cli-6201-2091

404.html

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     <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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</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

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     <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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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articles/AMR.html

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     <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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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articles/EUCAST.html

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     <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="">2.1.1.9053</small>
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articles/MDR.html

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     <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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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articles/PCA.html

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     <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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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articles/WHONET.html

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     <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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</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

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     <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="">2.1.1.9053</small>
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articles/index.html

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     <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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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articles/other_pkg.html

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     <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="">2.1.1.9053</small>
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articles/resistance_predict.html

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     <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="">2.1.1.9053</small>
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articles/welcome_to_AMR.html

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     <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="">2.1.1.9053</small>
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authors.html

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     <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="">2.1.1.9053</small>
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</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="2.1.1.9053" id="amr-2119053">AMR 2.1.1.9053<a class="anchor" aria-label="anchor" href="#amr-2119053"></a></h2>
+<h2 class="pkg-version" data-toc-text="2.1.1.9054" id="amr-2119054">AMR 2.1.1.9054<a class="anchor" aria-label="anchor" href="#amr-2119054"></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>
+<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! Install this beta using <a href="https://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p>
 <div class="section level5">
-<h5 id="a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9053">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-2-1-1-9053"></a></h5>
+<h5 id="a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9054">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-2-1-1-9054"></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-2-1-1-9053">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9053"></a></h3>
+<h3 id="breaking-2-1-1-9054">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9054"></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-2-1-1-9053">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9053"></a></h3>
+<h3 id="new-2-1-1-9054">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9054"></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>
@@ -180,15 +180,15 @@
 <li>
 <code><a href="../reference/ab_property.html">ab_url()</a></code> now supports retrieving the WHOCC url of their ATCvet pages</li>
 </ul></li>
+<li>EUCAST 2024 and CLSI 2024 are now supported, by adding all of their over 4,000 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 2024 (v14.0) is now the new default guideline for all MIC and disks diffusion interpretations.</li>
 <li>
 <code><a href="../reference/as.sir.html">as.sir()</a></code> now brings additional factor levels: “NI” for non-interpretable and “SDD” for susceptible dose-dependent. Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI. Also, to get quantitative values, <code><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double()</a></code> or a <code>sir</code> object will return 1 for S, 2 for SDD/I, and 3 for R (NI will become <code>NA</code>). Other functions using <code>sir</code> classes (e.g., <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code>) are updated to reflect the change to contain NI and SDD.</li>
 <li>The function group <code>scale_*_mic()</code>, namely: <code><a href="../reference/plot.html">scale_x_mic()</a></code>, <code><a href="../reference/plot.html">scale_y_mic()</a></code>, <code><a href="../reference/plot.html">scale_colour_mic()</a></code> and <code><a href="../reference/plot.html">scale_fill_mic()</a></code>. They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.</li>
 <li>Function <code><a href="../reference/as.mic.html">rescale_mic()</a></code>, which allows to rescale MIC values to a manually set range. This is the powerhouse behind the <code>scale_*_mic()</code> functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.</li>
 <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>
-<li>Clinical breakpoints and intrinsic resistance of EUCAST 2024 and CLSI 2024 have been added to the <code>clinical_breakpoints</code> data set for usage in <code><a href="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2024 (v14.0) is now the new default guideline for all MIC and disks diffusion interpretations.</li>
 </ul></div>
 <div class="section level3">
-<h3 id="changed-2-1-1-9053">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9053"></a></h3>
+<h3 id="changed-2-1-1-9054">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9054"></a></h3>
 <ul><li>For SIR interpretation, it is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
 <li>Extended the antibiotic selectors with <code><a href="../reference/antibiotic_class_selectors.html">nitrofurans()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">rifamycins()</a></code>
 </li>
@@ -221,7 +221,7 @@
 <li>Intermediate log2 levels used for MIC plotting are now more common values instead of following a strict dilution range</li>
 </ul></div>
 <div class="section level3">
-<h3 id="other-2-1-1-9053">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9053"></a></h3>
+<h3 id="other-2-1-1-9054">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9054"></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: 2024-06-17T08:43Z
+last_built: 2024-06-17T12:13Z
 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="">2.1.1.9053</small>
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     <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

