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2
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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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LICENSE-text.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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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="">2.1.1.9044</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 10 June 2024.</p>
generated on 12 June 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">2024-06-10</td>
<td align="center">2024-06-12</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">2024-06-10</td>
<td align="center">2024-06-12</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">2024-06-10</td>
<td align="center">2024-06-12</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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2
articles/MDR.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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@ -39,7 +39,7 @@
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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="">2.1.1.9044</small>
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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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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@ -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">10 June 2024</h4>
<h4 data-toc-skip class="date">12 June 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="">2.1.1.9044</small>
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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>
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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>
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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>
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authors.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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14
extra.css
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@ -89,13 +89,19 @@
box-shadow: none !important;
}
.endorse_img {
width: 0% !important;
}
.template-home img.logo {
width: 200px;
}
.template-home .endorse_img {
width: 150px;
}
.template-reference-index .section-desc {
font-style: italic;
text-align: justify;
font-size: 16px;
}
@media (max-width: 575.98px) {
.template-home img.logo {
width: 140px;

4
index.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</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">
@ -193,7 +193,6 @@
<a class="anchor" aria-label="anchor" href="#the-amr-package-for-r-"></a>
</h1>
</div>
<p><img src="./endorsement_clsi_eucast.jpg" class="endorse_img" align="right" height="120"></p>
<ul>
<li>Provides an <strong>all-in-one solution</strong> for AMR data analysis in a One Health approach</li>
<li>Generates <strong>antibiograms</strong> - traditional, combined, syndromic, and even WISCA</li>
@ -214,6 +213,7 @@
<small><a href="https://doi.org/10.18637/jss.v104.i03" target="_blank" class="external-link">https://doi.org/10.18637/jss.v104.i03</a></small>
</p>
</div>
<p><a href="./reference/clinical_breakpoints.html#response-from-clsi-and-eucast"><img src="./endorsement_clsi_eucast.jpg" class="endorse_img" align="right" height="120"></a></p>
<hr>
<div class="section level3">
<h3 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>

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>
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@ -159,18 +159,18 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9044" id="amr-2119044">AMR 2.1.1.9044<a class="anchor" aria-label="anchor" href="#amr-2119044"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9045" id="amr-2119045">AMR 2.1.1.9045<a class="anchor" aria-label="anchor" href="#amr-2119045"></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-2-1-1-9044">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-2-1-1-9044"></a></h5>
<h5 id="a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9045">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-2-1-1-9045"></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-2-1-1-9044">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9044"></a></h3>
<h3 id="breaking-2-1-1-9045">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9045"></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-2-1-1-9044">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9044"></a></h3>
<h3 id="new-2-1-1-9045">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9045"></a></h3>
<ul><li>One Health implementation
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for animal breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
<li>The <code>clinical_breakpoints</code> data set contains all these breakpoints, and can be downloaded on our <a href="https://msberends.github.io/AMR/articles/datasets.html">download page</a>.</li>
@ -187,7 +187,7 @@
<li>Function <code><a href="../reference/mo_property.html">mo_group_members()</a></code> to retrieve the member microorganisms of a microorganism group. For example, <code>mo_group_members("Strep group C")</code> returns a vector of all microorganisms that are in that group.</li>
</ul></div>
<div class="section level3">
<h3 id="changed-2-1-1-9044">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9044"></a></h3>
<h3 id="changed-2-1-1-9045">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9045"></a></h3>
<ul><li>For SIR interpretation, it is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
<li>Extended the antibiotic selectors with <code><a href="../reference/antibiotic_class_selectors.html">nitrofurans()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">rifamycins()</a></code>
</li>
@ -215,7 +215,7 @@
<li>Intermediate log2 levels used for MIC plotting are now more common values instead of following a strict dilution range</li>
</ul></div>
<div class="section level3">
<h3 id="other-2-1-1-9044">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9044"></a></h3>
<h3 id="other-2-1-1-9045">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9045"></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>

