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404.html
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@ -37,7 +37,7 @@
<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9016</small>
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LICENSE-text.html
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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articles/AMR.html
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@ -39,7 +39,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9016</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9017</small>
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@ -205,7 +205,7 @@
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 05 April 2024.</p>
generated on 07 April 2024.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -261,21 +261,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2024-04-05</td>
<td align="center">2024-04-07</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2024-04-05</td>
<td align="center">2024-04-07</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2024-04-05</td>
<td align="center">2024-04-07</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>

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articles/EUCAST.html
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@ -39,7 +39,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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articles/MDR.html
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@ -39,7 +39,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9016</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9017</small>
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@ -402,19 +402,19 @@ 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 S S S S R S</span></span>
<span><span class="co">#&gt; 2 R I R S R S</span></span>
<span><span class="co">#&gt; 3 S S I I S S</span></span>
<span><span class="co">#&gt; 4 I I I I I I</span></span>
<span><span class="co">#&gt; 5 R S I S I R</span></span>
<span><span class="co">#&gt; 6 I I I I R R</span></span>
<span><span class="co">#&gt; 1 S I R I R R</span></span>
<span><span class="co">#&gt; 2 I I S I S R</span></span>
<span><span class="co">#&gt; 3 S S S I S I</span></span>
<span><span class="co">#&gt; 4 I S I S S I</span></span>
<span><span class="co">#&gt; 5 R S S I R R</span></span>
<span><span class="co">#&gt; 6 S R I R S I</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 S</span></span>
<span><span class="co">#&gt; 2 R</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 S</span></span></code></pre></div>
<span><span class="co">#&gt; 2 I</span></span>
<span><span class="co">#&gt; 3 I</span></span>
<span><span class="co">#&gt; 4 R</span></span>
<span><span class="co">#&gt; 5 R</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>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -455,40 +455,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3272</td>
<td align="right">65.44%</td>
<td align="right">3272</td>
<td align="right">65.44%</td>
<td align="right">3221</td>
<td align="right">64.42%</td>
<td align="right">3221</td>
<td align="right">64.42%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">958</td>
<td align="right">19.16%</td>
<td align="right">4230</td>
<td align="right">84.60%</td>
<td align="right">960</td>
<td align="right">19.20%</td>
<td align="right">4181</td>
<td align="right">83.62%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">431</td>
<td align="right">8.62%</td>
<td align="right">4661</td>
<td align="right">93.22%</td>
<td align="right">451</td>
<td align="right">9.02%</td>
<td align="right">4632</td>
<td align="right">92.64%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">238</td>
<td align="right">4.76%</td>
<td align="right">4899</td>
<td align="right">97.98%</td>
<td align="right">262</td>
<td align="right">5.24%</td>
<td align="right">4894</td>
<td align="right">97.88%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">101</td>
<td align="right">2.02%</td>
<td align="right">106</td>
<td align="right">2.12%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

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articles/PCA.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9016</small>
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articles/WHONET.html
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@ -39,7 +39,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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4
articles/datasets.html
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@ -39,7 +39,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9016</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9017</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -194,7 +194,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">05 April 2024</h4>
<h4 data-toc-skip class="date">07 April 2024</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>

