Built site for AMR: 2.0.0.9031@1b499bf

2024-12-25 20:06:12 +01:00 · 2023-07-10 15:09:18 +00:00 · 2023-07-10 15:09:18 +00:00 · d8d9452d24
commit d8d9452d24
parent 97037aa011
82 changed files with 194 additions and 194 deletions
--- a/404.html
+++ b/404.html
@ -36,7 +36,7 @@
    
    <a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@ -10,7 +10,7 @@
    
    <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/articles/AMR.html
+++ b/articles/AMR.html
@ -38,7 +38,7 @@
    
    <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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@ -38,7 +38,7 @@
    
    <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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/articles/MDR.html
+++ b/articles/MDR.html
@ -38,7 +38,7 @@
    
    <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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
@ -402,18 +402,18 @@ names or codes, this would have worked exactly the same way:</p>
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
 <span><span class="co">#&gt;   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
-<span><span class="co">#&gt; 1          I         I            R          I            S            S</span></span>
-<span><span class="co">#&gt; 2          R         R            S          I            S            S</span></span>
-<span><span class="co">#&gt; 3          R         S            S          S            S            R</span></span>
-<span><span class="co">#&gt; 4          S         I            S          S            I            S</span></span>
-<span><span class="co">#&gt; 5          S         I            R          R            R            R</span></span>
-<span><span class="co">#&gt; 6          R         R            I          R            R            S</span></span>
+<span><span class="co">#&gt; 1          I         I            I          R            I            R</span></span>
+<span><span class="co">#&gt; 2          R         I            S          I            S            R</span></span>
+<span><span class="co">#&gt; 3          I         I            S          S            S            R</span></span>
+<span><span class="co">#&gt; 4          R         I            I          S            I            R</span></span>
+<span><span class="co">#&gt; 5          S         R            R          R            S            S</span></span>
+<span><span class="co">#&gt; 6          R         I            I          R            R            R</span></span>
 <span><span class="co">#&gt;   kanamycin</span></span>
-<span><span class="co">#&gt; 1         R</span></span>
-<span><span class="co">#&gt; 2         R</span></span>
-<span><span class="co">#&gt; 3         I</span></span>
-<span><span class="co">#&gt; 4         I</span></span>
-<span><span class="co">#&gt; 5         R</span></span>
+<span><span class="co">#&gt; 1         S</span></span>
+<span><span class="co">#&gt; 2         S</span></span>
+<span><span class="co">#&gt; 3         S</span></span>
+<span><span class="co">#&gt; 4         S</span></span>
+<span><span class="co">#&gt; 5         S</span></span>
 <span><span class="co">#&gt; 6         R</span></span></code></pre></div>
 <p>We can now add the interpretation of MDR-TB to our data set. You can
 use:</p>
@ -455,40 +455,40 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistant</td>
-<td align="right">3172</td>
-<td align="right">63.44%</td>
-<td align="right">3172</td>
-<td align="right">63.44%</td>
+<td align="right">3255</td>
+<td align="right">65.10%</td>
+<td align="right">3255</td>
+<td align="right">65.10%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">1056</td>
-<td align="right">21.12%</td>
-<td align="right">4228</td>
-<td align="right">84.56%</td>
+<td align="right">938</td>
+<td align="right">18.76%</td>
+<td align="right">4193</td>
+<td align="right">83.86%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Multi-drug-resistant</td>
-<td align="right">423</td>
-<td align="right">8.46%</td>
-<td align="right">4651</td>
-<td align="right">93.02%</td>
+<td align="right">436</td>
+<td align="right">8.72%</td>
+<td align="right">4629</td>
+<td align="right">92.58%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistant</td>
-<td align="right">251</td>
-<td align="right">5.02%</td>
-<td align="right">4902</td>
-<td align="right">98.04%</td>
+<td align="right">274</td>
+<td align="right">5.48%</td>
+<td align="right">4903</td>
+<td align="right">98.06%</td>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
 <td align="left">Extensively drug-resistant</td>
-<td align="right">98</td>
-<td align="right">1.96%</td>
+<td align="right">97</td>
+<td align="right">1.94%</td>
 <td align="right">5000</td>
 <td align="right">100.00%</td>
 </tr>
--- a/articles/PCA.html
+++ b/articles/PCA.html
@ -38,7 +38,7 @@
    
    <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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/articles/WHONET.html
+++ b/articles/WHONET.html
@ -38,7 +38,7 @@
    
    <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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/articles/datasets.html
+++ b/articles/datasets.html
@ -38,7 +38,7 @@
    
