cli-147-2126

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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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

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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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</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="">2.1.1.9056</small>
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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="">2.1.1.9056</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</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="">2.1.1.9056</small>
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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="">2.1.1.9056</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="">2.1.1.9056</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">

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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="2.1.1.9056" id="amr-2119056">AMR 2.1.1.9056<a class="anchor" aria-label="anchor" href="#amr-2119056"></a></h2>
+<h2 class="pkg-version" data-toc-text="2.1.1.9057" id="amr-2119057">AMR 2.1.1.9057<a class="anchor" aria-label="anchor" href="#amr-2119057"></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! 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-2-1-1-9056">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-2-1-1-9056"></a></h5>
+<h5 id="a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9057">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-2-1-1-9057"></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-2-1-1-9056">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9056"></a></h3>
+<h3 id="breaking-2-1-1-9057">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9057"></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-2-1-1-9056">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9056"></a></h3>
+<h3 id="new-2-1-1-9057">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9057"></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>
@@ -188,7 +188,7 @@
 <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-2-1-1-9056">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9056"></a></h3>
+<h3 id="changed-2-1-1-9057">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9057"></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-2-1-1-9056">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9056"></a></h3>
+<h3 id="other-2-1-1-9057">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9057"></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: 2024-06-17T12:55Z
+last_built: 2024-06-17T14:55Z
 urls:
   reference: https://msberends.github.io/AMR/reference
   article: https://msberends.github.io/AMR/articles

reference/AMR-options.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="">2.1.1.9056</small>
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reference/AMR.html

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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9056</small>
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reference/WHOCC.html

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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9056</small>
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reference/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="">2.1.1.9056</small>
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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="">2.1.1.9056</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="">2.1.1.9056</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="">2.1.1.9056</small>
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reference/add_custom_microorganisms.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="">2.1.1.9056</small>
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reference/age.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="">2.1.1.9056</small>
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reference/age_groups.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="">2.1.1.9056</small>
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reference/antibiogram.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="">2.1.1.9056</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
     
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9056</small>
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reference/antibiotics.html

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     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
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reference/as.ab.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="">2.1.1.9056</small>
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reference/as.av.html

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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9056</small>
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reference/as.disk.html

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reference/as.mic.html

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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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">
@@ -290,7 +290,7 @@
 <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: 'AMX' (amoxicillin), 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>  NOTE </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Multiple breakpoints available for amoxicillin (AMX) in Streptococcus 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] R</span>
@@ -303,7 +303,7 @@
 <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: 'AMX' (amoxicillin), 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>  NOTE </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Multiple breakpoints available for amoxicillin (AMX) in Streptococcus 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>