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     <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="">2.1.1.9053</small>
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reference/WHOCC.html

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     <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="">2.1.1.9053</small>
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     <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

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     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
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reference/ab_from_text.html

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     <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="">2.1.1.9053</small>
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reference/ab_property.html

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     <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="">2.1.1.9053</small>
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reference/add_custom_antimicrobials.html

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     <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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/age_groups.html

@@ -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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</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

@@ -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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</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">
@@ -574,32 +574,89 @@ 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"># For INTERPRETING disk diffusion and MIC values -----------------------</span></span></span>
 <span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># example data sets, with combined MIC values and disk zones</span></span></span>
+<span class="r-in"><span><span class="va">df_wide</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
+<span class="r-in"><span>  microorganism <span class="op">=</span> <span class="st">"Escherichia coli"</span>,</span></span>
+<span class="r-in"><span>  AMP <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">8</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  CIP <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">0.256</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  GEN <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">18</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  TOB <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">16</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  ERY <span class="op">=</span> <span class="st">"R"</span></span></span>
+<span class="r-in"><span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">df_long</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
+<span class="r-in"><span>  bacteria <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span>, <span class="fl">3</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  antibiotic <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="st">"amoxicillin"</span>, <span class="st">"cipro"</span>, <span class="st">"tobra"</span>, <span class="st">"genta"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  mics <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><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">0.01</span>, <span class="fl">1</span>, <span class="fl">4</span>, <span class="fl">8</span><span class="op">)</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  disks <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><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">6</span>, <span class="fl">10</span>, <span class="fl">14</span>, <span class="fl">18</span><span class="op">)</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(bacteria = rep("Escherichia coli", 3), antibiotic = c("amoxicillin",     "cipro", "tobra", "genta"), mics = as.mic(c(0.01, 1, 4, 8)),     disks = as.disk(c(6, 10, 14, 18))):</span> arguments imply differing number of rows: 3, 4</span>
+<span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># \donttest{</span></span></span>
 <span class="r-in"><span><span class="co">## Using dplyr -------------------------------------------------</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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="co"># approaches that all work without additional arguments:</span></span></span>
-<span class="r-in"><span>  <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
-<span class="r-in"><span>  <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="as.mic.html">is.mic</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">|</span> <span class="fu"><a href="as.disk.html">is.disk</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="as.mic.html">is.mic</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">|</span> <span class="fu"><a href="as.disk.html">is.disk</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
-<span class="r-in"><span>  <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-in"><span>  <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
-<span class="r-in"><span>  <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span>  </span></span>
 <span class="r-in"><span>  <span class="co"># approaches that all work with additional arguments:</span></span></span>
-<span class="r-in"><span>  <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span>, mo <span class="op">=</span> <span class="st">"column1"</span>, guideline <span class="op">=</span> <span class="st">"CLSI"</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">df_long</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
-<span class="r-in"><span>  <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>    <span class="co"># given a certain data type, e.g. MIC values</span></span></span>
-<span class="r-in"><span>                       <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, mo <span class="op">=</span> <span class="st">"column1"</span>, guideline <span class="op">=</span> <span class="st">"CLSI"</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://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span>,</span></span>
-<span class="r-in"><span>  <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.sir</span>, mo <span class="op">=</span> <span class="st">"column1"</span>, guideline <span class="op">=</span> <span class="st">"CLSI"</span><span class="op">)</span></span></span>
+<span class="r-in"><span>              mo <span class="op">=</span> <span class="st">"bacteria"</span>,</span></span>
-<span class="r-in"><span>  <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span>,</span></span>