2
articles/index.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9016</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9017</small>
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2
articles/other_pkg.html
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@ -39,7 +39,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9016</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9017</small>
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articles/resistance_predict.html
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@ -39,7 +39,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9016</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9017</small>
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articles/welcome_to_AMR.html
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@ -39,7 +39,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9016</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9017</small>
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2
authors.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9016</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9017</small>
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extra.css
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@ -30,19 +30,36 @@
*/
:root, .navbar * {
--bs-primary: #a7dbc3 !important;
--bs-primary-color: #a7dbc3 !important;
--bs-primary-rgb: 167, 219, 195 !important;
--amr-green-light: #a7dbc3;
--amr-green-light-rgb: 167, 219, 195;
--amr-green-dark: #128f76;
--amr-green-dark-rgb: 18, 143, 118;
--amr-green-middle: #60a799;
--amr-green-middle-rgb: 96, 167, 153;
--amr-blue-light: #a8d5ef
--amr-blue-light-rgb: 168, 213, 239
--bs-success: --amr-green-dark !important;
--bs-link-color: --amr-green-dark !important;
--bs-light: --amr-green-light !important;
/* --bs-light was this: #128f76a6; that's success with 60% alpha */
--bs-info: --amr-green-middle !important;
--bs-primary: --amr-green-dark !important;
--bs-primary-color: --amr-green-dark !important;
--bs-primary-rgb: --amr-green-light-rgb !important;
--bs-secondary: #ffffff !important;
--bs-secondary-color: var(--bs-success) !important;
--bs-secondary-color: var(--amr-green-dark) !important;
--bs-secondary-rgb: 255, 255, 255 !important;
--bs-navbar-brand-color: var(--bs-body-color) !important;
--bs-navbar-brand-color-hover: var(--bs-body-color) !important;
--bs-nav-link-color: var(--bs-body-color) !important;
--bs-bg-opacity: 1 !important;
}
.nav-text.text-muted {
color: var(--bs-success) !important;
color: var(--amr-green-dark) !important;
}
.template-home img.logo {
@ -78,7 +95,7 @@
/* marked words for after using the search box */
mark, .mark {
background: var(--bs-light) !important;
background: var(--amr-green-light) !important;
}
/* smaller tables */
@ -103,17 +120,17 @@ pre code {
}
pre .fu, .fu {
/* functions */
color: var(--bs-primary) !important;
color: var(--amr-green-dark) !important;
font-weight: bold !important;
letter-spacing: -1px !important;
}
pre .st, .st {
/* strings, regular text */
color: var(--bs-info) !important;
color: var(--amr-green-middle) !important;
}
pre .co, .co {
/* comments */
color: var(--bs-success) !important;
color: var(--amr-green-dark) !important;
font-style: italic !important;
}
pre code .r-out,
@ -128,7 +145,7 @@ pre a[href],
a code[href],
a pre[href] {
/* adjusted colour for all real links; having href attribute */
color: var(--bs-success);
color: var(--amr-green-dark);
text-decoration: none;
}
a[href] {

2
index.html
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@ -43,7 +43,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9016</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9017</small>
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14
news/index.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9016</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9017</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -159,18 +159,18 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9016" id="amr-2119016">AMR 2.1.1.9016<a class="anchor" aria-label="anchor" href="#amr-2119016"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9017" id="amr-2119017">AMR 2.1.1.9017<a class="anchor" aria-label="anchor" href="#amr-2119017"></a></h2>
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support!)</em></p>
<div class="section level5">
<h5 id="a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9016">A New Milestone: One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9016"></a></h5>
<h5 id="a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9017">A New Milestone: One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9017"></a></h5>
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
</div>
<div class="section level3">
<h3 id="breaking-2-1-1-9016">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9016"></a></h3>
<h3 id="breaking-2-1-1-9017">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9017"></a></h3>
<ul><li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over a year ago</li>
</ul></div>
<div class="section level3">
<h3 id="new-2-1-1-9016">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9016"></a></h3>
<h3 id="new-2-1-1-9017">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9017"></a></h3>
<ul><li>One Health implementation
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for animal breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
<li>The <code>clinical_breakpoints</code> data set contains all these breakpoints, and can be downloaded on our <a href="https://msberends.github.io/AMR/articles/datasets.html">download page</a>.</li>
@ -184,7 +184,7 @@
<li>Function <code><a href="../reference/as.mic.html">limit_mic_range()</a></code>, which allows to limit MIC values to a manually set range. This is the powerhouse behind the <code>scale_*_mic()</code> functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.</li>
</ul></div>
<div class="section level3">
<h3 id="changed-2-1-1-9016">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9016"></a></h3>
<h3 id="changed-2-1-1-9017">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9017"></a></h3>
<ul><li>For MICs:
<ul><li>Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960)</li>
<li>Added new argument <code>keep_operators</code> to <code><a href="../reference/as.mic.html">as.mic()</a></code>. This can be <code>"all"</code> (default), <code>"none"</code>, or <code>"edges"</code>. This argument is also available in the new <code><a href="../reference/as.mic.html">limit_mic_range()</a></code> and <code>scale_*_mic()</code> functions.</li>
@ -196,7 +196,7 @@
<li>Updated all antibiotic DDDs from WHOCC</li>
</ul></div>
<div class="section level3">
<h3 id="other-2-1-1-9016">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9016"></a></h3>
<h3 id="other-2-1-1-9017">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9017"></a></h3>
<ul><li>Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
</ul></div>
</div>