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pkgdown.yml
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@ -11,7 +11,7 @@ articles:
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
WHONET: WHONET.html
last_built: 2024-06-10T13:13Z
last_built: 2024-06-12T08:38Z
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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2
reference/AMR.html
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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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reference/WHOCC.html
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@ -10,7 +10,7 @@
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reference/WHONET.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/ab_from_text.html
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@ -10,7 +10,7 @@
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2
reference/ab_property.html
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@ -10,7 +10,7 @@
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2
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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2
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>
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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="">2.1.1.9044</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 58.51366 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.27596 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 74 74.60656 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.31967 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.30601 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.41530 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 26 26.78689 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.37158 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 51 51.98087 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 37 37.83333 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 58 58.51913 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.28142 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 74 74.61202 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.32514 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.31148 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.42077 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 26 26.79235 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.37705 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 51 51.98634 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 37 37.83880 13</span>
</code></pre></div>
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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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@ -307,7 +307,7 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: for AMX, EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMX' (amoxicillin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for amoxicillin (AMX) in Streptococcus</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> pneumoniae - assuming body site 'Meningitis'.</span>

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@ -24,7 +24,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
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@ -603,19 +603,19 @@ 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> 2024-06-10 <span style="color: #949494;">13:14:36</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> 2024-06-10 <span style="color: #949494;">13:14:36</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> 2024-06-10 <span style="color: #949494;">13:14:36</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> 2024-06-10 <span style="color: #949494;">13:14:36</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> 2024-06-10 <span style="color: #949494;">13:14:32</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> 2024-06-10 <span style="color: #949494;">13:14:32</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> 2024-06-10 <span style="color: #949494;">13:14:32</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> 2024-06-10 <span style="color: #949494;">13:14:32</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> 2024-06-10 <span style="color: #949494;">13:14:31</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> 2024-06-10 <span style="color: #949494;">13:14:31</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> 2024-06-10 <span style="color: #949494;">13:14:31</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> 2024-06-10 <span style="color: #949494;">13:14:31</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> 2024-06-10 <span style="color: #949494;">13:14:31</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> 2024-06-12 <span style="color: #949494;">08:38:59</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> 2024-06-12 <span style="color: #949494;">08:38:59</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> 2024-06-12 <span style="color: #949494;">08:38:59</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> 2024-06-12 <span style="color: #949494;">08:38:59</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> 2024-06-12 <span style="color: #949494;">08:38:55</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> 2024-06-12 <span style="color: #949494;">08:38:55</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> 2024-06-12 <span style="color: #949494;">08:38:55</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> 2024-06-12 <span style="color: #949494;">08:38:55</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> 2024-06-12 <span style="color: #949494;">08:38:54</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> 2024-06-12 <span style="color: #949494;">08:38:54</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> 2024-06-12 <span style="color: #949494;">08:38:54</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> 2024-06-12 <span style="color: #949494;">08:38:54</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> 2024-06-12 <span style="color: #949494;">08:38:54</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>
@ -782,7 +782,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column for NIT, EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'NIT' (nitrofurantoin), EUCAST 2023...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.sir(): interpretation of nitrofurantoin (NIT) is only available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (uncomplicated) urinary tract infections (UTI) for some microorganisms,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> thus assuming uti = TRUE. See ?as.sir.</span>
@ -794,7 +794,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column for NIT, EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'NIT' (nitrofurantoin), EUCAST 2023...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.sir(): interpretation of nitrofurantoin (NIT) is only available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (uncomplicated) urinary tract infections (UTI) for some microorganisms,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> thus assuming uti = TRUE. See ?as.sir.</span>

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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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@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@ -10,7 +10,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/eucast_rules.html
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@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/example_isolates.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/example_isolates_unclean.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/export_ncbi_biosample.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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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/first_isolate.html
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@ -12,7 +12,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/g.test.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/get_episode.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/ggplot_pca.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/ggplot_sir.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/guess_ab_col.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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reference/intrinsic_resistant.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/italicise_taxonomy.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/join.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/key_antimicrobials.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/kurtosis.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/like.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/mdro.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/mean_amr_distance.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/microorganisms.codes.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/microorganisms.groups.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/mo_matching_score.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/mo_property.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
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
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/pca.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/plot.html
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@ -12,7 +12,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/proportion.html
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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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/resistance_predict.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/skewness.html
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@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
reference/translate.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="">2.1.1.9044</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9045</small>
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2
search.json
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