+<span class="r-in"><span>              ab <span class="op">=</span> <span class="st">"antibiotic"</span>,</span></span>
-<span class="r-in"><span>                       <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, mo <span class="op">=</span> <span class="st">"column1"</span>, guideline <span class="op">=</span> <span class="st">"CLSI"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span>              guideline <span class="op">=</span> <span class="st">"CLSI"</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">df_long</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
+<span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>                  <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>,</span></span>
+<span class="r-in"><span>                                     mo <span class="op">=</span> <span class="st">"bacteria"</span>,</span></span>
+<span class="r-in"><span>                                     ab <span class="op">=</span> <span class="st">"antibiotic"</span>,</span></span>
+<span class="r-in"><span>                                     guideline <span class="op">=</span> <span class="st">"CLSI"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">df_long</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
+<span class="r-in"><span>    <span class="co"># given certain columns, e.g. from AMP to TOB</span></span></span>
+<span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.sir</span>,</span></span>
+<span class="r-in"><span>              mo <span class="op">=</span> <span class="st">"bacteria"</span>,</span></span>
+<span class="r-in"><span>              ab <span class="op">=</span> <span class="st">"antibiotic"</span>,</span></span>
+<span class="r-in"><span>              guideline <span class="op">=</span> <span class="st">"CLSI"</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">df_long</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
+<span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span>,</span></span>
+<span class="r-in"><span>                       <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>,</span></span>
+<span class="r-in"><span>                                          mo <span class="op">=</span> <span class="st">"bacteria"</span>,</span></span>
+<span class="r-in"><span>                                          ab <span class="op">=</span> <span class="st">"antibiotic"</span>,</span></span>
+<span class="r-in"><span>                                          guideline <span class="op">=</span> <span class="st">"CLSI"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span>                       </span></span>
 <span class="r-in"><span>  <span class="co"># for veterinary breakpoints, add 'host':</span></span></span>
-<span class="r-in"><span>  <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span>, guideline <span class="op">=</span> <span class="st">"CLSI"</span>, host <span class="op">=</span> <span class="st">"species_column"</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">df_long</span><span class="op">$</span><span class="va">animal_species</span> <span class="op">&lt;-</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="st">"cats"</span>, <span class="st">"dogs"</span>, <span class="st">"horses"</span>, <span class="st">"cattle"</span><span class="op">)</span></span></span>
-<span class="r-in"><span>  <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span>, guideline <span class="op">=</span> <span class="st">"CLSI"</span>, host <span class="op">=</span> <span class="st">"horse"</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">df_long</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
-<span class="r-in"><span>  <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>    <span class="co"># given a certain data type, e.g. MIC values</span></span></span>
-<span class="r-in"><span>                       <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, guideline <span class="op">=</span> <span class="st">"CLSI"</span>, host <span class="op">=</span> <span class="st">"species_column"</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://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span>,</span></span>
-<span class="r-in"><span>  <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.sir</span>, guideline <span class="op">=</span> <span class="st">"CLSI"</span>, host <span class="op">=</span> <span class="st">"species_column"</span><span class="op">)</span></span></span>
+<span class="r-in"><span>              mo <span class="op">=</span> <span class="st">"bacteria"</span>,</span></span>
-<span class="r-in"><span>  <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span>,</span></span>
+<span class="r-in"><span>              ab <span class="op">=</span> <span class="st">"antibiotic"</span>,</span></span>
-<span class="r-in"><span>                       <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, mo <span class="op">=</span> <span class="st">"column1"</span>, guideline <span class="op">=</span> <span class="st">"CLSI"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span>              host <span class="op">=</span> <span class="st">"animal_species"</span>,</span></span>
+<span class="r-in"><span>              guideline <span class="op">=</span> <span class="st">"CLSI"</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">df_long</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
+<span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>                  <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>,</span></span>
+<span class="r-in"><span>                                     mo <span class="op">=</span> <span class="st">"bacteria"</span>,</span></span>
+<span class="r-in"><span>                                     ab <span class="op">=</span> <span class="st">"antibiotic"</span>,</span></span>
+<span class="r-in"><span>                                     host <span class="op">=</span> <span class="st">"animal_species"</span>,</span></span>
+<span class="r-in"><span>                                     guideline <span class="op">=</span> <span class="st">"CLSI"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">df_long</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
+<span class="r-in"><span>    <span class="co"># given certain columns, e.g. from AMP to TOB</span></span></span>
+<span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.sir</span>,</span></span>
+<span class="r-in"><span>              mo <span class="op">=</span> <span class="st">"bacteria"</span>,</span></span>
+<span class="r-in"><span>              ab <span class="op">=</span> <span class="st">"antibiotic"</span>,</span></span>
+<span class="r-in"><span>              host <span class="op">=</span> <span class="st">"animal_species"</span>,</span></span>