    <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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/articles/index.html
+++ b/articles/index.html
@ -10,7 +10,7 @@
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/articles/other_pkg.html
+++ b/articles/other_pkg.html
@ -38,7 +38,7 @@
    
    <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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/articles/resistance_predict.html
+++ b/articles/resistance_predict.html
@ -38,7 +38,7 @@
    
    <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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/articles/welcome_to_AMR.html
+++ b/articles/welcome_to_AMR.html
@ -38,7 +38,7 @@
    
    <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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/authors.html
+++ b/authors.html
@ -10,7 +10,7 @@
    
    <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/index.html
+++ b/index.html
@ -42,7 +42,7 @@
    
    <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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/news/index.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
@ -159,9 +159,9 @@
    </div>

    <div class="section level2">
-<h2 class="pkg-version" data-toc-text="2.0.0.9030" id="amr-2009030">AMR 2.0.0.9030<a class="anchor" aria-label="anchor" href="#amr-2009030"></a></h2>
+<h2 class="pkg-version" data-toc-text="2.0.0.9031" id="amr-2009031">AMR 2.0.0.9031<a class="anchor" aria-label="anchor" href="#amr-2009031"></a></h2>
 <div class="section level3">
-<h3 id="new-2-0-0-9030">New<a class="anchor" aria-label="anchor" href="#new-2-0-0-9030"></a></h3>
+<h3 id="new-2-0-0-9031">New<a class="anchor" aria-label="anchor" href="#new-2-0-0-9031"></a></h3>
 <ul><li>Clinical breakpoints and intrinsic resistance of EUCAST 2023 and CLSI 2023 have been added for <code><a href="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2023 (v13.0) is now the new default guideline for all MIC and disks diffusion interpretations</li>
 <li>The EUCAST dosage guideline of v13.0 has been added to the <code>dosage</code> data set</li>
 <li>ECOFF: the <code>clinical_breakpoints</code> data set now contains epidemiological cut-off (ECOFF) values. These ECOFFs can be used for MIC/disk interpretation using <code>as.sir(..., breakpoint_type = "ECOFF")</code>, which is an important new addition for veterinary microbiology.</li>
@ -176,7 +176,7 @@
 <li>Added microbial codes for Gram-negative/positive anaerobic bacteria</li>
 </ul></div>
 <div class="section level3">
-<h3 id="changed-2-0-0-9030">Changed<a class="anchor" aria-label="anchor" href="#changed-2-0-0-9030"></a></h3>
+<h3 id="changed-2-0-0-9031">Changed<a class="anchor" aria-label="anchor" href="#changed-2-0-0-9031"></a></h3>
 <ul><li>Updated algorithm of <code><a href="../reference/as.mo.html">as.mo()</a></code> by giving more weight to fungi</li>
 <li>
 <code><a href="../reference/mo_property.html">mo_rank()</a></code> now returns <code>NA</code> for ‘unknown’ microorganisms (<code>B_ANAER</code>, <code>B_ANAER-NEG</code>, <code>B_ANAER-POS</code>, <code>B_GRAMN</code>, <code>B_GRAMP</code>, <code>F_FUNGUS</code>, <code>F_YEAST</code>, and <code>UNKNOWN</code>)</li>
--- a/pkgdown.yml
+++ b/pkgdown.yml
@ -11,7 +11,7 @@ articles:
  other_pkg: other_pkg.html
  resistance_predict: resistance_predict.html
  welcome_to_AMR: welcome_to_AMR.html
-last_built: 2023-07-10T14:49Z
+last_built: 2023-07-10T15:06Z
 urls:
  reference: https://msberends.github.io/AMR/reference
  article: https://msberends.github.io/AMR/articles
--- a/reference/AMR-deprecated.html
+++ b/reference/AMR-deprecated.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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/AMR-options.html
+++ b/reference/AMR-options.html
@ -10,7 +10,7 @@
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/AMR.html
+++ b/reference/AMR.html
@ -24,7 +24,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/WHOCC.html
+++ b/reference/WHOCC.html
@ -10,7 +10,7 @@
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/WHONET.html
+++ b/reference/WHONET.html
@ -10,7 +10,7 @@
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/ab_from_text.html
+++ b/reference/ab_from_text.html
@ -10,7 +10,7 @@
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/ab_property.html
+++ b/reference/ab_property.html
@ -10,7 +10,7 @@
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/add_custom_antimicrobials.html
+++ b/reference/add_custom_antimicrobials.html
@ -10,7 +10,7 @@
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/add_custom_microorganisms.html
+++ b/reference/add_custom_microorganisms.html
@ -10,7 +10,7 @@
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/age.html
+++ b/reference/age.html
@ -10,7 +10,7 @@
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</small>