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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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">
@@ -263,6 +263,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
 <li><p><strong>CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing</strong>, 2011-2024, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m100/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m100/</a>.</p></li>
 <li><p><strong>CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals</strong>, 2019-2024, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/veterinary-medicine/documents/vet01//" class="external-link">https://clsi.org/standards/products/veterinary-medicine/documents/vet01//</a>.</p></li>
 <li><p><strong>EUCAST Breakpoint tables for interpretation of MICs and zone diameters</strong>, 2011-2024, <em>European Committee on Antimicrobial Susceptibility Testing</em> (EUCAST). <a href="https://www.eucast.org/clinical_breakpoints" class="external-link">https://www.eucast.org/clinical_breakpoints</a>.</p></li>
+<li><p><strong>WHONET</strong> as a source for machine-reading clinical breakpoints ((read more here)https://msberends.github.io/AMR/reference/clinical_breakpoints.html#imported-from-whonet), 1989-2024, <em>WHO Collaborating Centre for Surveillance of Antimicrobial Resistance</em>. <a href="https://whonet.org/" class="external-link">https://whonet.org/</a>.</p></li>
 </ul></div>
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
@@ -577,10 +578,10 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <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>  amoxicillin <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>  cipro <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>  tobra <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>  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>  genta <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>  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>
@@ -597,8 +598,8 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <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_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_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_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_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">amoxicillin</span><span class="op">:</span><span class="va">tobra</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.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">amoxicillin</span><span class="op">:</span><span class="va">tobra</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_long</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -613,17 +614,15 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <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="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="co"># given certain columns, e.g. from 'cipro' to 'genta'</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">cipro</span><span class="op">:</span><span class="va">genta</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="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.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">cipro</span><span class="op">:</span><span class="va">genta</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>
@@ -642,18 +641,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <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="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="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">cipro</span><span class="op">:</span><span class="va">genta</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="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.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">cipro</span><span class="op">:</span><span class="va">genta</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>
@@ -673,66 +670,60 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-in"><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: 'AMP' (ampicillin) based on column</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'amoxicillin' (AMX) 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> Interpreting MIC values: 'cipro' (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>  NOTE </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> Interpreting MIC values: 'amoxicillin' (AMX) 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> Interpreting MIC values: 'cipro' (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>  NOTE </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> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin) based on</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> column '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> Interpreting disk diffusion zones: 'genta' (GEN, gentamicin) based on</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> column '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> Interpreting MIC values: 'amoxicillin' (AMX) 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> Interpreting MIC values: 'cipro' (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>  NOTE </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> Interpreting MIC values: 'amoxicillin' (AMX) 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> Interpreting MIC values: 'cipro' (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>  NOTE </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> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin) based on</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> column '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> Interpreting MIC values: 'amoxicillin' (AMX) 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> Interpreting MIC values: 'cipro' (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>  NOTE </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> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin) based on</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> column '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>
@@ -745,9 +736,104 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'amoxicillin' (AMX), 'cipro' (CIP, ciprofloxacin),</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> 'tobra' (TOB, tobramycin), and 'genta' (GEN, gentamicin) based on column</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> 'bacteria', CLSI 2024...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  WARNING </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   • Returned an empty result, which is unexpected. Are all of mo, ab, and host set and available?</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: 'cipro' (CIP, ciprofloxacin), CLSI 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 tbl_at_vars(tbl, vars, .include_group_vars = .include_group_vars,     error_call = error_call):</span> Can't select columns that don't exist.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin), CLSI 2024...</span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">✖</span> Column `cipro` doesn't exist.</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: 'genta' (GEN, gentamicin), CLSI 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: 'cipro' (CIP, ciprofloxacin), CLSI 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: 'tobra' (TOB, tobramycin), CLSI 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: 'genta' (GEN, gentamicin), CLSI 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> ℹ Assuming breakpoint_type = "animal", since host is set.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Please note that in the absence of specific veterinary breakpoints for</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   certain animal hosts, breakpoints for dogs, cattle, swine, cats, horse,</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   aquatic, and poultry, in that order, are used as substitutes.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'amoxicillin' (AMX), 'cipro' (CIP, ciprofloxacin),</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 'tobra' (TOB, tobramycin), and 'genta' (GEN, gentamicin) based on column</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 'bacteria', CLSI 2024...</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>   • Using dogs breakpoints since cattle for gentamicin (GEN) in Escherichia coli are not available.</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> ℹ Assuming breakpoint_type = "animal", since host is set.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Please note that in the absence of specific veterinary breakpoints for</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   certain animal hosts, breakpoints for dogs, cattle, swine, cats, horse,</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   aquatic, and poultry, in that order, are used as substitutes.