2
pkgdown.yml
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@ -11,7 +11,7 @@ articles:
other_pkg: other_pkg.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2024-04-05T14:56Z
last_built: 2024-04-07T22:55Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

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reference/AMR-options.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -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>
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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reference/add_custom_antimicrobials.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/add_custom_microorganisms.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9016</small>
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22
reference/age.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9016</small>
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@ -222,16 +222,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 58 58.33333 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.09563 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 74 74.42623 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.13934 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.12568 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.23497 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 26 26.60656 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.19126 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 51 51.80055 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 37 37.65301 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 58 58.33880 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.10109 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 74 74.43169 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.14481 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.13115 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.24044 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 26 26.61202 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.19672 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 51 51.80601 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 37 37.65847 13</span>
</code></pre></div>
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -10,7 +10,7 @@
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@ -12,7 +12,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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10
reference/as.mic.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9016</small>
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@ -316,18 +316,18 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># plot MIC values, see ?plot</span></span></span>
<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">mic_data</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="as.mic-1.png" alt="" width="700" height="433"></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error:</span> in plot.mic(): argument main must be of length 1, not 277</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-err co"><span class="r-pr">#&gt;</span> <span class="error">Error:</span> in plot.mic(): argument main must be of length 1, not 277</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-3.png" alt="" width="700" height="433"></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="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-4.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="as.mic-2.png" alt="" width="700" height="433"></span>
</code></pre></div>
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@ -10,7 +10,7 @@
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@ -24,7 +24,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
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@ -592,19 +592,19 @@ 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: 13 × 14</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_user mo_user ab mo input</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-04-05 <span style="color: #949494;">14:56:43</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-04-05 <span style="color: #949494;">14:56:43</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-04-05 <span style="color: #949494;">14:56:43</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR 0.256</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-04-05 <span style="color: #949494;">14:56:43</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-04-05 <span style="color: #949494;">14:56:39</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-04-05 <span style="color: #949494;">14:56:39</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-04-05 <span style="color: #949494;">14:56:39</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-04-05 <span style="color: #949494;">14:56:39</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-04-05 <span style="color: #949494;">14:56:39</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-04-05 <span style="color: #949494;">14:56:38</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> 2024-04-05 <span style="color: #949494;">14:56:38</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> 2024-04-05 <span style="color: #949494;">14:56:38</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> 2024-04-05 <span style="color: #949494;">14:56:38</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-04-07 <span style="color: #949494;">22:56:16</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-04-07 <span style="color: #949494;">22:56:16</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-04-07 <span style="color: #949494;">22:56:16</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR 0.256</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-04-07 <span style="color: #949494;">22:56:16</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-04-07 <span style="color: #949494;">22:56:11</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-04-07 <span style="color: #949494;">22:56:11</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-04-07 <span style="color: #949494;">22:56:11</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-04-07 <span style="color: #949494;">22:56:11</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-04-07 <span style="color: #949494;">22:56:11</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-04-07 <span style="color: #949494;">22:56:11</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> 2024-04-07 <span style="color: #949494;">22:56:11</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> 2024-04-07 <span style="color: #949494;">22:56:11</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> 2024-04-07 <span style="color: #949494;">22:56:10</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 7 more variables: outcome &lt;sir&gt;, method &lt;chr&gt;, breakpoint_S_R &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># guideline &lt;chr&gt;, host &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;</span></span>
<span class="r-in"><span></span></span>