    
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -222,16 +222,16 @@
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">df</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    birth_date age age_exact age_at_y2k</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1931-12-21  91  91.55068         68</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1942-05-14  81  81.15616         57</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1958-04-02  65  65.27123         41</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1947-07-06  76  76.01096         52</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1953-12-17  69  69.56164         46</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1988-05-23  35  35.13151         11</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1987-03-04  36  36.35068         12</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1945-08-19  77  77.89041         54</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1959-03-20  64  64.30685         40</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1957-04-12  66  66.24384         42</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1965-08-31  57  57.85753         34</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1959-01-07  64  64.50411         40</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1935-12-20  87  87.55342         64</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1943-06-23  80  80.04658         56</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1987-01-10  36  36.49589         12</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1998-12-26  24  24.53699          1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1992-10-01  30  30.77260          7</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1984-10-15  38  38.73425         15</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1936-11-01  86  86.68767         63</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-02-10  45  45.41096         21</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
--- a/reference/age_groups.html
+++ b/reference/age_groups.html
@ -10,7 +10,7 @@
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/antibiogram.html
+++ b/reference/antibiogram.html
@ -10,7 +10,7 @@
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/antibiotic_class_selectors.html
+++ b/reference/antibiotic_class_selectors.html
@ -12,7 +12,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
@ -627,10 +627,10 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
 <span class="r-out co"><span class="r-pr">#&gt;</span>   kefzol</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> R     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> R     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> I     </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> I     </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> R     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> I     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> S     </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="co"># get AMR for all aminoglycosides e.g., per ward:</span></span></span>
--- a/reference/antibiotics.html
+++ b/reference/antibiotics.html
@ -10,7 +10,7 @@
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/as.ab.html
+++ b/reference/as.ab.html
@ -10,7 +10,7 @@
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/as.av.html
+++ b/reference/as.av.html
@ -10,7 +10,7 @@
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/as.disk.html
+++ b/reference/as.disk.html
@ -10,7 +10,7 @@
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/as.mic-1.png
+++ b/reference/as.mic-1.png
--- a/reference/as.mic-2.png
+++ b/reference/as.mic-2.png
--- a/reference/as.mic-3.png
+++ b/reference/as.mic-3.png
--- a/reference/as.mic-4.png
+++ b/reference/as.mic-4.png
--- a/reference/as.mic-5.png
+++ b/reference/as.mic-5.png
--- a/reference/as.mic.html
+++ b/reference/as.mic.html
@ -10,7 +10,7 @@
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
@ -291,22 +291,22 @@
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># plot MIC values, see ?plot</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">mic_data</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in plot_colours_subtitle_guideline(x = x, mo = mo, ab = ab, guideline = guideline,     colours_SIR = colours_SIR, fn = as.mic, language = language,     method = "MIC", include_PKPD = include_PKPD, breakpoint_type = breakpoint_type,     ...):</span> object 'sir_history' not found</span>
-<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="as.mic-1.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="as.mic-2.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-plt img"><img src="as.mic-2.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="as.mic-3.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span> <span class="co"># Dutch</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-plt img"><img src="as.mic-3.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="as.mic-4.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>, language <span class="op">=</span> <span class="st">"uk"</span><span class="op">)</span> <span class="co"># Ukrainian</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-plt img"><img src="as.mic-4.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="as.mic-5.png" alt="" width="700" height="433"></span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
--- a/reference/as.mo.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/as.sir.html
+++ b/reference/as.sir.html
@ -14,7 +14,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
@ -556,14 +556,14 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 8 × 13</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   datetime            index ab_input   ab_guideline mo_input      mo_guideline</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span>              <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;chr&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> 2023-07-10 <span style="color: #949494;">14:50:29</span>     1 CIP        CIP          Escherichia …   UNKNOWN   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2023-07-10 <span style="color: #949494;">14:50:29</span>     1 AMP        AMP          Escherichia …   UNKNOWN   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2023-07-10 <span style="color: #949494;">14:50:21</span>     1 AMX        AMX          B_STRPT_PNMN  B_STRPT_PNMN</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2023-07-10 <span style="color: #949494;">14:50:21</span>     2 AMX        AMX          B_STRPT_PNMN  B_STRPT_PNMN</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> 2023-07-10 <span style="color: #949494;">14:50:21</span>     3 AMX        AMX          B_STRPT_PNMN  B_STRPT_PNMN</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> 2023-07-10 <span style="color: #949494;">14:50:21</span>     4 AMX        AMX          B_STRPT_PNMN  B_STRPT_PNMN</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">7</span> 2023-07-10 <span style="color: #949494;">14:50:21</span>     1 AMX        AMX          B_STRPT_PNMN  B_STRPT_PNMN</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">8</span> 2023-07-10 <span style="color: #949494;">14:50:20</span>     1 ampicillin AMP          Strep pneu    B_STRPT_PNMN</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2023-07-10 <span style="color: #949494;">15:07:05</span>     1 CIP        CIP          Escherichia …   UNKNOWN   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2023-07-10 <span style="color: #949494;">15:07:05</span>     1 AMP        AMP          Escherichia …   UNKNOWN   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2023-07-10 <span style="color: #949494;">15:06:57</span>     1 AMX        AMX          B_STRPT_PNMN  B_STRPT_PNMN</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2023-07-10 <span style="color: #949494;">15:06:57</span>     2 AMX        AMX          B_STRPT_PNMN  B_STRPT_PNMN</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> 2023-07-10 <span style="color: #949494;">15:06:57</span>     3 AMX        AMX          B_STRPT_PNMN  B_STRPT_PNMN</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> 2023-07-10 <span style="color: #949494;">15:06:57</span>     4 AMX        AMX          B_STRPT_PNMN  B_STRPT_PNMN</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">7</span> 2023-07-10 <span style="color: #949494;">15:06:57</span>     1 AMX        AMX          B_STRPT_PNMN  B_STRPT_PNMN</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">8</span> 2023-07-10 <span style="color: #949494;">15:06:56</span>     1 ampicillin AMP          Strep pneu    B_STRPT_PNMN</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 7 more variables: 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;">#   method &lt;chr&gt;, input &lt;dbl&gt;, outcome &lt;sir&gt;, breakpoint_S_R &lt;chr&gt;</span></span>