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'amoxicillin' (AMX), 'cipro' (CIP, ciprofloxacin),</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 'tobra' (TOB, tobramycin), and 'genta' (GEN, gentamicin) based on column</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 'bacteria', CLSI 2024...</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>   • Using dogs breakpoints since cattle for gentamicin (GEN) in Escherichia coli are not available.</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> ℹ Assuming breakpoint_type = "animal", since host is set.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Please note that in the absence of specific veterinary breakpoints for</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   certain animal hosts, breakpoints for dogs, cattle, swine, cats, horse,</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   aquatic, and poultry, in that order, are used as substitutes.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'antibiotic' (TESTAB, test Antibiotic), CLSI</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  WARNING </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   • No CLSI 2024 MIC breakpoints available for test Antibiotic (TESTAB).</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'antibiotic' (TESTAB, test Antibiotic),</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> CLSI 2024...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  WARNING </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   • No CLSI 2024 DISK breakpoints available for test Antibiotic (TESTAB).</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'antibiotic' (TESTAB, test Antibiotic),</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> CLSI 2024...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  WARNING </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   • No CLSI 2024 DISK breakpoints available for test Antibiotic (TESTAB).</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> ℹ Assuming breakpoint_type = "animal", since host is set.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Please note that in the absence of specific veterinary breakpoints for</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   certain animal hosts, breakpoints for dogs, cattle, swine, cats, horse,</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   aquatic, and poultry, in that order, are used as substitutes.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin), CLSI 2024...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  WARNING </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   • No CLSI 2024 MIC breakpoints available for ciprofloxacin (CIP).</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin), CLSI 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: 'genta' (GEN, gentamicin), CLSI 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: column 'nitrofuratoin' (NIT, nitrofurantoin),</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024...</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>   • Breakpoints for nitrofurantoin (NIT) in Escherichia coli are only available for (uncomplicated) urinary tract infections (UTI); assuming uti = TRUE.</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.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'nitrofuratoin' (NIT, nitrofurantoin),</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024...</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>   • Breakpoints for nitrofurantoin (NIT) in Escherichia coli are only available for (uncomplicated) urinary tract infections (UTI); assuming uti = TRUE.</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: 'cipro' (CIP, ciprofloxacin), 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: 'tobra' (TOB, tobramycin), EUCAST</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 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: 'genta' (GEN, gentamicin), EUCAST</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024...</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 amoxicillin cipro tobra genta ERY</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli           8  &lt;NA&gt;     S     S   R</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>
@@ -755,38 +841,39 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <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-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>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'amoxicillin' (AMX), 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: column 'CIP' (ciprofloxacin), EUCAST 2024...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'cipro' (CIP, ciprofloxacin), EUCAST</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> 2024...</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 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: column 'GEN' (gentamicin), EUCAST</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: column 'tobra' (TOB, tobramycin), EUCAST</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> 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: column 'TOB' (tobramycin), EUCAST</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: column 'genta' (GEN, gentamicin), EUCAST</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> 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> Assigning class 'sir' to already clean column 'ERY' (erythromycin)...</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>      microorganism amoxicillin cipro tobra genta ERY</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli   S   I   S   S   R</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli           S     I     S     S   R</span>
 <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: 37 × 16</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 55 × 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;">12:56:05</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;">14:56:02</span>     4 genta    Escheri… human      GEN  B_[ORD]_ENTRBCTR</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;">12:56:11</span>     4 genta    Escheri… human      GEN  B_[ORD]_ENTRBCTR</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;">14:56:02</span>     4 genta    Escheri… cattle     GEN  B_[ORD]_ENTRBCTR</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;">12:56:11</span>     4 genta    Escheri… human      GEN  B_[ORD]_ENTRBCTR</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;">14:56:02</span>     4 genta    Escheri… cattle     GEN  B_[ORD]_ENTRBCTR</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;">12:56:05</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;"> 4</span> 2024-06-17 <span style="color: #949494;">14:56:01</span>     3 tobra    Escheri… human      TOB  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;">12:56:11</span>     3 tobra    Escheri… human      TOB  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;">14:56:02</span>     3 tobra    Escheri… horse      TOB  B_ESCHR_COLI    </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;">12:56:11</span>     3 tobra    Escheri… human      TOB  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;">14:56:02</span>     3 tobra    Escheri… horse      TOB  B_ESCHR_COLI    </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;">12:56:05</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;"> 7</span> 2024-06-17 <span style="color: #949494;">14:56:01</span>     2 cipro    Escheri… human      CIP  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;">12:56:11</span>     2 cipro    Escheri… human      CIP  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;">14:56:02</span>     2 cipro    Escheri… dogs       CIP  B_ESCHR_COLI    </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;">12:56:11</span>     2 cipro    Escheri… human      CIP  B_[ORD]_ENTRBCTR</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;">14:56:02</span>     2 cipro    Escheri… dogs       CIP  B_ESCHR_COLI    </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;">12:56:04</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;">10</span> 2024-06-17 <span style="color: #949494;">14:56:03</span>     2 nitrofu… E. coli  human      NIT  B_ESCHR_COLI    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 27 more rows</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 45 more rows</span></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>
@@ -801,7 +888,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <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), 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>  NOTE </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Multiple breakpoints available for ampicillin (AMP) in Streptococcus pneumoniae - assuming body site 'Non-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] R</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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">
@@ -208,14 +208,14 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
 <h3 id="imported-from-whonet">Imported from WHONET<a class="anchor" aria-label="anchor" href="#imported-from-whonet"></a></h3>
 