+<span class="r-in"><span>              guideline <span class="op">=</span> <span class="st">"CLSI"</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">df_long</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
+<span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span>,</span></span>
+<span class="r-in"><span>                       <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>,</span></span>
+<span class="r-in"><span>                                          mo <span class="op">=</span> <span class="st">"bacteria"</span>,</span></span>
+<span class="r-in"><span>                                          ab <span class="op">=</span> <span class="st">"antibiotic"</span>,</span></span>
+<span class="r-in"><span>                                          host <span class="op">=</span> <span class="st">"animal_species"</span>,</span></span>
+<span class="r-in"><span>                                          guideline <span class="op">=</span> <span class="st">"CLSI"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span>  </span></span>
 <span class="r-in"><span>  <span class="co"># to include information about urinary tract infections (UTI)</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
@@ -612,24 +669,78 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-in"><span>             specimen <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="st">"urine"</span>, <span class="st">"blood"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>    <span class="fu">as.sir</span><span class="op">(</span><span class="op">)</span> <span class="co"># automatically determines urine isolates</span></span></span>
 <span class="r-in"><span></span></span>
-<span class="r-in"><span>  <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
+<span class="r-in"><span>  <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.sir</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, uti <span class="op">=</span> <span class="cn">TRUE</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 UseMethod("tbl_vars"):</span> no applicable method for 'tbl_vars' applied to an object of class "function"</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.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</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' (ciprofloxacin) based on column</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  NOTES </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.</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.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</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' (ciprofloxacin) based on column</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  NOTES </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</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' (tobramycin) based on column</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</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.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</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' (ciprofloxacin) based on column</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  NOTES </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.</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.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</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' (ciprofloxacin) based on column</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  NOTES </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</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' (tobramycin) based on column</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</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.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</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' (ciprofloxacin) based on column</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  NOTES </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</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' (tobramycin) based on column</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  OK </span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'df_long' not found</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co">## Using base R ------------------------------------------------</span></span></span>
 <span class="r-in"><span></span></span>
-<span class="r-in"><span><span class="co"># a whole data set, even with combined MIC values and disk zones</span></span></span>
+<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">df_wide</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
-<span class="r-in"><span>  microorganism <span class="op">=</span> <span class="st">"Escherichia coli"</span>,</span></span>
-<span class="r-in"><span>  AMP <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">8</span><span class="op">)</span>,</span></span>
-<span class="r-in"><span>  CIP <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">0.256</span><span class="op">)</span>,</span></span>
-<span class="r-in"><span>  GEN <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">18</span><span class="op">)</span>,</span></span>
-<span class="r-in"><span>  TOB <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">16</span><span class="op">)</span>,</span></span>
-<span class="r-in"><span>  ERY <span class="op">=</span> <span class="st">"R"</span></span></span>
-<span class="r-in"><span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">df</span><span class="op">)</span></span></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.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'AMP' (ampicillin), EUCAST 2024...</span>
@@ -650,22 +761,20 @@ 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: 13 × 16</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 29 × 16</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    datetime            index ab_given mo_given host_given ab   mo              </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  <span style="color: #BCBCBC;">*</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;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>            </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-06-17 <span style="color: #949494;">08:44:27</span>     4 AMX      B_STRPT… human      AMX  B_STRPT_PNMN    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-06-17 <span style="color: #949494;">12:14:06</span>     4 AMX      B_STRPT… human      AMX  B_STRPT_PNMN    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-06-17 <span style="color: #949494;">08:44:27</span>     3 AMX      B_STRPT… human      AMX  B_STRPT_PNMN    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-06-17 <span