 <span class="r-in"><span></span></span>
--- a/reference/atc_online.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/av_from_text.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/av_property.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/availability.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/bug_drug_combinations.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/clinical_breakpoints.html
+++ b/reference/clinical_breakpoints.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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/count.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/custom_eucast_rules.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/dosage.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/eucast_rules.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/example_isolates.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/example_isolates_unclean.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/first_isolate.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/g.test.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/get_episode.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
@ -263,28 +263,28 @@
 <span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">100</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="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   [1]  1 50 26 12 10 18 50 42 43 21 34 19 13 25 44 35 45 16 17  3 25 20  3 17 45</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [26]  6 10 28 42  9 47  1 11 27 18 45 17 14  6 22 31 42 41  2 23 38 16 46 29  8</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [51] 40 48  7 49 20 34 16  7 36 38 48  2 49 14 32 14 27 10 37 24 18 23  4 46  8</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [76] 36  6  7 32 22 28 49 16 47 38 21 30 27  6 22 14 24 48 33 21  5 48 39 16 15</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] 43 14  7  8 29  4 16 40  5 32  9 43 27  7 20 13 28  1  3 23 38 24 42  2 26</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [26] 44 21 36 11 35 25 31  6 17 27 28 19 46 35 14  6 48 47 47 29 32 16 15 46 45</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [51] 32  1 17 29 15 10 45 43 20 22 49  3 44 27 23 13 24 10 21 34 16 44  6 12  5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [76] 12 37  5 14 46 13 49 33 41 44 21 39 22  4 47 17 36 48 39 22 30 37 34 18 44</span>
 <span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   [1]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [13]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [25] FALSE  TRUE FALSE  TRUE FALSE  TRUE  TRUE FALSE  TRUE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [37] FALSE  TRUE FALSE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [49]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [61] FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [73]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [85] FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [97] FALSE  TRUE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   [1]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [13]  TRUE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [25]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [37]  TRUE  TRUE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [49] FALSE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [61]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [73] FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [85] FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [97] FALSE FALSE  TRUE FALSE</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
 <span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</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: 2 × 46</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&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;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-06-04 082413     78 M      ICU      B_STRPT_PNMN S     NA    NA    S    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-06-23 798871     82 M      Clinical B_ENTRC_FCLS NA    NA    NA    NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   date       patient   age gender ward  mo           PEN   OXA   FLC   AMX  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&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;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2003-04-20 6BC362     62 M      ICU   B_ENTRC      NA    NA    NA    NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2003-06-11 E35356     71 F      ICU   B_STPHY_CONS R     NA    R     R    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;,</span></span>
@ -318,19 +318,19 @@
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">condition</span>, <span class="va">date</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, condition [95]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, condition [99]</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    patient date       condition new_episode</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 008268  2007-02-20 B         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 051150  2007-01-02 B         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 067927  2002-01-07 A         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 074321  2015-09-20 A         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 078381  2014-07-17 B         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 078381  2014-08-17 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 082413  2002-06-04 C         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 0C0688  2014-09-05 B         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 0E2483  2007-05-29 A         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 15D386  2004-08-01 B         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 022060  2004-05-04 A         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 022060  2004-05-04 C         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 080086  2007-10-26 B         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 082622  2014-02-08 C         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 092034  2006-06-12 C         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 0D7D34  2011-03-16 C         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 0E2483  2007-05-29 A         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 0E2483  2007-05-29 C         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 126334  2009-11-26 B         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 155435  2014-06-18 C         TRUE       </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@ -344,19 +344,19 @@