 
-<p>Clinical breakpoints in this package were validated through and imported from <a href="https://whonet.org" class="external-link">WHONET</a>, a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on <a href="https://whonet.org" class="external-link">their website</a>. The developers of WHONET and this <code>AMR</code> package have been in contact about sharing their work. We highly appreciate their development on the WHONET software.</p>
+<p>Clinical breakpoints in this package were validated through and imported from <a href="https://whonet.org" class="external-link">WHONET</a>, a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on <a href="https://whonet.org" class="external-link">their website</a>. The developers of WHONET and this <code>AMR</code> package have been in contact about sharing their work. We highly appreciate their great development on the WHONET software.</p>
 </div>
 
 <div class="section">
 <h3 id="response-from-clsi-and-eucast">Response from CLSI and EUCAST<a class="anchor" aria-label="anchor" href="#response-from-clsi-and-eucast"></a></h3>
 
 
-<p>The CEO of CLSI and the chairman of EUCAST have endorsed the work and public use of this <code>AMR</code> package (and consequently the use of their breakpoints) in June 2023, when future development of distributing clinical breakpoints was discussed in a meeting between CLSI, EUCAST, the WHO, and developers of WHONET and the <code>AMR</code> package.</p>
+<p>The CEO of CLSI and the chairman of EUCAST have endorsed the work and public use of this <code>AMR</code> package (and consequently the use of their breakpoints) in June 2023, when future development of distributing clinical breakpoints was discussed in a meeting between CLSI, EUCAST, WHO, developers of WHONET software, and developers of this <code>AMR</code> package.</p>
 </div>
 
 <div class="section">

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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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">
@@ -428,16 +428,26 @@
 
       <dl><dt>
           
-          <code><a href="example_isolates.html">example_isolates</a></code> 
-        </dt>
-        <dd>Data Set with 2 000 Example Isolates</dd>
-      </dl><dl><dt>
-          
           <code><a href="microorganisms.html">microorganisms</a></code> 
         </dt>
         <dd>Data Set with 52 171 Microorganisms</dd>
       </dl><dl><dt>
           
+          <code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code> 
+        </dt>
+        <dd>Data Sets with 605 Antimicrobial Drugs</dd>
+      </dl><dl><dt>
+          
+          <code><a href="clinical_breakpoints.html">clinical_breakpoints</a></code> 
+        </dt>
+        <dd>Data Set with Clinical Breakpoints for SIR Interpretation</dd>
+      </dl><dl><dt>
+          
+          <code><a href="example_isolates.html">example_isolates</a></code> 
+        </dt>
+        <dd>Data Set with 2 000 Example Isolates</dd>
+      </dl><dl><dt>
+          
           <code><a href="microorganisms.codes.html">microorganisms.codes</a></code> 
         </dt>
         <dd>Data Set with 4 971 Common Microorganism Codes</dd>
@@ -448,11 +458,6 @@
         <dd>Data Set with 521 Microorganisms In Species Groups</dd>
       </dl><dl><dt>
           
-          <code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code> 
-        </dt>
-        <dd>Data Sets with 605 Antimicrobial Drugs</dd>
-      </dl><dl><dt>
-          
           <code><a href="intrinsic_resistant.html">intrinsic_resistant</a></code> 
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@@ -473,11 +478,6 @@
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-          <code><a href="clinical_breakpoints.html">clinical_breakpoints</a></code> 
-        </dt>
-        <dd>Data Set with Clinical Breakpoints for SIR Interpretation</dd>
-      </dl><dl><dt>
-          
           <code><a href="WHONET.html">WHONET</a></code> 
         </dt>
         <dd>Data Set with 500 Isolates - WHONET Example</dd>

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="">2.1.1.9056</small>
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reference/italicise_taxonomy.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="">2.1.1.9056</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</small>
 
     
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reference/mo_matching_score.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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</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="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</small>
 
     
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reference/resistance_predict.html

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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</small>
 
     
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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
     
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9056</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9057</small>
 
     
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reference/translate.html

@@ -10,7 +10,7 @@
     
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9056</small>
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