style="color: #949494;">12:14:06</span>     3 AMX      B_STRPT… human      AMX  B_STRPT_PNMN    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-06-17 <span style="color: #949494;">08:44:27</span>     2 AMX      B_STRPT… human      AMX  B_STRPT_PNMN    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-06-17 <span style="color: #949494;">12:14:06</span>     2 AMX      B_STRPT… human      AMX  B_STRPT_PNMN    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-06-17 <span style="color: #949494;">08:44:26</span>     1 ampicil… Strep p… human      AMP  B_STRPT_PNMN    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-06-17 <span style="color: #949494;">12:14:05</span>     1 ampicil… Strep p… human      AMP  B_STRPT_PNMN    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-06-17 <span style="color: #949494;">08:44:26</span>     1 AMP      Escheri… human      AMP  B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-06-17 <span style="color: #949494;">12:14:05</span>     1 AMP      Escheri… human      AMP  B_[ORD]_ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-06-17 <span style="color: #949494;">08:44:26</span>     1 GEN      Escheri… human      GEN  B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-06-17 <span style="color: #949494;">12:14:05</span>     1 GEN      Escheri… human      GEN  B_[ORD]_ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-06-17 <span style="color: #949494;">08:44:27</span>     1 TOB      Escheri… human      TOB  B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-06-17 <span style="color: #949494;">12:14:05</span>     1 TOB      Escheri… human      TOB  B_[ORD]_ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-06-17 <span style="color: #949494;">08:44:27</span>     1 AMX      B_STRPT… human      AMX  B_STRPT_PNMN    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-06-17 <span style="color: #949494;">12:14:06</span>     1 AMX      B_STRPT… human      AMX  B_STRPT_PNMN    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-06-17 <span style="color: #949494;">08:44:27</span>     1 AMX      B_STRPT… human      AMX  B_STRPT_PNMN    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-06-17 <span style="color: #949494;">12:14:06</span>     1 AMX      B_STRPT… human      AMX  B_STRPT_PNMN    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-06-17 <span style="color: #949494;">08:44:31</span>     1 AMP      Escheri… human      AMP  B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-06-17 <span style="color: #949494;">12:14:10</span>     1 AMP      Escheri… human      AMP  B_[ORD]_ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> 2024-06-17 <span style="color: #949494;">08:44:32</span>     1 CIP      Escheri… human      CIP  B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 19 more rows</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> 2024-06-17 <span style="color: #949494;">08:44:32</span>     1 GEN      Escheri… human      GEN  B_[ORD]_ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> 2024-06-17 <span style="color: #949494;">08:44:32</span>     1 TOB      Escheri… human      TOB  B_[ORD]_ENTRBCTR</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 9 more variables: host &lt;chr&gt;, method &lt;chr&gt;, input &lt;dbl&gt;, outcome &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   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;</span></span>
@@ -702,7 +811,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-in"><span><span class="co"># For CLEANING existing SIR values ------------------------------------</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">as.sir</span><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="st">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.sir(): 3 results in column '28' truncated (38%) that were invalid</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.sir(): 3 results in column '30' truncated (38%) that were invalid</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial interpretations: "A", "B", and "C"</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    SDD  I    R    NI   &lt;NA&gt; &lt;NA&gt; &lt;NA&gt;</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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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reference/export_ncbi_biosample.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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9054</small>
 
     
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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="">2.1.1.9053</small>
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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="">2.1.1.9053</small>
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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="">2.1.1.9053</small>
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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="">2.1.1.9053</small>
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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="">2.1.1.9053</small>
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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="">2.1.1.9053</small>
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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="">2.1.1.9053</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="">2.1.1.9053</small>
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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="">2.1.1.9053</small>
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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="">2.1.1.9053</small>
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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="">2.1.1.9053</small>
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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="">2.1.1.9053</small>
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reference/proportion.html

@@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
     
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9053</small>
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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="">2.1.1.9053</small>
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reference/resistance_predict.html

@@ -10,7 +10,7 @@
     
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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="">2.1.1.9053</small>
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reference/translate.html

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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9053</small>
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