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">ward</span>, <span class="va">date</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 5</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   ward, patient [94]</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    ward     date       patient new_index new_logical</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> ICU      2007-02-20 008268          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU      2007-01-02 051150          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ICU      2002-01-07 067927          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU      2015-09-20 074321          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU      2014-07-17 078381          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU      2014-08-17 078381          1 FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU      2002-06-04 082413          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2014-09-05 0C0688          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2007-05-29 0E2483          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> ICU      2004-08-01 15D386          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   ward, patient [93]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    ward       date       patient new_index new_logical</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> ICU        2004-05-04 022060          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU        2004-05-04 022060          1 FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical   2007-10-26 080086          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU        2014-02-08 082622          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU        2006-06-12 092034          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU        2011-03-16 0D7D34          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical   2007-05-29 0E2483          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical   2007-05-29 0E2483          1 FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Outpatient 2009-11-26 126334          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical   2014-06-18 155435          1 TRUE       </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@ -372,9 +372,9 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   ward       n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>           <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>          <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical           52             13            36            46</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU                38             12            28            35</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient          4              3             4             4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical           66             13            38            47</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU                24              9            20            24</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient          3              3             3             3</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
 <span class="r-in"><span><span class="co"># results as first_isolate() when using 'episode-based':</span></span></span>
@ -403,19 +403,19 @@
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, mo, ward [97]</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    patient mo           ward     flag_episode</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 067927  B_STPHY_EPDR ICU      TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> A85702  B_CTRBC_KOSR ICU      TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 949877  B_STRPT_PNMN Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> D43733  B_ESCHR_COLI ICU      TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> BB8157  B_STPHY_CONS Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 59C7F2  B_STRPT_PNMN Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 693199  B_STRPT_PNMN Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> A76045  B_ENTRC_FACM ICU      TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 559068  B_STPHY_CPTS Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 533225  B_ESCHR_COLI Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, mo, ward [98]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    patient mo            ward     flag_episode</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>          <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> F61180  B_ESCHR_COLI  ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 54890C  B_ESCHR_COLI  Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 869231  B_KLBSL_PNMN  Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> D52219  B_STRPT_GRPA  ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 690B42  B_ESCHR_COLI  Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 914520  B_STPHY_AURS  Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> C89738  B_STRPT_MITS  Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> D8D632  B_ESCHR_COLI  ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> F35553  B_ENTRBC_CLOC ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 905108  B_STRPT_PNMN  Clinical TRUE        </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
--- a/reference/ggplot_pca.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/ggplot_sir.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/guess_ab_col.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/index.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/intrinsic_resistant.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/italicise_taxonomy.html
+++ b/reference/italicise_taxonomy.html
@ -10,7 +10,7 @@
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/join.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/key_antimicrobials.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/kurtosis.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
@ -199,9 +199,9 @@
    <div class="section level2">
    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.993275</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.03876</span>
 <span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.005991136</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.05207763</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
--- a/reference/like.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/mdro.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/mean_amr_distance.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/microorganisms.codes.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/microorganisms.groups.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/microorganisms.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/mo_matching_score.html
+++ b/reference/mo_matching_score.html
@ -10,7 +10,7 @@
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/mo_property.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/mo_source.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/pca.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/plot.html
+++ b/reference/plot.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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/proportion.html
+++ b/reference/proportion.html
@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/random.html
+++ b/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="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/resistance_predict.html
+++ b/reference/resistance_predict.html
@ -10,7 +10,7 @@
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
--- a/reference/skewness.html
+++ b/reference/skewness.html
@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</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">
@ -198,7 +198,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
    <div class="section level2">
    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.01314082</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.0683066</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
--- a/reference/translate.html
+++ b/reference/translate.html
@ -10,7 +10,7 @@
    
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9031</small>

    
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--- a/search.json
+++ b/search.json