #949494;">14:05:20</span>     1 TOB        Escherich… TOB  B_[ORD]_ENTRBCTR 16    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2024-05-24 <span style="color: #949494;">13:11:09</span>     1 GEN     Escherichia c… GEN  B_[ORD]_ENTRBCTR 18    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-05-30 <span style="color: #949494;">14:05:20</span>     1 GEN        Escherich… GEN  B_[ORD]_ENTRBCTR 18    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2024-05-24 <span style="color: #949494;">13:11:09</span>     1 CIP     Escherichia c… CIP  B_[ORD]_ENTRBCTR  0.256</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-05-30 <span style="color: #949494;">14:05:20</span>     1 CIP        Escherich… CIP  B_[ORD]_ENTRBCTR  0.256</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2024-05-24 <span style="color: #949494;">13:11:09</span>     1 AMP     Escherichia c… AMP  B_[ORD]_ENTRBCTR  8    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-05-30 <span style="color: #949494;">14:05:20</span>     1 AMP        Escherich… AMP  B_[ORD]_ENTRBCTR  8    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-05-30 <span style="color: #949494;">14:05:15</span>     1 AMX        B_STRPT_P… AMX  B_STRPT_PNMN      0.01 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-05-30 <span style="color: #949494;">14:05:15</span>     2 AMX        B_STRPT_P… AMX  B_STRPT_PNMN      2    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-05-30 <span style="color: #949494;">14:05:15</span>     3 AMX        B_STRPT_P… AMX  B_STRPT_PNMN      4    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-05-30 <span style="color: #949494;">14:05:15</span>     4 AMX        B_STRPT_P… AMX  B_STRPT_PNMN      8    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-05-30 <span style="color: #949494;">14:05:15</span>     1 AMX        B_STRPT_P… AMX  B_STRPT_PNMN      2    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-05-30 <span style="color: #949494;">14:05:15</span>     1 TOB        Escherich… TOB  B_[ORD]_ENTRBCTR 16    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> 2024-05-30 <span style="color: #949494;">14:05:15</span>     1 GEN        Escherich… GEN  B_[ORD]_ENTRBCTR 18    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> 2024-05-30 <span style="color: #949494;">14:05:15</span>     1 AMP        Escherich… AMP  B_[ORD]_ENTRBCTR 20    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> 2024-05-30 <span style="color: #949494;">14:05:14</span>     1 ampicillin Strep pneu AMP  B_STRPT_PNMN     18    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 7 more variables: outcome &lt;sir&gt;, method &lt;chr&gt;, breakpoint_S_R &lt;chr&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   guideline &lt;chr&gt;, host &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;</span></span>
 <span class="r-in"><span></span></span>
@@ -818,8 +827,31 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   all the details of the breakpoint interpretations. Note that some</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   microorganisms might not have breakpoints for each antimicrobial drug in</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   EUCAST 2023.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'NIT', EUCAST 2023...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column , EUCAST 2023...</span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in data.frame(values = x, mo = mo, ab = ab, result = NA_sir_, uti = uti,     host = host, stringsAsFactors = FALSE):</span> arguments imply differing number of rows: 2, 1</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  OK </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Assuming value "urine" in column 'specimen' reflects a urinary tract</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   infection.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   Use as.sir(uti = FALSE) to prevent this.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   all the details of the breakpoint interpretations. Note that some</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   microorganisms might not have breakpoints for each antimicrobial drug in</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   EUCAST 2023.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column , EUCAST 2023...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  OK </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   all the details of the breakpoint interpretations. Note that some</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   microorganisms might not have breakpoints for each antimicrobial drug in</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   EUCAST 2023.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP', EUCAST 2023...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  OK </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP', EUCAST 2023...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  OK </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'GEN', EUCAST 2023...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  OK </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'TOB', EUCAST 2023...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  OK </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>      microorganism AMP  CIP GEN TOB ERY</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli   S &lt;NA&gt;   S   S   R</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># For CLEANING existing SIR values ------------------------------------</span></span></span>
 <span class="r-in"><span></span></span>

reference/atc_online.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -16,7 +16,7 @@ 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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -12,7 +12,7 @@ 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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</small>
 
     
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reference/eucast_rules.html

@@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -12,7 +12,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/g.test.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/get_episode.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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_pca.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/index.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/join.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/kurtosis.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/like.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/mdro.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/mean_amr_distance.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/microorganisms.codes.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/microorganisms.groups.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/microorganisms.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</small>
 
     
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reference/mo_matching_score.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/mo_property.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/mo_source.html

@@ -12,7 +12,7 @@ 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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/pca.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/plot.html

@@ -12,7 +12,7 @@ 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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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">
@@ -368,11 +368,11 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># when providing the microorganism and antibiotic, colours will show interpretations:</span></span></span>
 <span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_mic_values</span>, mo <span class="op">=</span> <span class="st">"S. aureus"</span>, ab <span class="op">=</span> <span class="st">"ampicillin"</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in data.frame(values = x, mo = mo, ab = ab, result = NA_sir_, uti = uti,     host = host, stringsAsFactors = FALSE):</span> arguments imply differing number of rows: 23, 1</span>
+<span class="r-plt img"><img src="plot-4.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_disk_values</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in data.frame(values = x, mo = mo, ab = ab, result = NA_sir_, uti = uti,     host = host, stringsAsFactors = FALSE):</span> arguments imply differing number of rows: 15, 1</span>
+<span class="r-plt img"><img src="plot-5.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_disk_values</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in data.frame(values = x, mo = mo, ab = ab, result = NA_sir_, uti = uti,     host = host, stringsAsFactors = FALSE):</span> arguments imply differing number of rows: 15, 1</span>
+<span class="r-plt img"><img src="plot-6.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Plotting using scale_x_mic()</span></span></span>
@@ -385,38 +385,38 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span class="r-in"><span>  <span class="va">mic_plot</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"without scale_x_mic()"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-plt img"><img src="plot-4.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-7.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">mic_plot</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu">scale_x_mic</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"with scale_x_mic()"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-plt img"><img src="plot-5.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-8.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">mic_plot</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu">scale_x_mic</span><span class="op">(</span>keep_operators <span class="op">=</span> <span class="st">"all"</span><span class="op">)</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"with scale_x_mic() keeping all operators"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-plt img"><img src="plot-6.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-9.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">mic_plot</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu">scale_x_mic</span><span class="op">(</span>mic_range <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">128</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"with scale_x_mic() using a manual range"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-plt img"><img src="plot-7.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-10.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">some_mic_values</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-plt img"><img src="plot-8.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-11.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">some_disk_values</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in data.frame(values = x, mo = mo, ab = ab, result = NA_sir_, uti = uti,     host = host, stringsAsFactors = FALSE):</span> arguments imply differing number of rows: 15, 1</span>
+<span class="r-plt img"><img src="plot-12.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">some_sir_values</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-plt img"><img src="plot-9.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-13.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
     </div>

reference/proportion.html

@@ -12,7 +12,7 @@ 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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/random.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/resistance_predict.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/skewness.html

@@ -12,7 +12,7 @@ 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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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/translate.html

@@ -10,7 +10,7 @@
     
     <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="">2.1.1.9033</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9034</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">