2
reference/atc_online.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9016</small>
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reference/av_from_text.html
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@ -10,7 +10,7 @@
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reference/av_property.html
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@ -10,7 +10,7 @@
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reference/availability.html
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@ -10,7 +10,7 @@
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reference/bug_drug_combinations.html
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@ -10,7 +10,7 @@
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reference/clinical_breakpoints.html
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@ -16,7 +16,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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reference/count.html
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@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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reference/custom_eucast_rules.html
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@ -10,7 +10,7 @@
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reference/dosage.html
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@ -10,7 +10,7 @@
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reference/eucast_rules.html
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@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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reference/example_isolates.html
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@ -10,7 +10,7 @@
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reference/example_isolates_unclean.html
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@ -10,7 +10,7 @@
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2
reference/first_isolate.html
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@ -12,7 +12,7 @@
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reference/g.test.html
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@ -10,7 +10,7 @@
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reference/get_episode.html
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@ -10,7 +10,7 @@
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reference/ggplot_pca.html
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@ -10,7 +10,7 @@
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reference/ggplot_sir.html
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@ -10,7 +10,7 @@
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reference/guess_ab_col.html
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@ -10,7 +10,7 @@
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2
reference/index.html
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@ -10,7 +10,7 @@
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reference/intrinsic_resistant.html
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@ -10,7 +10,7 @@
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reference/italicise_taxonomy.html
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@ -10,7 +10,7 @@
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reference/join.html
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@ -10,7 +10,7 @@
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reference/key_antimicrobials.html
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@ -10,7 +10,7 @@
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reference/kurtosis.html
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@ -10,7 +10,7 @@
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reference/like.html
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@ -10,7 +10,7 @@
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reference/mdro.html
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@ -10,7 +10,7 @@
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reference/mean_amr_distance.html
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@ -10,7 +10,7 @@
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reference/microorganisms.codes.html
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@ -10,7 +10,7 @@
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reference/microorganisms.groups.html
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@ -10,7 +10,7 @@
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reference/microorganisms.html
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@ -10,7 +10,7 @@
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reference/mo_matching_score.html
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@ -10,7 +10,7 @@
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2
reference/mo_property.html
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@ -10,7 +10,7 @@
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reference/mo_source.html
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@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -12,7 +12,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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@ -360,19 +360,19 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span class="r-in"><span><span class="va">some_sir_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">50</span>, prob_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.55</span>, <span class="fl">0.05</span>, <span class="fl">0.30</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">plot</span><span class="op">(</span><span class="va">some_mic_values</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="plot-1.png" alt="" width="700" height="433"></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error:</span> in plot.mic(): argument main must be of length 1, not 286</span>
<span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_disk_values</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="plot-2.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_sir_values</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="plot-3.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-2.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># when providing the microorganism and antibiotic, colours will show interpretations:</span></span></span>
<span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_mic_values</span>, mo <span class="op">=</span> <span class="st">"S. aureus"</span>, ab <span class="op">=</span> <span class="st">"ampicillin"</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="plot-4.png" alt="" width="700" height="433"></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error:</span> in plot.mic(): argument main must be of length 1, not 286</span>
<span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_disk_values</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="plot-5.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-3.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_disk_values</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="plot-6.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-4.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Plotting using scale_x_mic()</span></span></span>
@ -385,38 +385,38 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span class="r-in"><span> <span class="va">mic_plot</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"without scale_x_mic()"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="plot-7.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-5.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">mic_plot</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_x_mic</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"with scale_x_mic()"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="plot-8.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-6.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">mic_plot</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_x_mic</span><span class="op">(</span>keep_operators <span class="op">=</span> <span class="st">"all"</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"with scale_x_mic() keeping all operators"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="plot-9.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-7.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">mic_plot</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_x_mic</span><span class="op">(</span>mic_range <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">128</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"with scale_x_mic() using a manual range"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="plot-10.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-8.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">some_mic_values</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="plot-11.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-9.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">some_disk_values</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="plot-12.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-10.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">some_sir_values</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="plot-13.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-11.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>

2
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@ -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>
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reference/random.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9016</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9017</small>
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